Example usage for java.util HashMap values

Introduction

In this page you can find the example usage for java.util HashMap values.

Prototype

public Collection<V> values() 

Source Link

Document

Returns a Collection view of the values contained in this map.

Usage

From source file:net.bluehack.ui.ChatActivity.java

@Override
public void didReceivedNotification(int id, final Object... args) {
    if (id == NotificationCenter.messagesDidLoaded) {
        int guid = (Integer) args[10];
        if (guid == classGuid) {
            if (!openAnimationEnded) {
                NotificationCenter.getInstance().setAllowedNotificationsDutingAnimation(new int[] {
                        NotificationCenter.chatInfoDidLoaded, NotificationCenter.dialogsNeedReload,
                        NotificationCenter.closeChats,
                        NotificationCenter.botKeyboardDidLoaded/*, NotificationCenter.botInfoDidLoaded*/ });
            }//from  w w w.ja  va2s.com
            int queryLoadIndex = (Integer) args[11];
            int index = waitingForLoad.indexOf(queryLoadIndex);
            if (index == -1) {
                return;
            } else {
                waitingForLoad.remove(index);
            }
            ArrayList<MessageObject> messArr = (ArrayList<MessageObject>) args[2];
            if (waitingForReplyMessageLoad) {
                boolean found = false;
                for (int a = 0; a < messArr.size(); a++) {
                    if (messArr.get(a).getId() == startLoadFromMessageId) {
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    startLoadFromMessageId = 0;
                    return;
                }
                int startLoadFrom = startLoadFromMessageId;
                boolean needSelect = needSelectFromMessageId;
                clearChatData();
                startLoadFromMessageId = startLoadFrom;
                needSelectFromMessageId = needSelect;
            }

            loadsCount++;
            long did = (Long) args[0];
            int loadIndex = did == dialog_id ? 0 : 1;
            int count = (Integer) args[1];
            boolean isCache = (Boolean) args[3];
            int fnid = (Integer) args[4];
            int last_unread_date = (Integer) args[7];
            int load_type = (Integer) args[8];
            boolean wasUnread = false;
            if (fnid != 0) {
                first_unread_id = fnid;
                last_message_id = (Integer) args[5];
                unread_to_load = (Integer) args[6];
            } else if (startLoadFromMessageId != 0 && load_type == 3) {
                last_message_id = (Integer) args[5];
            }
            int newRowsCount = 0;

            forwardEndReached[loadIndex] = startLoadFromMessageId == 0 && last_message_id == 0;
            if ((load_type == 1 || load_type == 3) && loadIndex == 1) {
                endReached[0] = cacheEndReached[0] = true;
                forwardEndReached[0] = false;
                minMessageId[0] = 0;
            }

            if (loadsCount == 1 && messArr.size() > 20) {
                loadsCount++;
            }

            if (firstLoading) {
                if (!forwardEndReached[loadIndex]) {
                    messages.clear();
                    messagesByDays.clear();
                    for (int a = 0; a < 2; a++) {
                        messagesDict[a].clear();
                        if (currentEncryptedChat == null) {
                            maxMessageId[a] = Integer.MAX_VALUE;
                            minMessageId[a] = Integer.MIN_VALUE;
                        } else {
                            maxMessageId[a] = Integer.MIN_VALUE;
                            minMessageId[a] = Integer.MAX_VALUE;
                        }
                        maxDate[a] = Integer.MIN_VALUE;
                        minDate[a] = 0;
                    }
                }
                firstLoading = false;
                AndroidUtilities.runOnUIThread(new Runnable() {
                    @Override
                    public void run() {
                        if (parentLayout != null) {
                            parentLayout.resumeDelayedFragmentAnimation();
                        }
                    }
                });
            }

            if (load_type == 1) {
                Collections.reverse(messArr);
            }
            if (currentEncryptedChat == null) {
                MessagesQuery.loadReplyMessagesForMessages(messArr, dialog_id);
            }
            int approximateHeightSum = 0;
            for (int a = 0; a < messArr.size(); a++) {
                MessageObject obj = messArr.get(a);
                approximateHeightSum += obj.getApproximateHeight();
                if (currentUser != null) {
                    if (currentUser.self) {
                        obj.messageOwner.out = true;
                    }
                    if (currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                }
                if (messagesDict[loadIndex].containsKey(obj.getId())) {
                    continue;
                }
                if (loadIndex == 1) {
                    obj.setIsRead();
                }
                if (loadIndex == 0 && ChatObject.isChannel(currentChat) && obj.getId() == 1) {
                    endReached[loadIndex] = true;
                    cacheEndReached[loadIndex] = true;
                }
                if (obj.getId() > 0) {
                    maxMessageId[loadIndex] = Math.min(obj.getId(), maxMessageId[loadIndex]);
                    minMessageId[loadIndex] = Math.max(obj.getId(), minMessageId[loadIndex]);
                } else if (currentEncryptedChat != null) {
                    maxMessageId[loadIndex] = Math.max(obj.getId(), maxMessageId[loadIndex]);
                    minMessageId[loadIndex] = Math.min(obj.getId(), minMessageId[loadIndex]);
                }
                if (obj.messageOwner.date != 0) {
                    maxDate[loadIndex] = Math.max(maxDate[loadIndex], obj.messageOwner.date);
                    if (minDate[loadIndex] == 0 || obj.messageOwner.date < minDate[loadIndex]) {
                        minDate[loadIndex] = obj.messageOwner.date;
                    }
                }

                if (obj.type < 0 || loadIndex == 1
                        && obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                    continue;
                }

                if (!obj.isOut() && obj.isUnread()) {
                    wasUnread = true;
                }
                messagesDict[loadIndex].put(obj.getId(), obj);
                ArrayList<MessageObject> dayArray = messagesByDays.get(obj.dateKey);

                if (dayArray == null) {
                    dayArray = new ArrayList<>();
                    messagesByDays.put(obj.dateKey, dayArray);
                    TLRPC.Message dateMsg = new TLRPC.Message();
                    dateMsg.message = LocaleController.formatDateChat(obj.messageOwner.date);
                    dateMsg.id = 0;
                    dateMsg.date = obj.messageOwner.date;
                    MessageObject dateObj = new MessageObject(dateMsg, null, false);
                    dateObj.type = 10;
                    dateObj.contentType = 1;
                    if (load_type == 1) {
                        messages.add(0, dateObj);
                    } else {
                        messages.add(dateObj);
                    }
                    newRowsCount++;
                }

                newRowsCount++;
                if (load_type == 1) {
                    dayArray.add(obj);
                    messages.add(0, obj);
                }

                if (load_type != 1) {
                    dayArray.add(obj);
                    messages.add(messages.size() - 1, obj);
                }

                if (obj.getId() == last_message_id) {
                    forwardEndReached[loadIndex] = true;
                }

                if (load_type == 2 && obj.getId() == first_unread_id) {
                    if (approximateHeightSum > AndroidUtilities.displaySize.y / 2 || !forwardEndReached[0]) {
                        TLRPC.Message dateMsg = new TLRPC.Message();
                        dateMsg.message = "";
                        dateMsg.id = 0;
                        MessageObject dateObj = new MessageObject(dateMsg, null, false);
                        dateObj.type = 6;
                        dateObj.contentType = 2;
                        messages.add(messages.size() - 1, dateObj);
                        unreadMessageObject = dateObj;
                        scrollToMessage = unreadMessageObject;
                        scrollToMessagePosition = -10000;
                        newRowsCount++;
                    }
                } else if (load_type == 3 && obj.getId() == startLoadFromMessageId) {
                    if (needSelectFromMessageId) {
                        highlightMessageId = obj.getId();
                    } else {
                        highlightMessageId = Integer.MAX_VALUE;
                    }
                    scrollToMessage = obj;
                    startLoadFromMessageId = 0;
                    if (scrollToMessagePosition == -10000) {
                        scrollToMessagePosition = -9000;
                    }
                }
            }
            if (load_type == 0 && newRowsCount == 0) {
                loadsCount--;
            }

            if (forwardEndReached[loadIndex] && loadIndex != 1) {
                first_unread_id = 0;
                last_message_id = 0;
            }

            if (loadsCount <= 2) {
                if (!isCache) {
                    updateSpamView();
                }
            }

            if (load_type == 1) {
                if (messArr.size() != count && !isCache) {
                    forwardEndReached[loadIndex] = true;
                    if (loadIndex != 1) {
                        first_unread_id = 0;
                        last_message_id = 0;
                        chatAdapter.notifyItemRemoved(chatAdapter.getItemCount() - 1);
                        newRowsCount--;
                    }
                    startLoadFromMessageId = 0;
                }
                if (newRowsCount > 0) {
                    int firstVisPos = chatLayoutManager.findLastVisibleItemPosition();
                    int top = 0;
                    if (firstVisPos != chatLayoutManager.getItemCount() - 1) {
                        firstVisPos = RecyclerView.NO_POSITION;
                    } else {
                        View firstVisView = chatLayoutManager.findViewByPosition(firstVisPos);
                        top = ((firstVisView == null) ? 0 : firstVisView.getTop())
                                - chatListView.getPaddingTop();
                    }
                    chatAdapter.notifyItemRangeInserted(chatAdapter.getItemCount() - 1, newRowsCount);
                    if (firstVisPos != RecyclerView.NO_POSITION) {
                        chatLayoutManager.scrollToPositionWithOffset(firstVisPos, top);
                    }
                }
                loadingForward = false;
            } else {
                if (messArr.size() < count && load_type != 3) {
                    if (isCache) {
                        if (currentEncryptedChat != null || isBroadcast) {
                            endReached[loadIndex] = true;
                        }
                        if (load_type != 2) {
                            cacheEndReached[loadIndex] = true;
                        }
                    } else if (load_type != 2) {
                        endReached[loadIndex] = true;// =TODO if < 7 from unread
                    }
                }
                loading = false;

                if (chatListView != null) {
                    if (first || scrollToTopOnResume || forceScrollToTop) {
                        forceScrollToTop = false;
                        chatAdapter.notifyDataSetChanged();
                        if (scrollToMessage != null) {
                            int yOffset;
                            if (scrollToMessagePosition == -9000) {
                                yOffset = Math.max(0,
                                        (chatListView.getHeight() - scrollToMessage.getApproximateHeight())
                                                / 2);
                            } else if (scrollToMessagePosition == -10000) {
                                yOffset = 0;
                            } else {
                                yOffset = scrollToMessagePosition;
                            }
                            if (!messages.isEmpty()) {
                                if (messages.get(messages.size() - 1) == scrollToMessage
                                        || messages.get(messages.size() - 2) == scrollToMessage) {
                                    chatLayoutManager.scrollToPositionWithOffset((chatAdapter.isBot ? 1 : 0),
                                            -chatListView.getPaddingTop() - AndroidUtilities.dp(7) + yOffset);
                                } else {
                                    chatLayoutManager.scrollToPositionWithOffset(
                                            chatAdapter.messagesStartRow + messages.size()
                                                    - messages.indexOf(scrollToMessage) - 1,
                                            -chatListView.getPaddingTop() - AndroidUtilities.dp(7) + yOffset);
                                }
                            }
                            chatListView.invalidate();
                            if (scrollToMessagePosition == -10000 || scrollToMessagePosition == -9000) {
                                showPagedownButton(true, true);
                            }
                            scrollToMessagePosition = -10000;
                            scrollToMessage = null;
                        } else {
                            moveScrollToLastMessage();
                        }
                    } else {
                        if (newRowsCount != 0) {
                            boolean end = false;
                            if (endReached[loadIndex]
                                    && (loadIndex == 0 && mergeDialogId == 0 || loadIndex == 1)) {
                                end = true;
                                chatAdapter.notifyItemRangeChanged(chatAdapter.isBot ? 1 : 0, 2);
                            }
                            int firstVisPos = chatLayoutManager.findLastVisibleItemPosition();
                            View firstVisView = chatLayoutManager.findViewByPosition(firstVisPos);
                            int top = ((firstVisView == null) ? 0 : firstVisView.getTop())
                                    - chatListView.getPaddingTop();
                            if (newRowsCount - (end ? 1 : 0) > 0) {
                                chatAdapter.notifyItemRangeInserted((chatAdapter.isBot ? 2 : 1) + (end ? 0 : 1),
                                        newRowsCount - (end ? 1 : 0));
                            }
                            if (firstVisPos != -1) {
                                chatLayoutManager.scrollToPositionWithOffset(
                                        firstVisPos + newRowsCount - (end ? 1 : 0), top);
                            }
                        } else if (endReached[loadIndex]
                                && (loadIndex == 0 && mergeDialogId == 0 || loadIndex == 1)) {
                            chatAdapter.notifyItemRemoved(chatAdapter.isBot ? 1 : 0);
                        }
                    }

                    if (paused) {
                        scrollToTopOnResume = true;
                        if (scrollToMessage != null) {
                            scrollToTopUnReadOnResume = true;
                        }
                    }

                    if (first) {
                        if (chatListView != null) {
                            chatListView.setEmptyView(emptyViewContainer);
                        }
                    }
                } else {
                    scrollToTopOnResume = true;
                    if (scrollToMessage != null) {
                        scrollToTopUnReadOnResume = true;
                    }
                }
            }

            if (first && messages.size() > 0) {
                if (loadIndex == 0) {
                    final boolean wasUnreadFinal = wasUnread;
                    final int last_unread_date_final = last_unread_date;
                    final int lastid = messages.get(0).getId();
                    AndroidUtilities.runOnUIThread(new Runnable() {
                        @Override
                        public void run() {
                            if (last_message_id != 0) {
                                MessagesController.getInstance().markDialogAsRead(dialog_id, lastid,
                                        last_message_id, last_unread_date_final, wasUnreadFinal, false);
                            } else {
                                MessagesController.getInstance().markDialogAsRead(dialog_id, lastid,
                                        minMessageId[0], maxDate[0], wasUnreadFinal, false);
                            }
                        }
                    }, 700);
                }
                first = false;
            }
            if (messages.isEmpty() && currentEncryptedChat == null && currentUser != null && currentUser.bot
                    && botUser == null) {
                botUser = "";
                updateBottomOverlay();
            }

            if (newRowsCount == 0 && currentEncryptedChat != null && !endReached[0]) {
                first = true;
                if (chatListView != null) {
                    chatListView.setEmptyView(null);
                }
                if (emptyViewContainer != null) {
                    emptyViewContainer.setVisibility(View.INVISIBLE);
                }
            } else {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
            }
            checkScrollForLoad(false);
        }
    } else if (id == NotificationCenter.emojiDidLoaded) {
        if (chatListView != null) {
            chatListView.invalidateViews();
        }
        if (replyObjectTextView != null) {
            replyObjectTextView.invalidate();
        }
        if (alertTextView != null) {
            alertTextView.invalidate();
        }
        if (pinnedMessageTextView != null) {
            pinnedMessageTextView.invalidate();
        }
        if (mentionListView != null) {
            mentionListView.invalidateViews();
        }
    } else if (id == NotificationCenter.updateInterfaces) {
        int updateMask = (Integer) args[0];
        if ((updateMask & MessagesController.UPDATE_MASK_NAME) != 0
                || (updateMask & MessagesController.UPDATE_MASK_CHAT_NAME) != 0) {
            if (currentChat != null) {
                TLRPC.Chat chat = MessagesController.getInstance().getChat(currentChat.id);
                if (chat != null) {
                    currentChat = chat;
                }
            } else if (currentUser != null) {
                TLRPC.User user = MessagesController.getInstance().getUser(currentUser.id);
                if (user != null) {
                    currentUser = user;
                }
            }
            updateTitle();
        }
        boolean updateSubtitle = false;
        if ((updateMask & MessagesController.UPDATE_MASK_CHAT_MEMBERS) != 0
                || (updateMask & MessagesController.UPDATE_MASK_STATUS) != 0) {
            if (currentChat != null && avatarContainer != null) {
                avatarContainer.updateOnlineCount();
            }
            updateSubtitle = true;
        }
        if ((updateMask & MessagesController.UPDATE_MASK_AVATAR) != 0
                || (updateMask & MessagesController.UPDATE_MASK_CHAT_AVATAR) != 0
                || (updateMask & MessagesController.UPDATE_MASK_NAME) != 0) {
            checkAndUpdateAvatar();
            updateVisibleRows();
        }
        if ((updateMask & MessagesController.UPDATE_MASK_USER_PRINT) != 0) {
            updateSubtitle = true;
        }
        if ((updateMask & MessagesController.UPDATE_MASK_CHANNEL) != 0 && ChatObject.isChannel(currentChat)) {
            TLRPC.Chat chat = MessagesController.getInstance().getChat(currentChat.id);
            if (chat == null) {
                return;
            }
            currentChat = chat;
            updateSubtitle = true;
            updateBottomOverlay();
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setDialogId(dialog_id);
            }
        }
        if (avatarContainer != null && updateSubtitle) {
            avatarContainer.updateSubtitle();
        }
        if ((updateMask & MessagesController.UPDATE_MASK_USER_PHONE) != 0) {
            updateContactStatus();
        }
    } else if (id == NotificationCenter.didReceivedNewMessages) {
        long did = (Long) args[0];
        if (did == dialog_id) {

            boolean updateChat = false;
            boolean hasFromMe = false;
            ArrayList<MessageObject> arr = (ArrayList<MessageObject>) args[1];
            if (currentEncryptedChat != null && arr.size() == 1) {
                MessageObject obj = arr.get(0);

                if (currentEncryptedChat != null && obj.isOut() && obj.messageOwner.action != null
                        && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                        && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL
                        && getParentActivity() != null) {
                    if (AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) < 17
                            && currentEncryptedChat.ttl > 0 && currentEncryptedChat.ttl <= 60) {
                        AlertDialog.Builder builder = new AlertDialog.Builder(getParentActivity());
                        builder.setTitle(LocaleController.getString("AppName", R.string.AppName));
                        builder.setPositiveButton(LocaleController.getString("OK", R.string.OK), null);
                        builder.setMessage(LocaleController.formatString("CompatibilityChat",
                                R.string.CompatibilityChat, currentUser.first_name, currentUser.first_name));
                        showDialog(builder.create());
                    }
                }
            }
            if (currentChat != null || inlineReturn != 0) {
                for (int a = 0; a < arr.size(); a++) {
                    MessageObject messageObject = arr.get(a);
                    if (currentChat != null) {
                        if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser
                                && messageObject.messageOwner.action.user_id == UserConfig.getClientUserId()
                                || messageObject.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                        && messageObject.messageOwner.action.users
                                                .contains(UserConfig.getClientUserId())) {
                            TLRPC.Chat newChat = MessagesController.getInstance().getChat(currentChat.id);
                            if (newChat != null) {
                                currentChat = newChat;
                                checkActionBarMenu();
                                updateBottomOverlay();
                                if (avatarContainer != null) {
                                    avatarContainer.updateSubtitle();
                                }
                            }
                        } else if (messageObject.messageOwner.reply_to_msg_id != 0
                                && messageObject.replyMessageObject == null) {
                            messageObject.replyMessageObject = messagesDict[0]
                                    .get(messageObject.messageOwner.reply_to_msg_id);
                            if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionPinMessage) {
                                messageObject.generatePinMessageText(null, null);
                            } else if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionGameScore) {
                                messageObject.generateGameMessageText(null);
                            }
                        }
                    } else if (inlineReturn != 0) {
                        if (messageObject.messageOwner.reply_markup != null) {
                            for (int b = 0; b < messageObject.messageOwner.reply_markup.rows.size(); b++) {
                                TLRPC.TL_keyboardButtonRow row = messageObject.messageOwner.reply_markup.rows
                                        .get(b);
                                for (int c = 0; c < row.buttons.size(); c++) {
                                    TLRPC.KeyboardButton button = row.buttons.get(c);
                                    if (button instanceof TLRPC.TL_keyboardButtonSwitchInline) {
                                        processSwitchButton((TLRPC.TL_keyboardButtonSwitchInline) button);
                                        break;
                                    }
                                }
                            }
                        }
                    }
                }
            }

            boolean reloadMegagroup = false;
            if (!forwardEndReached[0]) {
                int currentMaxDate = Integer.MIN_VALUE;
                int currentMinMsgId = Integer.MIN_VALUE;
                if (currentEncryptedChat != null) {
                    currentMinMsgId = Integer.MAX_VALUE;
                }
                boolean currentMarkAsRead = false;

                for (int a = 0; a < arr.size(); a++) {
                    MessageObject obj = arr.get(a);
                    if (currentUser != null && currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                    if (avatarContainer != null && currentEncryptedChat != null
                            && obj.messageOwner.action != null
                            && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                            && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL) {
                        avatarContainer.setTime(
                                ((TLRPC.TL_decryptedMessageActionSetMessageTTL) obj.messageOwner.action.encryptedAction).ttl_seconds);
                    }
                    if (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                        final Bundle bundle = new Bundle();
                        bundle.putInt("chat_id", obj.messageOwner.action.channel_id);
                        final BaseFragment lastFragment = parentLayout.fragmentsStack.size() > 0
                                ? parentLayout.fragmentsStack.get(parentLayout.fragmentsStack.size() - 1)
                                : null;
                        final int channel_id = obj.messageOwner.action.channel_id;
                        AndroidUtilities.runOnUIThread(new Runnable() {
                            @Override
                            public void run() {
                                ActionBarLayout parentLayout = ChatActivity.this.parentLayout;
                                if (lastFragment != null) {
                                    NotificationCenter.getInstance().removeObserver(lastFragment,
                                            NotificationCenter.closeChats);
                                }
                                NotificationCenter.getInstance()
                                        .postNotificationName(NotificationCenter.closeChats);
                                parentLayout.presentFragment(new ChatActivity(bundle), true);
                                AndroidUtilities.runOnUIThread(new Runnable() {
                                    @Override
                                    public void run() {
                                        MessagesController.getInstance().loadFullChat(channel_id, 0, true);
                                    }
                                }, 1000);
                            }
                        });
                        return;
                    } else if (currentChat != null && currentChat.megagroup
                            && (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                    || obj.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser)) {
                        reloadMegagroup = true;
                    }
                    if (obj.isOut() && obj.isSending()) {
                        scrollToLastMessage(false);
                        return;
                    }
                    if (obj.type < 0 || messagesDict[0].containsKey(obj.getId())) {
                        continue;
                    }
                    obj.checkLayout();
                    currentMaxDate = Math.max(currentMaxDate, obj.messageOwner.date);
                    if (obj.getId() > 0) {
                        currentMinMsgId = Math.max(obj.getId(), currentMinMsgId);
                        last_message_id = Math.max(last_message_id, obj.getId());
                    } else if (currentEncryptedChat != null) {
                        currentMinMsgId = Math.min(obj.getId(), currentMinMsgId);
                        last_message_id = Math.min(last_message_id, obj.getId());
                    }

                    if (!obj.isOut() && obj.isUnread()) {
                        unread_to_load++;
                        currentMarkAsRead = true;
                    }
                    if (obj.type == 10 || obj.type == 11) {
                        updateChat = true;
                    }
                }

                if (currentMarkAsRead) {
                    if (paused) {
                        readWhenResume = true;
                        readWithDate = currentMaxDate;
                        readWithMid = currentMinMsgId;
                    } else {
                        if (messages.size() > 0) {
                            MessagesController.getInstance().markDialogAsRead(dialog_id,
                                    messages.get(0).getId(), currentMinMsgId, currentMaxDate, true, false);
                        }
                    }
                }
                updateVisibleRows();
            } else {
                boolean markAsRead = false;
                boolean unreadUpdated = true;
                int oldCount = messages.size();
                int addedCount = 0;
                HashMap<String, ArrayList<MessageObject>> webpagesToReload = null;
                int placeToPaste = -1;
                for (int a = 0; a < arr.size(); a++) {
                    MessageObject obj = arr.get(a);
                    if (a == 0) {
                        if (obj.messageOwner.id < 0) {
                            placeToPaste = 0;
                        } else {
                            if (!messages.isEmpty()) {
                                int size = messages.size();
                                for (int b = 0; b < size; b++) {
                                    MessageObject lastMessage = messages.get(b);
                                    if (lastMessage.type >= 0 && lastMessage.messageOwner.date > 0) {
                                        if (lastMessage.messageOwner.id > 0 && obj.messageOwner.id > 0) {
                                            if (lastMessage.messageOwner.id < obj.messageOwner.id) {
                                                placeToPaste = b;
                                                break;
                                            }
                                        } else {
                                            if (lastMessage.messageOwner.date < obj.messageOwner.date) {
                                                placeToPaste = b;
                                                break;
                                            }
                                        }
                                    }
                                }
                                if (placeToPaste == -1 || placeToPaste > messages.size()) {
                                    placeToPaste = messages.size();
                                }
                            } else {
                                placeToPaste = 0;
                            }
                        }
                    }
                    if (currentUser != null && currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                    if (avatarContainer != null && currentEncryptedChat != null
                            && obj.messageOwner.action != null
                            && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                            && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL) {
                        avatarContainer.setTime(
                                ((TLRPC.TL_decryptedMessageActionSetMessageTTL) obj.messageOwner.action.encryptedAction).ttl_seconds);
                    }
                    if (obj.type < 0 || messagesDict[0].containsKey(obj.getId())) {
                        continue;
                    }
                    if (currentEncryptedChat != null
                            && obj.messageOwner.media instanceof TLRPC.TL_messageMediaWebPage
                            && obj.messageOwner.media.webpage instanceof TLRPC.TL_webPageUrlPending) {
                        if (webpagesToReload == null) {
                            webpagesToReload = new HashMap<>();
                        }
                        ArrayList<MessageObject> arrayList = webpagesToReload
                                .get(obj.messageOwner.media.webpage.url);
                        if (arrayList == null) {
                            arrayList = new ArrayList<>();
                            webpagesToReload.put(obj.messageOwner.media.webpage.url, arrayList);
                        }
                        arrayList.add(obj);
                    }
                    obj.checkLayout();
                    if (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                        final Bundle bundle = new Bundle();
                        bundle.putInt("chat_id", obj.messageOwner.action.channel_id);
                        final BaseFragment lastFragment = parentLayout.fragmentsStack.size() > 0
                                ? parentLayout.fragmentsStack.get(parentLayout.fragmentsStack.size() - 1)
                                : null;
                        final int channel_id = obj.messageOwner.action.channel_id;
                        AndroidUtilities.runOnUIThread(new Runnable() {
                            @Override
                            public void run() {
                                ActionBarLayout parentLayout = ChatActivity.this.parentLayout;
                                if (lastFragment != null) {
                                    NotificationCenter.getInstance().removeObserver(lastFragment,
                                            NotificationCenter.closeChats);
                                }
                                NotificationCenter.getInstance()
                                        .postNotificationName(NotificationCenter.closeChats);
                                parentLayout.presentFragment(new ChatActivity(bundle), true);
                                AndroidUtilities.runOnUIThread(new Runnable() {
                                    @Override
                                    public void run() {
                                        MessagesController.getInstance().loadFullChat(channel_id, 0, true);
                                    }
                                }, 1000);
                            }
                        });
                        return;
                    } else if (currentChat != null && currentChat.megagroup
                            && (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                    || obj.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser)) {
                        reloadMegagroup = true;
                    }
                    if (minDate[0] == 0 || obj.messageOwner.date < minDate[0]) {
                        minDate[0] = obj.messageOwner.date;
                    }

                    if (obj.isOut()) {
                        removeUnreadPlane();
                        hasFromMe = true;
                    }

                    if (obj.getId() > 0) {
                        maxMessageId[0] = Math.min(obj.getId(), maxMessageId[0]);
                        minMessageId[0] = Math.max(obj.getId(), minMessageId[0]);
                    } else if (currentEncryptedChat != null) {
                        maxMessageId[0] = Math.max(obj.getId(), maxMessageId[0]);
                        minMessageId[0] = Math.min(obj.getId(), minMessageId[0]);
                    }
                    maxDate[0] = Math.max(maxDate[0], obj.messageOwner.date);
                    messagesDict[0].put(obj.getId(), obj);
                    ArrayList<MessageObject> dayArray = messagesByDays.get(obj.dateKey);
                    if (dayArray == null) {
                        dayArray = new ArrayList<>();
                        messagesByDays.put(obj.dateKey, dayArray);
                        TLRPC.Message dateMsg = new TLRPC.Message();
                        dateMsg.message = LocaleController.formatDateChat(obj.messageOwner.date);
                        dateMsg.id = 0;
                        dateMsg.date = obj.messageOwner.date;
                        MessageObject dateObj = new MessageObject(dateMsg, null, false);
                        dateObj.type = 10;
                        dateObj.contentType = 1;
                        messages.add(placeToPaste, dateObj);
                        addedCount++;
                    }
                    if (!obj.isOut()) {
                        if (paused && placeToPaste == 0) {
                            if (!scrollToTopUnReadOnResume && unreadMessageObject != null) {
                                removeMessageObject(unreadMessageObject);
                                if (placeToPaste > 0) {
                                    placeToPaste--;
                                }
                                unreadMessageObject = null;
                            }
                            if (unreadMessageObject == null) {
                                TLRPC.Message dateMsg = new TLRPC.Message();
                                dateMsg.message = "";
                                dateMsg.id = 0;
                                MessageObject dateObj = new MessageObject(dateMsg, null, false);
                                dateObj.type = 6;
                                dateObj.contentType = 2;
                                messages.add(0, dateObj);
                                unreadMessageObject = dateObj;
                                scrollToMessage = unreadMessageObject;
                                scrollToMessagePosition = -10000;
                                unreadUpdated = false;
                                unread_to_load = 0;
                                scrollToTopUnReadOnResume = true;
                                addedCount++;
                            }
                        }
                        if (unreadMessageObject != null) {
                            unread_to_load++;
                            unreadUpdated = true;
                        }
                        if (obj.isUnread()) {
                            if (!paused) {
                                obj.setIsRead();
                            }
                            markAsRead = true;
                        }
                    }

                    dayArray.add(0, obj);
                    if (placeToPaste > messages.size()) {
                        placeToPaste = messages.size();
                    }
                    messages.add(placeToPaste, obj);
                    addedCount++;
                    newUnreadMessageCount++;
                    if (obj.type == 10 || obj.type == 11) {
                        updateChat = true;
                    }
                }
                if (webpagesToReload != null) {
                    MessagesController.getInstance().reloadWebPages(dialog_id, webpagesToReload);
                }

                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
                if (chatAdapter != null) {
                    if (unreadUpdated) {
                        chatAdapter.updateRowWithMessageObject(unreadMessageObject);
                    }
                    if (addedCount != 0) {
                        chatAdapter.notifyItemRangeInserted(chatAdapter.getItemCount() - placeToPaste,
                                addedCount);
                    }
                } else {
                    scrollToTopOnResume = true;
                }

                if (chatListView != null && chatAdapter != null) {
                    int lastVisible = chatLayoutManager.findLastVisibleItemPosition();
                    if (lastVisible == RecyclerView.NO_POSITION) {
                        lastVisible = 0;
                    }
                    if (endReached[0]) {
                        lastVisible++;
                    }
                    if (chatAdapter.isBot) {
                        oldCount++;
                    }
                    if (lastVisible >= oldCount || hasFromMe) {
                        newUnreadMessageCount = 0;
                        if (!firstLoading) {
                            if (paused) {
                                scrollToTopOnResume = true;
                            } else {
                                forceScrollToTop = true;
                                moveScrollToLastMessage();
                            }
                        }
                    } else {
                        if (newUnreadMessageCount != 0 && pagedownButtonCounter != null) {
                            pagedownButtonCounter.setVisibility(View.VISIBLE);
                            pagedownButtonCounter.setText(String.format("%d", newUnreadMessageCount));
                        }
                        showPagedownButton(true, true);
                    }
                } else {
                    scrollToTopOnResume = true;
                }

                if (markAsRead) {
                    if (paused) {
                        readWhenResume = true;
                        readWithDate = maxDate[0];
                        readWithMid = minMessageId[0];
                    } else {
                        MessagesController.getInstance().markDialogAsRead(dialog_id, messages.get(0).getId(),
                                minMessageId[0], maxDate[0], true, false);
                    }
                }
            }
            if (!messages.isEmpty() && botUser != null && botUser.length() == 0) {
                botUser = null;
                updateBottomOverlay();
            }
            if (updateChat) {
                updateTitle();
                checkAndUpdateAvatar();
            }
            if (reloadMegagroup) {
                MessagesController.getInstance().loadFullChat(currentChat.id, 0, true);
            }
        }
    } else if (id == NotificationCenter.closeChats) {
        if (args != null && args.length > 0) {
            long did = (Long) args[0];
            if (did == dialog_id) {
                finishFragment();
            }
        } else {
            removeSelfFromStack();
        }
    } else if (id == NotificationCenter.messagesRead) {
        SparseArray<Long> inbox = (SparseArray<Long>) args[0];
        SparseArray<Long> outbox = (SparseArray<Long>) args[1];
        boolean updated = false;
        for (int b = 0; b < inbox.size(); b++) {
            int key = inbox.keyAt(b);
            long messageId = inbox.get(key);
            if (key != dialog_id) {
                continue;
            }
            for (int a = 0; a < messages.size(); a++) {
                MessageObject obj = messages.get(a);
                if (!obj.isOut() && obj.getId() > 0 && obj.getId() <= (int) messageId) {
                    if (!obj.isUnread()) {
                        break;
                    }
                    obj.setIsRead();
                    updated = true;
                }
            }
            break;
        }
        for (int b = 0; b < outbox.size(); b++) {
            int key = outbox.keyAt(b);
            int messageId = (int) ((long) outbox.get(key));
            if (key != dialog_id) {
                continue;
            }
            for (int a = 0; a < messages.size(); a++) {
                MessageObject obj = messages.get(a);
                if (obj.isOut() && obj.getId() > 0 && obj.getId() <= messageId) {
                    if (!obj.isUnread()) {
                        break;
                    }
                    obj.setIsRead();
                    updated = true;
                }
            }
            break;
        }
        if (updated) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.messagesDeleted) {
        ArrayList<Integer> markAsDeletedMessages = (ArrayList<Integer>) args[0];
        int channelId = (Integer) args[1];
        int loadIndex = 0;
        if (ChatObject.isChannel(currentChat)) {
            if (channelId == 0 && mergeDialogId != 0) {
                loadIndex = 1;
            } else if (channelId == currentChat.id) {
                loadIndex = 0;
            } else {
                return;
            }
        } else if (channelId != 0) {
            return;
        }
        boolean updated = false;
        for (int a = 0; a < markAsDeletedMessages.size(); a++) {
            Integer ids = markAsDeletedMessages.get(a);
            MessageObject obj = messagesDict[loadIndex].get(ids);
            if (loadIndex == 0 && info != null && info.pinned_msg_id == ids) {
                pinnedMessageObject = null;
                info.pinned_msg_id = 0;
                MessagesStorage.getInstance().updateChannelPinnedMessage(channelId, 0);
                updatePinnedMessageView(true);
            }
            if (obj != null) {
                int index = messages.indexOf(obj);
                if (index != -1) {
                    messages.remove(index);
                    messagesDict[loadIndex].remove(ids);
                    ArrayList<MessageObject> dayArr = messagesByDays.get(obj.dateKey);
                    if (dayArr != null) {
                        dayArr.remove(obj);
                        if (dayArr.isEmpty()) {
                            messagesByDays.remove(obj.dateKey);
                            if (index >= 0 && index < messages.size()) {
                                messages.remove(index);
                            }
                        }
                    }
                    updated = true;
                }
            }
        }
        if (messages.isEmpty()) {
            if (!endReached[0] && !loading) {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
                if (chatListView != null) {
                    chatListView.setEmptyView(null);
                }
                if (currentEncryptedChat == null) {
                    maxMessageId[0] = maxMessageId[1] = Integer.MAX_VALUE;
                    minMessageId[0] = minMessageId[1] = Integer.MIN_VALUE;
                } else {
                    maxMessageId[0] = maxMessageId[1] = Integer.MIN_VALUE;
                    minMessageId[0] = minMessageId[1] = Integer.MAX_VALUE;
                }
                maxDate[0] = maxDate[1] = Integer.MIN_VALUE;
                minDate[0] = minDate[1] = 0;
                waitingForLoad.add(lastLoadIndex);
                MessagesController.getInstance().loadMessages(dialog_id, 30, 0, !cacheEndReached[0], minDate[0],
                        classGuid, 0, 0, ChatObject.isChannel(currentChat), lastLoadIndex++);
                loading = true;
            } else {
                if (botButtons != null) {
                    botButtons = null;
                    if (chatActivityEnterView != null) {
                        chatActivityEnterView.setButtons(null, false);
                    }
                }
                if (currentEncryptedChat == null && currentUser != null && currentUser.bot && botUser == null) {
                    botUser = "";
                    updateBottomOverlay();
                }
            }
        }
        if (updated && chatAdapter != null) {
            removeUnreadPlane();
            chatAdapter.notifyDataSetChanged();
        }
    } else if (id == NotificationCenter.messageReceivedByServer) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            Integer newMsgId = (Integer) args[1];
            if (!newMsgId.equals(msgId) && messagesDict[0].containsKey(newMsgId)) {
                MessageObject removed = messagesDict[0].remove(msgId);
                if (removed != null) {
                    int index = messages.indexOf(removed);
                    messages.remove(index);
                    ArrayList<MessageObject> dayArr = messagesByDays.get(removed.dateKey);
                    dayArr.remove(obj);
                    if (dayArr.isEmpty()) {
                        messagesByDays.remove(obj.dateKey);
                        if (index >= 0 && index < messages.size()) {
                            messages.remove(index);
                        }
                    }
                    if (chatAdapter != null) {
                        chatAdapter.notifyDataSetChanged();
                    }
                }
                return;
            }
            TLRPC.Message newMsgObj = (TLRPC.Message) args[2];
            boolean mediaUpdated = false;
            boolean updatedForward = false;
            if (newMsgObj != null) {
                try {
                    updatedForward = obj.isForwarded()
                            && (obj.messageOwner.reply_markup == null && newMsgObj.reply_markup != null
                                    || !obj.messageOwner.message.equals(newMsgObj.message));
                    mediaUpdated = updatedForward
                            || obj.messageOwner.params != null
                                    && obj.messageOwner.params.containsKey("query_id")
                            || newMsgObj.media != null && obj.messageOwner.media != null
                                    && !newMsgObj.media.getClass().equals(obj.messageOwner.media.getClass());
                } catch (Exception e) {
                    FileLog.e("tmessages", e);
                }
                obj.messageOwner = newMsgObj;
                obj.generateThumbs(true);
                obj.setType();
                if (newMsgObj.media instanceof TLRPC.TL_messageMediaGame) {
                    obj.applyNewText();
                }
            }
            if (updatedForward) {
                obj.measureInlineBotButtons();
            }
            messagesDict[0].remove(msgId);
            messagesDict[0].put(newMsgId, obj);
            obj.messageOwner.id = newMsgId;
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SENT;
            obj.forceUpdate = mediaUpdated;
            ArrayList<MessageObject> messArr = new ArrayList<>();
            messArr.add(obj);
            if (currentEncryptedChat == null) {
                MessagesQuery.loadReplyMessagesForMessages(messArr, dialog_id);
            }
            if (chatAdapter != null) {
                chatAdapter.updateRowWithMessageObject(obj);
            }
            if (chatLayoutManager != null) {
                if (mediaUpdated && chatLayoutManager.findLastVisibleItemPosition() >= messages.size() - 1) {
                    moveScrollToLastMessage();
                }
            }
            NotificationsController.getInstance().playOutChatSound();
        }
    } else if (id == NotificationCenter.messageReceivedByAck) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SENT;
            if (chatAdapter != null) {
                chatAdapter.updateRowWithMessageObject(obj);
            }
        }
    } else if (id == NotificationCenter.messageSendError) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SEND_ERROR;
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.chatInfoDidLoaded) {
        TLRPC.ChatFull chatFull = (TLRPC.ChatFull) args[0];
        if (currentChat != null && chatFull.id == currentChat.id) {
            if (chatFull instanceof TLRPC.TL_channelFull) {
                if (currentChat.megagroup) {
                    int lastDate = 0;
                    if (chatFull.participants != null) {
                        for (int a = 0; a < chatFull.participants.participants.size(); a++) {
                            lastDate = Math.max(chatFull.participants.participants.get(a).date, lastDate);
                        }
                    }
                    if (lastDate == 0 || Math.abs(System.currentTimeMillis() / 1000 - lastDate) > 60 * 60) {
                        MessagesController.getInstance().loadChannelParticipants(currentChat.id);
                    }
                }
                if (chatFull.participants == null && info != null) {
                    chatFull.participants = info.participants;
                }
            }
            info = chatFull;
            if (mentionsAdapter != null) {
                mentionsAdapter.setChatInfo(info);
            }
            if (args[3] instanceof MessageObject) {
                pinnedMessageObject = (MessageObject) args[3];
                updatePinnedMessageView(false);
            } else {
                updatePinnedMessageView(true);
            }
            if (avatarContainer != null) {
                avatarContainer.updateOnlineCount();
                avatarContainer.updateSubtitle();
            }
            if (isBroadcast) {
                SendMessagesHelper.getInstance().setCurrentChatInfo(info);
            }
            if (info instanceof TLRPC.TL_chatFull) {
                hasBotsCommands = false;
                botInfo.clear();
                botsCount = 0;
                URLSpanBotCommand.enabled = false;
                for (int a = 0; a < info.participants.participants.size(); a++) {
                    TLRPC.ChatParticipant participant = info.participants.participants.get(a);
                    TLRPC.User user = MessagesController.getInstance().getUser(participant.user_id);
                    if (user != null && user.bot) {
                        URLSpanBotCommand.enabled = true;
                        botsCount++;
                        BotQuery.loadBotInfo(user.id, true, classGuid);
                    }
                }
                if (chatListView != null) {
                    chatListView.invalidateViews();
                }
            } else if (info instanceof TLRPC.TL_channelFull) {
                hasBotsCommands = false;
                botInfo.clear();
                botsCount = 0;
                URLSpanBotCommand.enabled = !info.bot_info.isEmpty();
                botsCount = info.bot_info.size();
                for (int a = 0; a < info.bot_info.size(); a++) {
                    TLRPC.BotInfo bot = info.bot_info.get(a);
                    if (!bot.commands.isEmpty() && (!ChatObject.isChannel(currentChat)
                            || currentChat != null && currentChat.megagroup)) {
                        hasBotsCommands = true;
                    }
                    botInfo.put(bot.user_id, bot);
                }
                if (chatListView != null) {
                    chatListView.invalidateViews();
                }
                if (mentionsAdapter != null && (!ChatObject.isChannel(currentChat)
                        || currentChat != null && currentChat.megagroup)) {
                    mentionsAdapter.setBotInfo(botInfo);
                }
            }
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setBotsCount(botsCount, hasBotsCommands);
            }
            if (mentionsAdapter != null) {
                mentionsAdapter.setBotsCount(botsCount);
            }
            if (ChatObject.isChannel(currentChat) && mergeDialogId == 0 && info.migrated_from_chat_id != 0) {
                mergeDialogId = -info.migrated_from_chat_id;
                maxMessageId[1] = info.migrated_from_max_id;
                if (chatAdapter != null) {
                    chatAdapter.notifyDataSetChanged();
                }
            }
        }
    } else if (id == NotificationCenter.chatInfoCantLoad) {
        int chatId = (Integer) args[0];
        if (currentChat != null && currentChat.id == chatId) {
            int reason = (Integer) args[1];
            if (getParentActivity() == null || closeChatDialog != null) {
                return;
            }
            AlertDialog.Builder builder = new AlertDialog.Builder(getParentActivity());
            builder.setTitle(LocaleController.getString("AppName", R.string.AppName));
            if (reason == 0) {
                builder.setMessage(
                        LocaleController.getString("ChannelCantOpenPrivate", R.string.ChannelCantOpenPrivate));
            } else if (reason == 1) {
                builder.setMessage(LocaleController.getString("ChannelCantOpenNa", R.string.ChannelCantOpenNa));
            } else if (reason == 2) {
                builder.setMessage(
                        LocaleController.getString("ChannelCantOpenBanned", R.string.ChannelCantOpenBanned));
            }
            builder.setPositiveButton(LocaleController.getString("OK", R.string.OK), null);
            showDialog(closeChatDialog = builder.create());

            loading = false;
            if (progressView != null) {
                progressView.setVisibility(View.INVISIBLE);
            }
            if (chatAdapter != null) {
                chatAdapter.notifyDataSetChanged();
            }
        }
    } else if (id == NotificationCenter.contactsDidLoaded) {
        updateContactStatus();
        if (avatarContainer != null) {
            avatarContainer.updateSubtitle();
        }
    } else if (id == NotificationCenter.encryptedChatUpdated) {
        TLRPC.EncryptedChat chat = (TLRPC.EncryptedChat) args[0];
        if (currentEncryptedChat != null && chat.id == currentEncryptedChat.id) {
            currentEncryptedChat = chat;
            updateContactStatus();
            updateSecretStatus();
            initStickers();
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setAllowStickersAndGifs(
                        currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 23,
                        currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 46);
            }
            if (mentionsAdapter != null) {
                mentionsAdapter.setNeedBotContext(
                        !chatActivityEnterView.isEditingMessage() && (currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 46));
            }
        }
    } else if (id == NotificationCenter.messagesReadEncrypted) {
        int encId = (Integer) args[0];
        if (currentEncryptedChat != null && currentEncryptedChat.id == encId) {
            int date = (Integer) args[1];
            for (MessageObject obj : messages) {
                if (!obj.isOut()) {
                    continue;
                } else if (obj.isOut() && !obj.isUnread()) {
                    break;
                }
                if (obj.messageOwner.date - 1 <= date) {
                    obj.setIsRead();
                }
            }
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.audioDidReset || id == NotificationCenter.audioPlayStateChanged) {
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    MessageObject messageObject = cell.getMessageObject();
                    if (messageObject != null && (messageObject.isVoice() || messageObject.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
            count = mentionListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = mentionListView.getChildAt(a);
                if (view instanceof ContextLinkCell) {
                    ContextLinkCell cell = (ContextLinkCell) view;
                    MessageObject messageObject = cell.getMessageObject();
                    if (messageObject != null && (messageObject.isVoice() || messageObject.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
        }
    } else if (id == NotificationCenter.audioProgressDidChanged) {
        Integer mid = (Integer) args[0];
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    if (cell.getMessageObject() != null && cell.getMessageObject().getId() == mid) {
                        MessageObject playing = cell.getMessageObject();
                        MessageObject player = MediaController.getInstance().getPlayingMessageObject();
                        if (player != null) {
                            playing.audioProgress = player.audioProgress;
                            playing.audioProgressSec = player.audioProgressSec;
                            cell.updateAudioProgress();
                        }
                        break;
                    }
                }
            }
        }
    } else if (id == NotificationCenter.removeAllMessagesFromDialog) {
        long did = (Long) args[0];
        if (dialog_id == did) {
            messages.clear();
            waitingForLoad.clear();
            messagesByDays.clear();
            for (int a = 1; a >= 0; a--) {
                messagesDict[a].clear();
                if (currentEncryptedChat == null) {
                    maxMessageId[a] = Integer.MAX_VALUE;
                    minMessageId[a] = Integer.MIN_VALUE;
                } else {
                    maxMessageId[a] = Integer.MIN_VALUE;
                    minMessageId[a] = Integer.MAX_VALUE;
                }
                maxDate[a] = Integer.MIN_VALUE;
                minDate[a] = 0;
                selectedMessagesIds[a].clear();
                selectedMessagesCanCopyIds[a].clear();
            }
            cantDeleteMessagesCount = 0;
            actionBar.hideActionMode();
            updatePinnedMessageView(true);

            if (botButtons != null) {
                botButtons = null;
                if (chatActivityEnterView != null) {
                    chatActivityEnterView.setButtons(null, false);
                }
            }
            if (currentEncryptedChat == null && currentUser != null && currentUser.bot && botUser == null) {
                botUser = "";
                updateBottomOverlay();
            }
            if ((Boolean) args[1]) {
                if (chatAdapter != null) {
                    progressView.setVisibility(chatAdapter.botInfoRow == -1 ? View.VISIBLE : View.INVISIBLE);
                    chatListView.setEmptyView(null);
                }
                for (int a = 0; a < 2; a++) {
                    endReached[a] = false;
                    cacheEndReached[a] = false;
                    forwardEndReached[a] = true;
                }
                first = true;
                firstLoading = true;
                loading = true;
                startLoadFromMessageId = 0;
                needSelectFromMessageId = false;
                waitingForLoad.add(lastLoadIndex);
                MessagesController.getInstance().loadMessages(dialog_id, AndroidUtilities.isTablet() ? 30 : 20,
                        0, true, 0, classGuid, 2, 0, ChatObject.isChannel(currentChat), lastLoadIndex++);
            } else {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                    chatListView.setEmptyView(emptyViewContainer);
                }
            }

            if (chatAdapter != null) {
                chatAdapter.notifyDataSetChanged();
            }
        }
    } else if (id == NotificationCenter.screenshotTook) {
        updateInformationForScreenshotDetector();
    } else if (id == NotificationCenter.blockedUsersDidLoaded) {
        if (currentUser != null) {
            boolean oldValue = userBlocked;
            userBlocked = MessagesController.getInstance().blockedUsers.contains(currentUser.id);
            if (oldValue != userBlocked) {
                updateBottomOverlay();
            }
        }
    } else if (id == NotificationCenter.FileNewChunkAvailable) {
        MessageObject messageObject = (MessageObject) args[0];
        long finalSize = (Long) args[2];
        if (finalSize != 0 && dialog_id == messageObject.getDialogId()) {
            MessageObject currentObject = messagesDict[0].get(messageObject.getId());
            if (currentObject != null) {
                currentObject.messageOwner.media.document.size = (int) finalSize;
                updateVisibleRows();
            }
        }
    } else if (id == NotificationCenter.didCreatedNewDeleteTask) {
        SparseArray<ArrayList<Integer>> mids = (SparseArray<ArrayList<Integer>>) args[0];
        boolean changed = false;
        for (int i = 0; i < mids.size(); i++) {
            int key = mids.keyAt(i);
            ArrayList<Integer> arr = mids.get(key);
            for (Integer mid : arr) {
                MessageObject messageObject = messagesDict[0].get(mid);
                if (messageObject != null) {
                    messageObject.messageOwner.destroyTime = key;
                    changed = true;
                }
            }
        }
        if (changed) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.audioDidStarted) {
        MessageObject messageObject = (MessageObject) args[0];
        sendSecretMessageRead(messageObject);
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    MessageObject messageObject1 = cell.getMessageObject();
                    if (messageObject1 != null && (messageObject1.isVoice() || messageObject1.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
        }
    } else if (id == NotificationCenter.updateMessageMedia) {
        MessageObject messageObject = (MessageObject) args[0];
        MessageObject existMessageObject = messagesDict[0].get(messageObject.getId());
        if (existMessageObject != null) {
            existMessageObject.messageOwner.media = messageObject.messageOwner.media;
            existMessageObject.messageOwner.attachPath = messageObject.messageOwner.attachPath;
            existMessageObject.generateThumbs(false);
        }
        updateVisibleRows();
    } else if (id == NotificationCenter.replaceMessagesObjects) {
        long did = (long) args[0];
        if (did != dialog_id && did != mergeDialogId) {
            return;
        }
        int loadIndex = did == dialog_id ? 0 : 1;
        boolean changed = false;
        boolean mediaUpdated = false;
        ArrayList<MessageObject> messageObjects = (ArrayList<MessageObject>) args[1];
        for (int a = 0; a < messageObjects.size(); a++) {
            MessageObject messageObject = messageObjects.get(a);
            MessageObject old = messagesDict[loadIndex].get(messageObject.getId());
            if (pinnedMessageObject != null && pinnedMessageObject.getId() == messageObject.getId()) {
                pinnedMessageObject = messageObject;
                updatePinnedMessageView(true);
            }
            if (old != null) {
                if (messageObject.type >= 0) {
                    if (!mediaUpdated
                            && messageObject.messageOwner.media instanceof TLRPC.TL_messageMediaWebPage) {
                        mediaUpdated = true;
                    }
                    if (old.replyMessageObject != null) {
                        messageObject.replyMessageObject = old.replyMessageObject;
                        if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionGameScore) {
                            messageObject.generateGameMessageText(null);
                        }
                    }
                    messageObject.messageOwner.attachPath = old.messageOwner.attachPath;
                    messageObject.attachPathExists = old.attachPathExists;
                    messageObject.mediaExists = old.mediaExists;
                    messagesDict[loadIndex].put(old.getId(), messageObject);
                } else {
                    messagesDict[loadIndex].remove(old.getId());
                }
                int index = messages.indexOf(old);
                if (index >= 0) {
                    ArrayList<MessageObject> dayArr = messagesByDays.get(old.dateKey);
                    int index2 = -1;
                    if (dayArr != null) {
                        index2 = dayArr.indexOf(old);
                    }
                    if (messageObject.type >= 0) {
                        messages.set(index, messageObject);
                        if (chatAdapter != null) {
                            chatAdapter.notifyItemChanged(
                                    chatAdapter.messagesStartRow + messages.size() - index - 1);
                        }
                        if (index2 >= 0) {
                            dayArr.set(index2, messageObject);
                        }
                    } else {
                        messages.remove(index);
                        if (chatAdapter != null) {
                            chatAdapter.notifyItemRemoved(
                                    chatAdapter.messagesStartRow + messages.size() - index - 1);
                        }
                        if (index2 >= 0) {
                            dayArr.remove(index2);
                            if (dayArr.isEmpty()) {
                                messagesByDays.remove(old.dateKey);
                                messages.remove(index);
                                chatAdapter.notifyItemRemoved(chatAdapter.messagesStartRow + messages.size());
                            }
                        }
                    }
                    changed = true;
                }
            }
        }
        if (changed && chatLayoutManager != null) {
            if (mediaUpdated && chatLayoutManager.findLastVisibleItemPosition() >= messages.size()
                    - (chatAdapter.isBot ? 2 : 1)) {
                moveScrollToLastMessage();
            }
        }
    } else if (id == NotificationCenter.notificationsSettingsUpdated) {
        updateTitleIcons();
        if (ChatObject.isChannel(currentChat)) {
            updateBottomOverlay();
        }
    } else if (id == NotificationCenter.didLoadedReplyMessages) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.didLoadedPinnedMessage) {
        MessageObject message = (MessageObject) args[0];
        if (message.getDialogId() == dialog_id && info != null && info.pinned_msg_id == message.getId()) {
            pinnedMessageObject = message;
            loadingPinnedMessage = 0;
            updatePinnedMessageView(true);
        }
    } else if (id == NotificationCenter.didReceivedWebpages) {
        ArrayList<TLRPC.Message> arrayList = (ArrayList<TLRPC.Message>) args[0];
        boolean updated = false;
        for (int a = 0; a < arrayList.size(); a++) {
            TLRPC.Message message = arrayList.get(a);
            long did = MessageObject.getDialogId(message);
            if (did != dialog_id && did != mergeDialogId) {
                continue;
            }
            MessageObject currentMessage = messagesDict[did == dialog_id ? 0 : 1].get(message.id);
            if (currentMessage != null) {
                currentMessage.messageOwner.media = new TLRPC.TL_messageMediaWebPage();
                currentMessage.messageOwner.media.webpage = message.media.webpage;
                currentMessage.generateThumbs(true);
                updated = true;
            }
        }
        if (updated) {
            updateVisibleRows();
            if (chatLayoutManager != null
                    && chatLayoutManager.findLastVisibleItemPosition() >= messages.size() - 1) {
                moveScrollToLastMessage();
            }
        }
    } else if (id == NotificationCenter.didReceivedWebpagesInUpdates) {
        if (foundWebPage != null) {
            HashMap<Long, TLRPC.WebPage> hashMap = (HashMap<Long, TLRPC.WebPage>) args[0];
            for (TLRPC.WebPage webPage : hashMap.values()) {
                if (webPage.id == foundWebPage.id) {
                    showReplyPanel(!(webPage instanceof TLRPC.TL_webPageEmpty), null, null, webPage, false,
                            true);
                    break;
                }
            }
        }
    } else if (id == NotificationCenter.messagesReadContent) {
        ArrayList<Long> arrayList = (ArrayList<Long>) args[0];
        boolean updated = false;
        for (int a = 0; a < arrayList.size(); a++) {
            long mid = arrayList.get(a);
            MessageObject currentMessage = messagesDict[mergeDialogId == 0 ? 0 : 1].get((int) mid);
            if (currentMessage != null) {
                currentMessage.setContentIsRead();
                updated = true;
            }
        }
        if (updated) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.botInfoDidLoaded) {
        int guid = (Integer) args[1];
        if (classGuid == guid) {
            TLRPC.BotInfo info = (TLRPC.BotInfo) args[0];
            if (currentEncryptedChat == null) {
                if (!info.commands.isEmpty() && !ChatObject.isChannel(currentChat)) {
                    hasBotsCommands = true;
                }
                botInfo.put(info.user_id, info);
                if (chatAdapter != null) {
                    chatAdapter.notifyItemChanged(0);
                }
                if (mentionsAdapter != null && (!ChatObject.isChannel(currentChat)
                        || currentChat != null && currentChat.megagroup)) {
                    mentionsAdapter.setBotInfo(botInfo);
                }
                if (chatActivityEnterView != null) {
                    chatActivityEnterView.setBotsCount(botsCount, hasBotsCommands);
                }
            }
            updateBotButtons();
        }
    } else if (id == NotificationCenter.botKeyboardDidLoaded) {
        if (dialog_id == (Long) args[1]) {
            TLRPC.Message message = (TLRPC.Message) args[0];
            if (message != null && !userBlocked) {
                botButtons = new MessageObject(message, null, false);
                if (chatActivityEnterView != null) {
                    if (botButtons.messageOwner.reply_markup instanceof TLRPC.TL_replyKeyboardForceReply) {
                        SharedPreferences preferences = ApplicationLoader.applicationContext
                                .getSharedPreferences("mainconfig", Activity.MODE_PRIVATE);
                        if (preferences.getInt("answered_" + dialog_id, 0) != botButtons.getId()
                                && (replyingMessageObject == null
                                        || chatActivityEnterView.getFieldText() == null)) {
                            botReplyButtons = botButtons;
                            chatActivityEnterView.setButtons(botButtons);
                            showReplyPanel(true, botButtons, null, null, false, true);
                        }
                    } else {
                        if (replyingMessageObject != null && botReplyButtons == replyingMessageObject) {
                            botReplyButtons = null;
                            showReplyPanel(false, null, null, null, false, true);
                        }
                        chatActivityEnterView.setButtons(botButtons);
                    }
                }
            } else {
                botButtons = null;
                if (chatActivityEnterView != null) {
                    if (replyingMessageObject != null && botReplyButtons == replyingMessageObject) {
                        botReplyButtons = null;
                        showReplyPanel(false, null, null, null, false, true);
                    }
                    chatActivityEnterView.setButtons(botButtons);
                }
            }
        }
    } else if (id == NotificationCenter.chatSearchResultsAvailable) {
        if (classGuid == (Integer) args[0]) {
            int messageId = (Integer) args[1];
            long did = (Long) args[3];
            if (messageId != 0) {
                scrollToMessageId(messageId, 0, true, did == dialog_id ? 0 : 1);
            }
            updateSearchButtons((Integer) args[2], (Integer) args[4], (Integer) args[5]);
        }
    } else if (id == NotificationCenter.didUpdatedMessagesViews) {
        SparseArray<SparseIntArray> channelViews = (SparseArray<SparseIntArray>) args[0];
        SparseIntArray array = channelViews.get((int) dialog_id);
        if (array != null) {
            boolean updated = false;
            for (int a = 0; a < array.size(); a++) {
                int messageId = array.keyAt(a);
                MessageObject messageObject = messagesDict[0].get(messageId);
                if (messageObject != null) {
                    int newValue = array.get(messageId);
                    if (newValue > messageObject.messageOwner.views) {
                        messageObject.messageOwner.views = newValue;
                        updated = true;
                    }
                }
            }
            if (updated) {
                updateVisibleRows();
            }
        }
    } else if (id == NotificationCenter.peerSettingsDidLoaded) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            updateSpamView();
        }
    } else if (id == NotificationCenter.newDraftReceived) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            applyDraftMaybe(true);
        }
    }
}

---

From source file:kr.wdream.ui.ChatActivity.java

@Override
public void didReceivedNotification(int id, final Object... args) {
    if (id == NotificationCenter.messagesDidLoaded) {
        int guid = (Integer) args[10];
        if (guid == classGuid) {
            if (!openAnimationEnded) {
                NotificationCenter.getInstance().setAllowedNotificationsDutingAnimation(new int[] {
                        NotificationCenter.chatInfoDidLoaded, NotificationCenter.dialogsNeedReload,
                        NotificationCenter.closeChats,
                        NotificationCenter.botKeyboardDidLoaded/*, NotificationCenter.botInfoDidLoaded*/ });
            }//from  w  ww  .  j a v  a  2s. co m
            int queryLoadIndex = (Integer) args[11];
            int index = waitingForLoad.indexOf(queryLoadIndex);
            if (index == -1) {
                return;
            } else {
                waitingForLoad.remove(index);
            }
            ArrayList<MessageObject> messArr = (ArrayList<MessageObject>) args[2];
            if (waitingForReplyMessageLoad) {
                boolean found = false;
                for (int a = 0; a < messArr.size(); a++) {
                    if (messArr.get(a).getId() == startLoadFromMessageId) {
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    startLoadFromMessageId = 0;
                    return;
                }
                int startLoadFrom = startLoadFromMessageId;
                boolean needSelect = needSelectFromMessageId;
                clearChatData();
                startLoadFromMessageId = startLoadFrom;
                needSelectFromMessageId = needSelect;
            }

            loadsCount++;
            long did = (Long) args[0];
            int loadIndex = did == dialog_id ? 0 : 1;
            int count = (Integer) args[1];
            boolean isCache = (Boolean) args[3];
            int fnid = (Integer) args[4];
            int last_unread_date = (Integer) args[7];
            int load_type = (Integer) args[8];
            boolean wasUnread = false;
            if (fnid != 0) {
                first_unread_id = fnid;
                last_message_id = (Integer) args[5];
                unread_to_load = (Integer) args[6];
            } else if (startLoadFromMessageId != 0 && load_type == 3) {
                last_message_id = (Integer) args[5];
            }
            int newRowsCount = 0;

            forwardEndReached[loadIndex] = startLoadFromMessageId == 0 && last_message_id == 0;
            if ((load_type == 1 || load_type == 3) && loadIndex == 1) {
                endReached[0] = cacheEndReached[0] = true;
                forwardEndReached[0] = false;
                minMessageId[0] = 0;
            }

            if (loadsCount == 1 && messArr.size() > 20) {
                loadsCount++;
            }

            if (firstLoading) {
                if (!forwardEndReached[loadIndex]) {
                    messages.clear();
                    messagesByDays.clear();
                    for (int a = 0; a < 2; a++) {
                        messagesDict[a].clear();
                        if (currentEncryptedChat == null) {
                            maxMessageId[a] = Integer.MAX_VALUE;
                            minMessageId[a] = Integer.MIN_VALUE;
                        } else {
                            maxMessageId[a] = Integer.MIN_VALUE;
                            minMessageId[a] = Integer.MAX_VALUE;
                        }
                        maxDate[a] = Integer.MIN_VALUE;
                        minDate[a] = 0;
                    }
                }
                firstLoading = false;
                AndroidUtilities.runOnUIThread(new Runnable() {
                    @Override
                    public void run() {
                        if (parentLayout != null) {
                            parentLayout.resumeDelayedFragmentAnimation();
                        }
                    }
                });
            }

            if (load_type == 1) {
                Collections.reverse(messArr);
            }
            if (currentEncryptedChat == null) {
                MessagesQuery.loadReplyMessagesForMessages(messArr, dialog_id);
            }
            int approximateHeightSum = 0;
            for (int a = 0; a < messArr.size(); a++) {
                MessageObject obj = messArr.get(a);
                approximateHeightSum += obj.getApproximateHeight();
                if (currentUser != null) {
                    if (currentUser.self) {
                        obj.messageOwner.out = true;
                    }
                    if (currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                }
                if (messagesDict[loadIndex].containsKey(obj.getId())) {
                    continue;
                }
                if (loadIndex == 1) {
                    obj.setIsRead();
                }
                if (loadIndex == 0 && ChatObject.isChannel(currentChat) && obj.getId() == 1) {
                    endReached[loadIndex] = true;
                    cacheEndReached[loadIndex] = true;
                }
                if (obj.getId() > 0) {
                    maxMessageId[loadIndex] = Math.min(obj.getId(), maxMessageId[loadIndex]);
                    minMessageId[loadIndex] = Math.max(obj.getId(), minMessageId[loadIndex]);
                } else if (currentEncryptedChat != null) {
                    maxMessageId[loadIndex] = Math.max(obj.getId(), maxMessageId[loadIndex]);
                    minMessageId[loadIndex] = Math.min(obj.getId(), minMessageId[loadIndex]);
                }
                if (obj.messageOwner.date != 0) {
                    maxDate[loadIndex] = Math.max(maxDate[loadIndex], obj.messageOwner.date);
                    if (minDate[loadIndex] == 0 || obj.messageOwner.date < minDate[loadIndex]) {
                        minDate[loadIndex] = obj.messageOwner.date;
                    }
                }

                if (obj.type < 0 || loadIndex == 1
                        && obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                    continue;
                }

                if (!obj.isOut() && obj.isUnread()) {
                    wasUnread = true;
                }
                messagesDict[loadIndex].put(obj.getId(), obj);
                ArrayList<MessageObject> dayArray = messagesByDays.get(obj.dateKey);

                if (dayArray == null) {
                    dayArray = new ArrayList<>();
                    messagesByDays.put(obj.dateKey, dayArray);
                    TLRPC.Message dateMsg = new TLRPC.Message();
                    dateMsg.message = LocaleController.formatDateChat(obj.messageOwner.date);
                    dateMsg.id = 0;
                    dateMsg.date = obj.messageOwner.date;
                    MessageObject dateObj = new MessageObject(dateMsg, null, false);
                    dateObj.type = 10;
                    dateObj.contentType = 1;
                    if (load_type == 1) {
                        messages.add(0, dateObj);
                    } else {
                        messages.add(dateObj);
                    }
                    newRowsCount++;
                }

                newRowsCount++;
                if (load_type == 1) {
                    dayArray.add(obj);
                    messages.add(0, obj);
                }

                if (load_type != 1) {
                    dayArray.add(obj);
                    messages.add(messages.size() - 1, obj);
                }

                if (obj.getId() == last_message_id) {
                    forwardEndReached[loadIndex] = true;
                }

                if (load_type == 2 && obj.getId() == first_unread_id) {
                    if (approximateHeightSum > AndroidUtilities.displaySize.y / 2 || !forwardEndReached[0]) {
                        TLRPC.Message dateMsg = new TLRPC.Message();
                        dateMsg.message = "";
                        dateMsg.id = 0;
                        MessageObject dateObj = new MessageObject(dateMsg, null, false);
                        dateObj.type = 6;
                        dateObj.contentType = 2;
                        messages.add(messages.size() - 1, dateObj);
                        unreadMessageObject = dateObj;
                        scrollToMessage = unreadMessageObject;
                        scrollToMessagePosition = -10000;
                        newRowsCount++;
                    }
                } else if (load_type == 3 && obj.getId() == startLoadFromMessageId) {
                    if (needSelectFromMessageId) {
                        highlightMessageId = obj.getId();
                    } else {
                        highlightMessageId = Integer.MAX_VALUE;
                    }
                    scrollToMessage = obj;
                    startLoadFromMessageId = 0;
                    if (scrollToMessagePosition == -10000) {
                        scrollToMessagePosition = -9000;
                    }
                }
            }
            if (load_type == 0 && newRowsCount == 0) {
                loadsCount--;
            }

            if (forwardEndReached[loadIndex] && loadIndex != 1) {
                first_unread_id = 0;
                last_message_id = 0;
            }

            if (loadsCount <= 2) {
                if (!isCache) {
                    updateSpamView();
                }
            }

            if (load_type == 1) {
                if (messArr.size() != count && !isCache) {
                    forwardEndReached[loadIndex] = true;
                    if (loadIndex != 1) {
                        first_unread_id = 0;
                        last_message_id = 0;
                        chatAdapter.notifyItemRemoved(chatAdapter.getItemCount() - 1);
                        newRowsCount--;
                    }
                    startLoadFromMessageId = 0;
                }
                if (newRowsCount > 0) {
                    int firstVisPos = chatLayoutManager.findLastVisibleItemPosition();
                    int top = 0;
                    if (firstVisPos != chatLayoutManager.getItemCount() - 1) {
                        firstVisPos = RecyclerView.NO_POSITION;
                    } else {
                        View firstVisView = chatLayoutManager.findViewByPosition(firstVisPos);
                        top = ((firstVisView == null) ? 0 : firstVisView.getTop())
                                - chatListView.getPaddingTop();
                    }
                    chatAdapter.notifyItemRangeInserted(chatAdapter.getItemCount() - 1, newRowsCount);
                    if (firstVisPos != RecyclerView.NO_POSITION) {
                        chatLayoutManager.scrollToPositionWithOffset(firstVisPos, top);
                    }
                }
                loadingForward = false;
            } else {
                if (messArr.size() < count && load_type != 3) {
                    if (isCache) {
                        if (currentEncryptedChat != null || isBroadcast) {
                            endReached[loadIndex] = true;
                        }
                        if (load_type != 2) {
                            cacheEndReached[loadIndex] = true;
                        }
                    } else if (load_type != 2) {
                        endReached[loadIndex] = true;// =TODO if < 7 from unread
                    }
                }
                loading = false;

                if (chatListView != null) {
                    if (first || scrollToTopOnResume || forceScrollToTop) {
                        forceScrollToTop = false;
                        chatAdapter.notifyDataSetChanged();
                        if (scrollToMessage != null) {
                            int yOffset;
                            if (scrollToMessagePosition == -9000) {
                                yOffset = Math.max(0,
                                        (chatListView.getHeight() - scrollToMessage.getApproximateHeight())
                                                / 2);
                            } else if (scrollToMessagePosition == -10000) {
                                yOffset = 0;
                            } else {
                                yOffset = scrollToMessagePosition;
                            }
                            if (!messages.isEmpty()) {
                                if (messages.get(messages.size() - 1) == scrollToMessage
                                        || messages.get(messages.size() - 2) == scrollToMessage) {
                                    chatLayoutManager.scrollToPositionWithOffset((chatAdapter.isBot ? 1 : 0),
                                            -chatListView.getPaddingTop() - AndroidUtilities.dp(7) + yOffset);
                                } else {
                                    chatLayoutManager.scrollToPositionWithOffset(
                                            chatAdapter.messagesStartRow + messages.size()
                                                    - messages.indexOf(scrollToMessage) - 1,
                                            -chatListView.getPaddingTop() - AndroidUtilities.dp(7) + yOffset);
                                }
                            }
                            chatListView.invalidate();
                            if (scrollToMessagePosition == -10000 || scrollToMessagePosition == -9000) {
                                showPagedownButton(true, true);
                            }
                            scrollToMessagePosition = -10000;
                            scrollToMessage = null;
                        } else {
                            moveScrollToLastMessage();
                        }
                    } else {
                        if (newRowsCount != 0) {
                            boolean end = false;
                            if (endReached[loadIndex]
                                    && (loadIndex == 0 && mergeDialogId == 0 || loadIndex == 1)) {
                                end = true;
                                chatAdapter.notifyItemRangeChanged(chatAdapter.isBot ? 1 : 0, 2);
                            }
                            int firstVisPos = chatLayoutManager.findLastVisibleItemPosition();
                            View firstVisView = chatLayoutManager.findViewByPosition(firstVisPos);
                            int top = ((firstVisView == null) ? 0 : firstVisView.getTop())
                                    - chatListView.getPaddingTop();
                            if (newRowsCount - (end ? 1 : 0) > 0) {
                                chatAdapter.notifyItemRangeInserted((chatAdapter.isBot ? 2 : 1) + (end ? 0 : 1),
                                        newRowsCount - (end ? 1 : 0));
                            }
                            if (firstVisPos != -1) {
                                chatLayoutManager.scrollToPositionWithOffset(
                                        firstVisPos + newRowsCount - (end ? 1 : 0), top);
                            }
                        } else if (endReached[loadIndex]
                                && (loadIndex == 0 && mergeDialogId == 0 || loadIndex == 1)) {
                            chatAdapter.notifyItemRemoved(chatAdapter.isBot ? 1 : 0);
                        }
                    }

                    if (paused) {
                        scrollToTopOnResume = true;
                        if (scrollToMessage != null) {
                            scrollToTopUnReadOnResume = true;
                        }
                    }

                    if (first) {
                        if (chatListView != null) {
                            chatListView.setEmptyView(emptyViewContainer);
                        }
                    }
                } else {
                    scrollToTopOnResume = true;
                    if (scrollToMessage != null) {
                        scrollToTopUnReadOnResume = true;
                    }
                }
            }

            if (first && messages.size() > 0) {
                if (loadIndex == 0) {
                    final boolean wasUnreadFinal = wasUnread;
                    final int last_unread_date_final = last_unread_date;
                    final int lastid = messages.get(0).getId();
                    AndroidUtilities.runOnUIThread(new Runnable() {
                        @Override
                        public void run() {
                            if (last_message_id != 0) {
                                MessagesController.getInstance().markDialogAsRead(dialog_id, lastid,
                                        last_message_id, last_unread_date_final, wasUnreadFinal, false);
                            } else {
                                MessagesController.getInstance().markDialogAsRead(dialog_id, lastid,
                                        minMessageId[0], maxDate[0], wasUnreadFinal, false);
                            }
                        }
                    }, 700);
                }
                first = false;
            }
            if (messages.isEmpty() && currentEncryptedChat == null && currentUser != null && currentUser.bot
                    && botUser == null) {
                botUser = "";
                updateBottomOverlay();
            }

            if (newRowsCount == 0 && currentEncryptedChat != null && !endReached[0]) {
                first = true;
                if (chatListView != null) {
                    chatListView.setEmptyView(null);
                }
                if (emptyViewContainer != null) {
                    emptyViewContainer.setVisibility(View.INVISIBLE);
                }
            } else {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
            }
            checkScrollForLoad(false);
        }
    } else if (id == NotificationCenter.emojiDidLoaded) {
        if (chatListView != null) {
            chatListView.invalidateViews();
        }
        if (replyObjectTextView != null) {
            replyObjectTextView.invalidate();
        }
        if (alertTextView != null) {
            alertTextView.invalidate();
        }
        if (pinnedMessageTextView != null) {
            pinnedMessageTextView.invalidate();
        }
        if (mentionListView != null) {
            mentionListView.invalidateViews();
        }
    } else if (id == NotificationCenter.updateInterfaces) {
        int updateMask = (Integer) args[0];
        if ((updateMask & MessagesController.UPDATE_MASK_NAME) != 0
                || (updateMask & MessagesController.UPDATE_MASK_CHAT_NAME) != 0) {
            if (currentChat != null) {
                TLRPC.Chat chat = MessagesController.getInstance().getChat(currentChat.id);
                if (chat != null) {
                    currentChat = chat;
                }
            } else if (currentUser != null) {
                TLRPC.User user = MessagesController.getInstance().getUser(currentUser.id);
                if (user != null) {
                    currentUser = user;
                }
            }
            updateTitle();
        }
        boolean updateSubtitle = false;
        if ((updateMask & MessagesController.UPDATE_MASK_CHAT_MEMBERS) != 0
                || (updateMask & MessagesController.UPDATE_MASK_STATUS) != 0) {
            if (currentChat != null && avatarContainer != null) {
                avatarContainer.updateOnlineCount();
            }
            updateSubtitle = true;
        }
        if ((updateMask & MessagesController.UPDATE_MASK_AVATAR) != 0
                || (updateMask & MessagesController.UPDATE_MASK_CHAT_AVATAR) != 0
                || (updateMask & MessagesController.UPDATE_MASK_NAME) != 0) {
            checkAndUpdateAvatar();
            updateVisibleRows();
        }
        if ((updateMask & MessagesController.UPDATE_MASK_USER_PRINT) != 0) {
            updateSubtitle = true;
        }
        if ((updateMask & MessagesController.UPDATE_MASK_CHANNEL) != 0 && ChatObject.isChannel(currentChat)) {
            TLRPC.Chat chat = MessagesController.getInstance().getChat(currentChat.id);
            if (chat == null) {
                return;
            }
            currentChat = chat;
            updateSubtitle = true;
            updateBottomOverlay();
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setDialogId(dialog_id);
            }
        }
        if (avatarContainer != null && updateSubtitle) {
            avatarContainer.updateSubtitle();
        }
        if ((updateMask & MessagesController.UPDATE_MASK_USER_PHONE) != 0) {
            updateContactStatus();
        }
    } else if (id == NotificationCenter.didReceivedNewMessages) {

        //   (  ?  ?
        Log.d(LOG_TAG, "didReceivedNewMessage : " + id);
        long did = (Long) args[0];
        if (did == dialog_id) {

            boolean updateChat = false;
            boolean hasFromMe = false;
            ArrayList<MessageObject> arr = (ArrayList<MessageObject>) args[1];
            if (currentEncryptedChat != null && arr.size() == 1) {
                MessageObject obj = arr.get(0);

                if (currentEncryptedChat != null && obj.isOut() && obj.messageOwner.action != null
                        && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                        && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL
                        && getParentActivity() != null) {
                    if (AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) < 17
                            && currentEncryptedChat.ttl > 0 && currentEncryptedChat.ttl <= 60) {
                        AlertDialog.Builder builder = new AlertDialog.Builder(getParentActivity());
                        builder.setTitle(
                                LocaleController.getString("AppName", kr.wdream.storyshop.R.string.AppName));
                        builder.setPositiveButton(
                                LocaleController.getString("OK", kr.wdream.storyshop.R.string.OK), null);
                        builder.setMessage(LocaleController.formatString("CompatibilityChat",
                                kr.wdream.storyshop.R.string.CompatibilityChat, currentUser.first_name,
                                currentUser.first_name));
                        showDialog(builder.create());
                    }
                }
            }
            if (currentChat != null || inlineReturn != 0) {
                for (int a = 0; a < arr.size(); a++) {
                    MessageObject messageObject = arr.get(a);
                    if (currentChat != null) {
                        if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser
                                && messageObject.messageOwner.action.user_id == UserConfig.getClientUserId()
                                || messageObject.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                        && messageObject.messageOwner.action.users
                                                .contains(UserConfig.getClientUserId())) {
                            TLRPC.Chat newChat = MessagesController.getInstance().getChat(currentChat.id);
                            if (newChat != null) {
                                currentChat = newChat;
                                checkActionBarMenu();
                                updateBottomOverlay();
                                if (avatarContainer != null) {
                                    avatarContainer.updateSubtitle();
                                }
                            }
                        } else if (messageObject.messageOwner.reply_to_msg_id != 0
                                && messageObject.replyMessageObject == null) {
                            messageObject.replyMessageObject = messagesDict[0]
                                    .get(messageObject.messageOwner.reply_to_msg_id);
                            if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionPinMessage) {
                                messageObject.generatePinMessageText(null, null);
                            } else if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionGameScore) {
                                messageObject.generateGameMessageText(null);
                            }
                        }
                    } else if (inlineReturn != 0) {
                        if (messageObject.messageOwner.reply_markup != null) {
                            for (int b = 0; b < messageObject.messageOwner.reply_markup.rows.size(); b++) {
                                TLRPC.TL_keyboardButtonRow row = messageObject.messageOwner.reply_markup.rows
                                        .get(b);
                                for (int c = 0; c < row.buttons.size(); c++) {
                                    TLRPC.KeyboardButton button = row.buttons.get(c);
                                    if (button instanceof TLRPC.TL_keyboardButtonSwitchInline) {
                                        processSwitchButton((TLRPC.TL_keyboardButtonSwitchInline) button);
                                        break;
                                    }
                                }
                            }
                        }
                    }
                }
            }

            boolean reloadMegagroup = false;
            if (!forwardEndReached[0]) {
                int currentMaxDate = Integer.MIN_VALUE;
                int currentMinMsgId = Integer.MIN_VALUE;
                if (currentEncryptedChat != null) {
                    currentMinMsgId = Integer.MAX_VALUE;
                }
                boolean currentMarkAsRead = false;

                for (int a = 0; a < arr.size(); a++) {
                    MessageObject obj = arr.get(a);
                    if (currentUser != null && currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                    if (avatarContainer != null && currentEncryptedChat != null
                            && obj.messageOwner.action != null
                            && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                            && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL) {
                        avatarContainer.setTime(
                                ((TLRPC.TL_decryptedMessageActionSetMessageTTL) obj.messageOwner.action.encryptedAction).ttl_seconds);
                    }
                    if (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                        final Bundle bundle = new Bundle();
                        bundle.putInt("chat_id", obj.messageOwner.action.channel_id);
                        final BaseFragment lastFragment = parentLayout.fragmentsStack.size() > 0
                                ? parentLayout.fragmentsStack.get(parentLayout.fragmentsStack.size() - 1)
                                : null;
                        final int channel_id = obj.messageOwner.action.channel_id;
                        AndroidUtilities.runOnUIThread(new Runnable() {
                            @Override
                            public void run() {
                                ActionBarLayout parentLayout = ChatActivity.this.parentLayout;
                                if (lastFragment != null) {
                                    NotificationCenter.getInstance().removeObserver(lastFragment,
                                            NotificationCenter.closeChats);
                                }
                                NotificationCenter.getInstance()
                                        .postNotificationName(NotificationCenter.closeChats);
                                parentLayout.presentFragment(new ChatActivity(bundle), true);
                                AndroidUtilities.runOnUIThread(new Runnable() {
                                    @Override
                                    public void run() {
                                        MessagesController.getInstance().loadFullChat(channel_id, 0, true);
                                    }
                                }, 1000);
                            }
                        });
                        return;
                    } else if (currentChat != null && currentChat.megagroup
                            && (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                    || obj.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser)) {
                        reloadMegagroup = true;
                    }
                    if (obj.isOut() && obj.isSending()) {
                        scrollToLastMessage(false);
                        return;
                    }
                    if (obj.type < 0 || messagesDict[0].containsKey(obj.getId())) {
                        continue;
                    }
                    obj.checkLayout();
                    currentMaxDate = Math.max(currentMaxDate, obj.messageOwner.date);
                    if (obj.getId() > 0) {
                        currentMinMsgId = Math.max(obj.getId(), currentMinMsgId);
                        last_message_id = Math.max(last_message_id, obj.getId());
                    } else if (currentEncryptedChat != null) {
                        currentMinMsgId = Math.min(obj.getId(), currentMinMsgId);
                        last_message_id = Math.min(last_message_id, obj.getId());
                    }

                    if (!obj.isOut() && obj.isUnread()) {
                        unread_to_load++;
                        currentMarkAsRead = true;
                    }
                    if (obj.type == 10 || obj.type == 11) {
                        updateChat = true;
                    }
                }

                if (currentMarkAsRead) {
                    if (paused) {
                        readWhenResume = true;
                        readWithDate = currentMaxDate;
                        readWithMid = currentMinMsgId;
                    } else {
                        if (messages.size() > 0) {
                            MessagesController.getInstance().markDialogAsRead(dialog_id,
                                    messages.get(0).getId(), currentMinMsgId, currentMaxDate, true, false);
                        }
                    }
                }
                updateVisibleRows();
            } else {
                boolean markAsRead = false;
                boolean unreadUpdated = true;
                int oldCount = messages.size();
                int addedCount = 0;
                HashMap<String, ArrayList<MessageObject>> webpagesToReload = null;
                int placeToPaste = -1;
                for (int a = 0; a < arr.size(); a++) {
                    MessageObject obj = arr.get(a);
                    if (a == 0) {
                        if (obj.messageOwner.id < 0) {
                            placeToPaste = 0;
                        } else {
                            if (!messages.isEmpty()) {
                                int size = messages.size();
                                for (int b = 0; b < size; b++) {
                                    MessageObject lastMessage = messages.get(b);
                                    if (lastMessage.type >= 0 && lastMessage.messageOwner.date > 0) {
                                        if (lastMessage.messageOwner.id > 0 && obj.messageOwner.id > 0) {
                                            if (lastMessage.messageOwner.id < obj.messageOwner.id) {
                                                placeToPaste = b;
                                                break;
                                            }
                                        } else {
                                            if (lastMessage.messageOwner.date < obj.messageOwner.date) {
                                                placeToPaste = b;
                                                break;
                                            }
                                        }
                                    }
                                }
                                if (placeToPaste == -1 || placeToPaste > messages.size()) {
                                    placeToPaste = messages.size();
                                }
                            } else {
                                placeToPaste = 0;
                            }
                        }
                    }
                    if (currentUser != null && currentUser.bot && obj.isOut()) {
                        obj.setIsRead();
                    }
                    if (avatarContainer != null && currentEncryptedChat != null
                            && obj.messageOwner.action != null
                            && obj.messageOwner.action instanceof TLRPC.TL_messageEncryptedAction
                            && obj.messageOwner.action.encryptedAction instanceof TLRPC.TL_decryptedMessageActionSetMessageTTL) {
                        avatarContainer.setTime(
                                ((TLRPC.TL_decryptedMessageActionSetMessageTTL) obj.messageOwner.action.encryptedAction).ttl_seconds);
                    }
                    if (obj.type < 0 || messagesDict[0].containsKey(obj.getId())) {
                        continue;
                    }
                    if (currentEncryptedChat != null
                            && obj.messageOwner.media instanceof TLRPC.TL_messageMediaWebPage
                            && obj.messageOwner.media.webpage instanceof TLRPC.TL_webPageUrlPending) {
                        if (webpagesToReload == null) {
                            webpagesToReload = new HashMap<>();
                        }
                        ArrayList<MessageObject> arrayList = webpagesToReload
                                .get(obj.messageOwner.media.webpage.url);
                        if (arrayList == null) {
                            arrayList = new ArrayList<>();
                            webpagesToReload.put(obj.messageOwner.media.webpage.url, arrayList);
                        }
                        arrayList.add(obj);
                    }
                    obj.checkLayout();
                    if (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatMigrateTo) {
                        final Bundle bundle = new Bundle();
                        bundle.putInt("chat_id", obj.messageOwner.action.channel_id);
                        final BaseFragment lastFragment = parentLayout.fragmentsStack.size() > 0
                                ? parentLayout.fragmentsStack.get(parentLayout.fragmentsStack.size() - 1)
                                : null;
                        final int channel_id = obj.messageOwner.action.channel_id;
                        AndroidUtilities.runOnUIThread(new Runnable() {
                            @Override
                            public void run() {
                                ActionBarLayout parentLayout = ChatActivity.this.parentLayout;
                                if (lastFragment != null) {
                                    NotificationCenter.getInstance().removeObserver(lastFragment,
                                            NotificationCenter.closeChats);
                                }
                                NotificationCenter.getInstance()
                                        .postNotificationName(NotificationCenter.closeChats);
                                parentLayout.presentFragment(new ChatActivity(bundle), true);
                                AndroidUtilities.runOnUIThread(new Runnable() {
                                    @Override
                                    public void run() {
                                        MessagesController.getInstance().loadFullChat(channel_id, 0, true);
                                    }
                                }, 1000);
                            }
                        });
                        return;
                    } else if (currentChat != null && currentChat.megagroup
                            && (obj.messageOwner.action instanceof TLRPC.TL_messageActionChatAddUser
                                    || obj.messageOwner.action instanceof TLRPC.TL_messageActionChatDeleteUser)) {
                        reloadMegagroup = true;
                    }
                    if (minDate[0] == 0 || obj.messageOwner.date < minDate[0]) {
                        minDate[0] = obj.messageOwner.date;
                    }

                    if (obj.isOut()) {
                        removeUnreadPlane();
                        hasFromMe = true;
                    }

                    if (obj.getId() > 0) {
                        maxMessageId[0] = Math.min(obj.getId(), maxMessageId[0]);
                        minMessageId[0] = Math.max(obj.getId(), minMessageId[0]);
                    } else if (currentEncryptedChat != null) {
                        maxMessageId[0] = Math.max(obj.getId(), maxMessageId[0]);
                        minMessageId[0] = Math.min(obj.getId(), minMessageId[0]);
                    }
                    maxDate[0] = Math.max(maxDate[0], obj.messageOwner.date);
                    messagesDict[0].put(obj.getId(), obj);
                    ArrayList<MessageObject> dayArray = messagesByDays.get(obj.dateKey);
                    if (dayArray == null) {
                        dayArray = new ArrayList<>();
                        messagesByDays.put(obj.dateKey, dayArray);
                        TLRPC.Message dateMsg = new TLRPC.Message();
                        dateMsg.message = LocaleController.formatDateChat(obj.messageOwner.date);
                        dateMsg.id = 0;
                        dateMsg.date = obj.messageOwner.date;
                        MessageObject dateObj = new MessageObject(dateMsg, null, false);
                        dateObj.type = 10;
                        dateObj.contentType = 1;
                        messages.add(placeToPaste, dateObj);
                        addedCount++;
                    }
                    if (!obj.isOut()) {
                        if (paused && placeToPaste == 0) {
                            if (!scrollToTopUnReadOnResume && unreadMessageObject != null) {
                                removeMessageObject(unreadMessageObject);
                                if (placeToPaste > 0) {
                                    placeToPaste--;
                                }
                                unreadMessageObject = null;
                            }
                            if (unreadMessageObject == null) {
                                TLRPC.Message dateMsg = new TLRPC.Message();
                                dateMsg.message = "";
                                dateMsg.id = 0;
                                MessageObject dateObj = new MessageObject(dateMsg, null, false);
                                dateObj.type = 6;
                                dateObj.contentType = 2;
                                messages.add(0, dateObj);
                                unreadMessageObject = dateObj;
                                scrollToMessage = unreadMessageObject;
                                scrollToMessagePosition = -10000;
                                unreadUpdated = false;
                                unread_to_load = 0;
                                scrollToTopUnReadOnResume = true;
                                addedCount++;
                            }
                        }
                        if (unreadMessageObject != null) {
                            unread_to_load++;
                            unreadUpdated = true;
                        }
                        if (obj.isUnread()) {
                            if (!paused) {
                                obj.setIsRead();
                            }
                            markAsRead = true;
                        }
                    }

                    dayArray.add(0, obj);
                    if (placeToPaste > messages.size()) {
                        placeToPaste = messages.size();
                    }
                    messages.add(placeToPaste, obj);
                    addedCount++;
                    newUnreadMessageCount++;
                    if (obj.type == 10 || obj.type == 11) {
                        updateChat = true;
                    }
                }
                if (webpagesToReload != null) {
                    MessagesController.getInstance().reloadWebPages(dialog_id, webpagesToReload);
                }

                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
                if (chatAdapter != null) {
                    if (unreadUpdated) {
                        chatAdapter.updateRowWithMessageObject(unreadMessageObject);
                    }
                    if (addedCount != 0) {
                        chatAdapter.notifyItemRangeInserted(chatAdapter.getItemCount() - placeToPaste,
                                addedCount);
                    }
                } else {
                    scrollToTopOnResume = true;
                }

                if (chatListView != null && chatAdapter != null) {
                    int lastVisible = chatLayoutManager.findLastVisibleItemPosition();
                    if (lastVisible == RecyclerView.NO_POSITION) {
                        lastVisible = 0;
                    }
                    if (endReached[0]) {
                        lastVisible++;
                    }
                    if (chatAdapter.isBot) {
                        oldCount++;
                    }
                    if (lastVisible >= oldCount || hasFromMe) {
                        newUnreadMessageCount = 0;
                        if (!firstLoading) {
                            if (paused) {
                                scrollToTopOnResume = true;
                            } else {
                                forceScrollToTop = true;
                                moveScrollToLastMessage();
                            }
                        }
                    } else {
                        if (newUnreadMessageCount != 0 && pagedownButtonCounter != null) {
                            pagedownButtonCounter.setVisibility(View.VISIBLE);
                            pagedownButtonCounter.setText(String.format("%d", newUnreadMessageCount));
                        }
                        showPagedownButton(true, true);
                    }
                } else {
                    scrollToTopOnResume = true;
                }

                if (markAsRead) {
                    if (paused) {
                        readWhenResume = true;
                        readWithDate = maxDate[0];
                        readWithMid = minMessageId[0];
                    } else {
                        MessagesController.getInstance().markDialogAsRead(dialog_id, messages.get(0).getId(),
                                minMessageId[0], maxDate[0], true, false);
                    }
                }
            }
            if (!messages.isEmpty() && botUser != null && botUser.length() == 0) {
                botUser = null;
                updateBottomOverlay();
            }
            if (updateChat) {
                updateTitle();
                checkAndUpdateAvatar();
            }
            if (reloadMegagroup) {
                MessagesController.getInstance().loadFullChat(currentChat.id, 0, true);
            }
        }
    } else if (id == NotificationCenter.closeChats) {
        if (args != null && args.length > 0) {
            long did = (Long) args[0];
            if (did == dialog_id) {
                finishFragment();
            }
        } else {
            removeSelfFromStack();
        }
    } else if (id == NotificationCenter.messagesRead) {
        SparseArray<Long> inbox = (SparseArray<Long>) args[0];
        SparseArray<Long> outbox = (SparseArray<Long>) args[1];
        boolean updated = false;
        for (int b = 0; b < inbox.size(); b++) {
            int key = inbox.keyAt(b);
            long messageId = inbox.get(key);
            if (key != dialog_id) {
                continue;
            }
            for (int a = 0; a < messages.size(); a++) {
                MessageObject obj = messages.get(a);
                if (!obj.isOut() && obj.getId() > 0 && obj.getId() <= (int) messageId) {
                    if (!obj.isUnread()) {
                        break;
                    }
                    obj.setIsRead();
                    updated = true;
                }
            }
            break;
        }
        for (int b = 0; b < outbox.size(); b++) {
            int key = outbox.keyAt(b);
            int messageId = (int) ((long) outbox.get(key));
            if (key != dialog_id) {
                continue;
            }
            for (int a = 0; a < messages.size(); a++) {
                MessageObject obj = messages.get(a);
                if (obj.isOut() && obj.getId() > 0 && obj.getId() <= messageId) {
                    if (!obj.isUnread()) {
                        break;
                    }
                    obj.setIsRead();
                    updated = true;
                }
            }
            break;
        }
        if (updated) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.messagesDeleted) {
        ArrayList<Integer> markAsDeletedMessages = (ArrayList<Integer>) args[0];
        int channelId = (Integer) args[1];
        int loadIndex = 0;
        if (ChatObject.isChannel(currentChat)) {
            if (channelId == 0 && mergeDialogId != 0) {
                loadIndex = 1;
            } else if (channelId == currentChat.id) {
                loadIndex = 0;
            } else {
                return;
            }
        } else if (channelId != 0) {
            return;
        }
        boolean updated = false;
        for (int a = 0; a < markAsDeletedMessages.size(); a++) {
            Integer ids = markAsDeletedMessages.get(a);
            MessageObject obj = messagesDict[loadIndex].get(ids);
            if (loadIndex == 0 && info != null && info.pinned_msg_id == ids) {
                pinnedMessageObject = null;
                info.pinned_msg_id = 0;
                MessagesStorage.getInstance().updateChannelPinnedMessage(channelId, 0);
                updatePinnedMessageView(true);
            }
            if (obj != null) {
                int index = messages.indexOf(obj);
                if (index != -1) {
                    messages.remove(index);
                    messagesDict[loadIndex].remove(ids);
                    ArrayList<MessageObject> dayArr = messagesByDays.get(obj.dateKey);
                    if (dayArr != null) {
                        dayArr.remove(obj);
                        if (dayArr.isEmpty()) {
                            messagesByDays.remove(obj.dateKey);
                            if (index >= 0 && index < messages.size()) {
                                messages.remove(index);
                            }
                        }
                    }
                    updated = true;
                }
            }
        }
        if (messages.isEmpty()) {
            if (!endReached[0] && !loading) {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                }
                if (chatListView != null) {
                    chatListView.setEmptyView(null);
                }
                if (currentEncryptedChat == null) {
                    maxMessageId[0] = maxMessageId[1] = Integer.MAX_VALUE;
                    minMessageId[0] = minMessageId[1] = Integer.MIN_VALUE;
                } else {
                    maxMessageId[0] = maxMessageId[1] = Integer.MIN_VALUE;
                    minMessageId[0] = minMessageId[1] = Integer.MAX_VALUE;
                }
                maxDate[0] = maxDate[1] = Integer.MIN_VALUE;
                minDate[0] = minDate[1] = 0;
                waitingForLoad.add(lastLoadIndex);
                MessagesController.getInstance().loadMessages(dialog_id, 30, 0, !cacheEndReached[0], minDate[0],
                        classGuid, 0, 0, ChatObject.isChannel(currentChat), lastLoadIndex++);
                loading = true;
            } else {
                if (botButtons != null) {
                    botButtons = null;
                    if (chatActivityEnterView != null) {
                        chatActivityEnterView.setButtons(null, false);
                    }
                }
                if (currentEncryptedChat == null && currentUser != null && currentUser.bot && botUser == null) {
                    botUser = "";
                    updateBottomOverlay();
                }
            }
        }
        if (updated && chatAdapter != null) {
            removeUnreadPlane();
            chatAdapter.notifyDataSetChanged();
        }
    } else if (id == NotificationCenter.messageReceivedByServer) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            Integer newMsgId = (Integer) args[1];
            if (!newMsgId.equals(msgId) && messagesDict[0].containsKey(newMsgId)) {
                MessageObject removed = messagesDict[0].remove(msgId);
                if (removed != null) {
                    int index = messages.indexOf(removed);
                    messages.remove(index);
                    ArrayList<MessageObject> dayArr = messagesByDays.get(removed.dateKey);
                    dayArr.remove(obj);
                    if (dayArr.isEmpty()) {
                        messagesByDays.remove(obj.dateKey);
                        if (index >= 0 && index < messages.size()) {
                            messages.remove(index);
                        }
                    }
                    if (chatAdapter != null) {
                        chatAdapter.notifyDataSetChanged();
                    }
                }
                return;
            }
            TLRPC.Message newMsgObj = (TLRPC.Message) args[2];
            boolean mediaUpdated = false;
            boolean updatedForward = false;
            if (newMsgObj != null) {
                try {
                    updatedForward = obj.isForwarded()
                            && (obj.messageOwner.reply_markup == null && newMsgObj.reply_markup != null
                                    || !obj.messageOwner.message.equals(newMsgObj.message));
                    mediaUpdated = updatedForward
                            || obj.messageOwner.params != null
                                    && obj.messageOwner.params.containsKey("query_id")
                            || newMsgObj.media != null && obj.messageOwner.media != null
                                    && !newMsgObj.media.getClass().equals(obj.messageOwner.media.getClass());
                } catch (Exception e) {
                    FileLog.e("tmessages", e);
                }
                obj.messageOwner = newMsgObj;
                obj.generateThumbs(true);
                obj.setType();
                if (newMsgObj.media instanceof TLRPC.TL_messageMediaGame) {
                    obj.applyNewText();
                }
            }
            if (updatedForward) {
                obj.measureInlineBotButtons();
            }
            messagesDict[0].remove(msgId);
            messagesDict[0].put(newMsgId, obj);
            obj.messageOwner.id = newMsgId;
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SENT;
            obj.forceUpdate = mediaUpdated;
            ArrayList<MessageObject> messArr = new ArrayList<>();
            messArr.add(obj);
            if (currentEncryptedChat == null) {
                MessagesQuery.loadReplyMessagesForMessages(messArr, dialog_id);
            }
            if (chatAdapter != null) {
                chatAdapter.updateRowWithMessageObject(obj);
            }
            if (chatLayoutManager != null) {
                if (mediaUpdated && chatLayoutManager.findLastVisibleItemPosition() >= messages.size() - 1) {
                    moveScrollToLastMessage();
                }
            }
            NotificationsController.getInstance().playOutChatSound();
        }
    } else if (id == NotificationCenter.messageReceivedByAck) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SENT;
            if (chatAdapter != null) {
                chatAdapter.updateRowWithMessageObject(obj);
            }
        }
    } else if (id == NotificationCenter.messageSendError) {
        Integer msgId = (Integer) args[0];
        MessageObject obj = messagesDict[0].get(msgId);
        if (obj != null) {
            obj.messageOwner.send_state = MessageObject.MESSAGE_SEND_STATE_SEND_ERROR;
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.chatInfoDidLoaded) {
        TLRPC.ChatFull chatFull = (TLRPC.ChatFull) args[0];
        if (currentChat != null && chatFull.id == currentChat.id) {
            if (chatFull instanceof TLRPC.TL_channelFull) {
                if (currentChat.megagroup) {
                    int lastDate = 0;
                    if (chatFull.participants != null) {
                        for (int a = 0; a < chatFull.participants.participants.size(); a++) {
                            lastDate = Math.max(chatFull.participants.participants.get(a).date, lastDate);
                        }
                    }
                    if (lastDate == 0 || Math.abs(System.currentTimeMillis() / 1000 - lastDate) > 60 * 60) {
                        MessagesController.getInstance().loadChannelParticipants(currentChat.id);
                    }
                }
                if (chatFull.participants == null && info != null) {
                    chatFull.participants = info.participants;
                }
            }
            info = chatFull;
            if (mentionsAdapter != null) {
                mentionsAdapter.setChatInfo(info);
            }
            if (args[3] instanceof MessageObject) {
                pinnedMessageObject = (MessageObject) args[3];
                updatePinnedMessageView(false);
            } else {
                updatePinnedMessageView(true);
            }
            if (avatarContainer != null) {
                avatarContainer.updateOnlineCount();
                avatarContainer.updateSubtitle();
            }
            if (isBroadcast) {
                SendMessagesHelper.getInstance().setCurrentChatInfo(info);
            }
            if (info instanceof TLRPC.TL_chatFull) {
                hasBotsCommands = false;
                botInfo.clear();
                botsCount = 0;
                URLSpanBotCommand.enabled = false;
                for (int a = 0; a < info.participants.participants.size(); a++) {
                    TLRPC.ChatParticipant participant = info.participants.participants.get(a);
                    TLRPC.User user = MessagesController.getInstance().getUser(participant.user_id);
                    if (user != null && user.bot) {
                        URLSpanBotCommand.enabled = true;
                        botsCount++;
                        BotQuery.loadBotInfo(user.id, true, classGuid);
                    }
                }
                if (chatListView != null) {
                    chatListView.invalidateViews();
                }
            } else if (info instanceof TLRPC.TL_channelFull) {
                hasBotsCommands = false;
                botInfo.clear();
                botsCount = 0;
                URLSpanBotCommand.enabled = !info.bot_info.isEmpty();
                botsCount = info.bot_info.size();
                for (int a = 0; a < info.bot_info.size(); a++) {
                    TLRPC.BotInfo bot = info.bot_info.get(a);
                    if (!bot.commands.isEmpty() && (!ChatObject.isChannel(currentChat)
                            || currentChat != null && currentChat.megagroup)) {
                        hasBotsCommands = true;
                    }
                    botInfo.put(bot.user_id, bot);
                }
                if (chatListView != null) {
                    chatListView.invalidateViews();
                }
                if (mentionsAdapter != null && (!ChatObject.isChannel(currentChat)
                        || currentChat != null && currentChat.megagroup)) {
                    mentionsAdapter.setBotInfo(botInfo);
                }
            }
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setBotsCount(botsCount, hasBotsCommands);
            }
            if (mentionsAdapter != null) {
                mentionsAdapter.setBotsCount(botsCount);
            }
            if (ChatObject.isChannel(currentChat) && mergeDialogId == 0 && info.migrated_from_chat_id != 0) {
                mergeDialogId = -info.migrated_from_chat_id;
                maxMessageId[1] = info.migrated_from_max_id;
                if (chatAdapter != null) {
                    chatAdapter.notifyDataSetChanged();
                }
            }
        }
    } else if (id == NotificationCenter.chatInfoCantLoad) {
        int chatId = (Integer) args[0];
        if (currentChat != null && currentChat.id == chatId) {
            int reason = (Integer) args[1];
            if (getParentActivity() == null || closeChatDialog != null) {
                return;
            }
            AlertDialog.Builder builder = new AlertDialog.Builder(getParentActivity());
            builder.setTitle(LocaleController.getString("AppName", kr.wdream.storyshop.R.string.AppName));
            if (reason == 0) {
                builder.setMessage(LocaleController.getString("ChannelCantOpenPrivate",
                        kr.wdream.storyshop.R.string.ChannelCantOpenPrivate));
            } else if (reason == 1) {
                builder.setMessage(LocaleController.getString("ChannelCantOpenNa",
                        kr.wdream.storyshop.R.string.ChannelCantOpenNa));
            } else if (reason == 2) {
                builder.setMessage(LocaleController.getString("ChannelCantOpenBanned",
                        kr.wdream.storyshop.R.string.ChannelCantOpenBanned));
            }
            builder.setPositiveButton(LocaleController.getString("OK", kr.wdream.storyshop.R.string.OK), null);
            showDialog(closeChatDialog = builder.create());

            loading = false;
            if (progressView != null) {
                progressView.setVisibility(View.INVISIBLE);
            }
            if (chatAdapter != null) {
                chatAdapter.notifyDataSetChanged();
            }
        }
    } else if (id == NotificationCenter.contactsDidLoaded) {
        updateContactStatus();
        if (avatarContainer != null) {
            avatarContainer.updateSubtitle();
        }
    } else if (id == NotificationCenter.encryptedChatUpdated) {
        TLRPC.EncryptedChat chat = (TLRPC.EncryptedChat) args[0];
        if (currentEncryptedChat != null && chat.id == currentEncryptedChat.id) {
            currentEncryptedChat = chat;
            updateContactStatus();
            updateSecretStatus();
            initStickers();
            if (chatActivityEnterView != null) {
                chatActivityEnterView.setAllowStickersAndGifs(
                        currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 23,
                        currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 46);
            }
            if (mentionsAdapter != null) {
                mentionsAdapter.setNeedBotContext(
                        !chatActivityEnterView.isEditingMessage() && (currentEncryptedChat == null
                                || AndroidUtilities.getPeerLayerVersion(currentEncryptedChat.layer) >= 46));
            }
        }
    } else if (id == NotificationCenter.messagesReadEncrypted) {
        int encId = (Integer) args[0];
        if (currentEncryptedChat != null && currentEncryptedChat.id == encId) {
            int date = (Integer) args[1];
            for (MessageObject obj : messages) {
                if (!obj.isOut()) {
                    continue;
                } else if (obj.isOut() && !obj.isUnread()) {
                    break;
                }
                if (obj.messageOwner.date - 1 <= date) {
                    obj.setIsRead();
                }
            }
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.audioDidReset || id == NotificationCenter.audioPlayStateChanged) {
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    MessageObject messageObject = cell.getMessageObject();
                    if (messageObject != null && (messageObject.isVoice() || messageObject.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
            count = mentionListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = mentionListView.getChildAt(a);
                if (view instanceof ContextLinkCell) {
                    ContextLinkCell cell = (ContextLinkCell) view;
                    MessageObject messageObject = cell.getMessageObject();
                    if (messageObject != null && (messageObject.isVoice() || messageObject.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
        }
    } else if (id == NotificationCenter.audioProgressDidChanged) {
        Integer mid = (Integer) args[0];
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    if (cell.getMessageObject() != null && cell.getMessageObject().getId() == mid) {
                        MessageObject playing = cell.getMessageObject();
                        MessageObject player = MediaController.getInstance().getPlayingMessageObject();
                        if (player != null) {
                            playing.audioProgress = player.audioProgress;
                            playing.audioProgressSec = player.audioProgressSec;
                            cell.updateAudioProgress();
                        }
                        break;
                    }
                }
            }
        }
    } else if (id == NotificationCenter.removeAllMessagesFromDialog) {
        long did = (Long) args[0];
        if (dialog_id == did) {
            messages.clear();
            waitingForLoad.clear();
            messagesByDays.clear();
            for (int a = 1; a >= 0; a--) {
                messagesDict[a].clear();
                if (currentEncryptedChat == null) {
                    maxMessageId[a] = Integer.MAX_VALUE;
                    minMessageId[a] = Integer.MIN_VALUE;
                } else {
                    maxMessageId[a] = Integer.MIN_VALUE;
                    minMessageId[a] = Integer.MAX_VALUE;
                }
                maxDate[a] = Integer.MIN_VALUE;
                minDate[a] = 0;
                selectedMessagesIds[a].clear();
                selectedMessagesCanCopyIds[a].clear();
            }
            cantDeleteMessagesCount = 0;
            actionBar.hideActionMode();
            updatePinnedMessageView(true);

            if (botButtons != null) {
                botButtons = null;
                if (chatActivityEnterView != null) {
                    chatActivityEnterView.setButtons(null, false);
                }
            }
            if (currentEncryptedChat == null && currentUser != null && currentUser.bot && botUser == null) {
                botUser = "";
                updateBottomOverlay();
            }
            if ((Boolean) args[1]) {
                if (chatAdapter != null) {
                    progressView.setVisibility(chatAdapter.botInfoRow == -1 ? View.VISIBLE : View.INVISIBLE);
                    chatListView.setEmptyView(null);
                }
                for (int a = 0; a < 2; a++) {
                    endReached[a] = false;
                    cacheEndReached[a] = false;
                    forwardEndReached[a] = true;
                }
                first = true;
                firstLoading = true;
                loading = true;
                startLoadFromMessageId = 0;
                needSelectFromMessageId = false;
                waitingForLoad.add(lastLoadIndex);
                MessagesController.getInstance().loadMessages(dialog_id, AndroidUtilities.isTablet() ? 30 : 20,
                        0, true, 0, classGuid, 2, 0, ChatObject.isChannel(currentChat), lastLoadIndex++);
            } else {
                if (progressView != null) {
                    progressView.setVisibility(View.INVISIBLE);
                    chatListView.setEmptyView(emptyViewContainer);
                }
            }

            if (chatAdapter != null) {
                chatAdapter.notifyDataSetChanged();
            }
        }
    } else if (id == NotificationCenter.screenshotTook) {
        updateInformationForScreenshotDetector();
    } else if (id == NotificationCenter.blockedUsersDidLoaded) {
        if (currentUser != null) {
            boolean oldValue = userBlocked;
            userBlocked = MessagesController.getInstance().blockedUsers.contains(currentUser.id);
            if (oldValue != userBlocked) {
                updateBottomOverlay();
            }
        }
    } else if (id == NotificationCenter.FileNewChunkAvailable) {
        MessageObject messageObject = (MessageObject) args[0];
        long finalSize = (Long) args[2];
        if (finalSize != 0 && dialog_id == messageObject.getDialogId()) {
            MessageObject currentObject = messagesDict[0].get(messageObject.getId());
            if (currentObject != null) {
                currentObject.messageOwner.media.document.size = (int) finalSize;
                updateVisibleRows();
            }
        }
    } else if (id == NotificationCenter.didCreatedNewDeleteTask) {
        SparseArray<ArrayList<Integer>> mids = (SparseArray<ArrayList<Integer>>) args[0];
        boolean changed = false;
        for (int i = 0; i < mids.size(); i++) {
            int key = mids.keyAt(i);
            ArrayList<Integer> arr = mids.get(key);
            for (Integer mid : arr) {
                MessageObject messageObject = messagesDict[0].get(mid);
                if (messageObject != null) {
                    messageObject.messageOwner.destroyTime = key;
                    changed = true;
                }
            }
        }
        if (changed) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.audioDidStarted) {
        MessageObject messageObject = (MessageObject) args[0];
        sendSecretMessageRead(messageObject);
        if (chatListView != null) {
            int count = chatListView.getChildCount();
            for (int a = 0; a < count; a++) {
                View view = chatListView.getChildAt(a);
                if (view instanceof ChatMessageCell) {
                    ChatMessageCell cell = (ChatMessageCell) view;
                    MessageObject messageObject1 = cell.getMessageObject();
                    if (messageObject1 != null && (messageObject1.isVoice() || messageObject1.isMusic())) {
                        cell.updateButtonState(false);
                    }
                }
            }
        }
    } else if (id == NotificationCenter.updateMessageMedia) {
        MessageObject messageObject = (MessageObject) args[0];
        MessageObject existMessageObject = messagesDict[0].get(messageObject.getId());
        if (existMessageObject != null) {
            existMessageObject.messageOwner.media = messageObject.messageOwner.media;
            existMessageObject.messageOwner.attachPath = messageObject.messageOwner.attachPath;
            existMessageObject.generateThumbs(false);
        }
        updateVisibleRows();
    } else if (id == NotificationCenter.replaceMessagesObjects) {
        long did = (long) args[0];
        if (did != dialog_id && did != mergeDialogId) {
            return;
        }
        int loadIndex = did == dialog_id ? 0 : 1;
        boolean changed = false;
        boolean mediaUpdated = false;
        ArrayList<MessageObject> messageObjects = (ArrayList<MessageObject>) args[1];
        for (int a = 0; a < messageObjects.size(); a++) {
            MessageObject messageObject = messageObjects.get(a);
            MessageObject old = messagesDict[loadIndex].get(messageObject.getId());
            if (pinnedMessageObject != null && pinnedMessageObject.getId() == messageObject.getId()) {
                pinnedMessageObject = messageObject;
                updatePinnedMessageView(true);
            }
            if (old != null) {
                if (messageObject.type >= 0) {
                    if (!mediaUpdated
                            && messageObject.messageOwner.media instanceof TLRPC.TL_messageMediaWebPage) {
                        mediaUpdated = true;
                    }
                    if (old.replyMessageObject != null) {
                        messageObject.replyMessageObject = old.replyMessageObject;
                        if (messageObject.messageOwner.action instanceof TLRPC.TL_messageActionGameScore) {
                            messageObject.generateGameMessageText(null);
                        }
                    }
                    messageObject.messageOwner.attachPath = old.messageOwner.attachPath;
                    messageObject.attachPathExists = old.attachPathExists;
                    messageObject.mediaExists = old.mediaExists;
                    messagesDict[loadIndex].put(old.getId(), messageObject);
                } else {
                    messagesDict[loadIndex].remove(old.getId());
                }
                int index = messages.indexOf(old);
                if (index >= 0) {
                    ArrayList<MessageObject> dayArr = messagesByDays.get(old.dateKey);
                    int index2 = -1;
                    if (dayArr != null) {
                        index2 = dayArr.indexOf(old);
                    }
                    if (messageObject.type >= 0) {
                        messages.set(index, messageObject);
                        if (chatAdapter != null) {
                            chatAdapter.notifyItemChanged(
                                    chatAdapter.messagesStartRow + messages.size() - index - 1);
                        }
                        if (index2 >= 0) {
                            dayArr.set(index2, messageObject);
                        }
                    } else {
                        messages.remove(index);
                        if (chatAdapter != null) {
                            chatAdapter.notifyItemRemoved(
                                    chatAdapter.messagesStartRow + messages.size() - index - 1);
                        }
                        if (index2 >= 0) {
                            dayArr.remove(index2);
                            if (dayArr.isEmpty()) {
                                messagesByDays.remove(old.dateKey);
                                messages.remove(index);
                                chatAdapter.notifyItemRemoved(chatAdapter.messagesStartRow + messages.size());
                            }
                        }
                    }
                    changed = true;
                }
            }
        }
        if (changed && chatLayoutManager != null) {
            if (mediaUpdated && chatLayoutManager.findLastVisibleItemPosition() >= messages.size()
                    - (chatAdapter.isBot ? 2 : 1)) {
                moveScrollToLastMessage();
            }
        }
    } else if (id == NotificationCenter.notificationsSettingsUpdated) {
        updateTitleIcons();
        if (ChatObject.isChannel(currentChat)) {
            updateBottomOverlay();
        }
    } else if (id == NotificationCenter.didLoadedReplyMessages) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.didLoadedPinnedMessage) {
        MessageObject message = (MessageObject) args[0];
        if (message.getDialogId() == dialog_id && info != null && info.pinned_msg_id == message.getId()) {
            pinnedMessageObject = message;
            loadingPinnedMessage = 0;
            updatePinnedMessageView(true);
        }
    } else if (id == NotificationCenter.didReceivedWebpages) {
        ArrayList<TLRPC.Message> arrayList = (ArrayList<TLRPC.Message>) args[0];
        boolean updated = false;
        for (int a = 0; a < arrayList.size(); a++) {
            TLRPC.Message message = arrayList.get(a);
            long did = MessageObject.getDialogId(message);
            if (did != dialog_id && did != mergeDialogId) {
                continue;
            }
            MessageObject currentMessage = messagesDict[did == dialog_id ? 0 : 1].get(message.id);
            if (currentMessage != null) {
                currentMessage.messageOwner.media = new TLRPC.TL_messageMediaWebPage();
                currentMessage.messageOwner.media.webpage = message.media.webpage;
                currentMessage.generateThumbs(true);
                updated = true;
            }
        }
        if (updated) {
            updateVisibleRows();
            if (chatLayoutManager != null
                    && chatLayoutManager.findLastVisibleItemPosition() >= messages.size() - 1) {
                moveScrollToLastMessage();
            }
        }
    } else if (id == NotificationCenter.didReceivedWebpagesInUpdates) {
        if (foundWebPage != null) {
            HashMap<Long, TLRPC.WebPage> hashMap = (HashMap<Long, TLRPC.WebPage>) args[0];
            for (TLRPC.WebPage webPage : hashMap.values()) {
                if (webPage.id == foundWebPage.id) {
                    showReplyPanel(!(webPage instanceof TLRPC.TL_webPageEmpty), null, null, webPage, false,
                            true);
                    break;
                }
            }
        }
    } else if (id == NotificationCenter.messagesReadContent) {
        ArrayList<Long> arrayList = (ArrayList<Long>) args[0];
        boolean updated = false;
        for (int a = 0; a < arrayList.size(); a++) {
            long mid = arrayList.get(a);
            MessageObject currentMessage = messagesDict[mergeDialogId == 0 ? 0 : 1].get((int) mid);
            if (currentMessage != null) {
                currentMessage.setContentIsRead();
                updated = true;
            }
        }
        if (updated) {
            updateVisibleRows();
        }
    } else if (id == NotificationCenter.botInfoDidLoaded) {
        int guid = (Integer) args[1];
        if (classGuid == guid) {
            TLRPC.BotInfo info = (TLRPC.BotInfo) args[0];
            if (currentEncryptedChat == null) {
                if (!info.commands.isEmpty() && !ChatObject.isChannel(currentChat)) {
                    hasBotsCommands = true;
                }
                botInfo.put(info.user_id, info);
                if (chatAdapter != null) {
                    chatAdapter.notifyItemChanged(0);
                }
                if (mentionsAdapter != null && (!ChatObject.isChannel(currentChat)
                        || currentChat != null && currentChat.megagroup)) {
                    mentionsAdapter.setBotInfo(botInfo);
                }
                if (chatActivityEnterView != null) {
                    chatActivityEnterView.setBotsCount(botsCount, hasBotsCommands);
                }
            }
            updateBotButtons();
        }
    } else if (id == NotificationCenter.botKeyboardDidLoaded) {
        if (dialog_id == (Long) args[1]) {
            TLRPC.Message message = (TLRPC.Message) args[0];
            if (message != null && !userBlocked) {
                botButtons = new MessageObject(message, null, false);
                if (chatActivityEnterView != null) {
                    if (botButtons.messageOwner.reply_markup instanceof TLRPC.TL_replyKeyboardForceReply) {
                        SharedPreferences preferences = ApplicationLoader.applicationContext
                                .getSharedPreferences("mainconfig", Activity.MODE_PRIVATE);
                        if (preferences.getInt("answered_" + dialog_id, 0) != botButtons.getId()
                                && (replyingMessageObject == null
                                        || chatActivityEnterView.getFieldText() == null)) {
                            botReplyButtons = botButtons;
                            chatActivityEnterView.setButtons(botButtons);
                            showReplyPanel(true, botButtons, null, null, false, true);
                        }
                    } else {
                        if (replyingMessageObject != null && botReplyButtons == replyingMessageObject) {
                            botReplyButtons = null;
                            showReplyPanel(false, null, null, null, false, true);
                        }
                        chatActivityEnterView.setButtons(botButtons);
                    }
                }
            } else {
                botButtons = null;
                if (chatActivityEnterView != null) {
                    if (replyingMessageObject != null && botReplyButtons == replyingMessageObject) {
                        botReplyButtons = null;
                        showReplyPanel(false, null, null, null, false, true);
                    }
                    chatActivityEnterView.setButtons(botButtons);
                }
            }
        }
    } else if (id == NotificationCenter.chatSearchResultsAvailable) {
        if (classGuid == (Integer) args[0]) {
            int messageId = (Integer) args[1];
            long did = (Long) args[3];
            if (messageId != 0) {
                scrollToMessageId(messageId, 0, true, did == dialog_id ? 0 : 1);
            }
            updateSearchButtons((Integer) args[2], (Integer) args[4], (Integer) args[5]);
        }
    } else if (id == NotificationCenter.didUpdatedMessagesViews) {
        SparseArray<SparseIntArray> channelViews = (SparseArray<SparseIntArray>) args[0];
        SparseIntArray array = channelViews.get((int) dialog_id);
        if (array != null) {
            boolean updated = false;
            for (int a = 0; a < array.size(); a++) {
                int messageId = array.keyAt(a);
                MessageObject messageObject = messagesDict[0].get(messageId);
                if (messageObject != null) {
                    int newValue = array.get(messageId);
                    if (newValue > messageObject.messageOwner.views) {
                        messageObject.messageOwner.views = newValue;
                        updated = true;
                    }
                }
            }
            if (updated) {
                updateVisibleRows();
            }
        }
    } else if (id == NotificationCenter.peerSettingsDidLoaded) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            updateSpamView();
        }
    } else if (id == NotificationCenter.newDraftReceived) {
        long did = (Long) args[0];
        if (did == dialog_id) {
            applyDraftMaybe(true);
        }
    }
}

---

From source file:com.jhh.hdb.sqlparser.MySemanticAnalyzer.java

/**
 * Generates a select operator which can go between the original input operator and the union
 * operator. This select casts columns to match the type of the associated column in the union,
 * other columns pass through unchanged. The new operator's only parent is the original input
 * operator to the union, and it's only child is the union. If the input does not need to be
 * cast, the original operator is returned, and no new select operator is added.
 *
 * @param origInputOp/*  w  w w  .j  a v  a2  s  .  c o m*/
 *          The original input operator to the union.
 * @param origInputFieldMap
 *          A map from field name to ColumnInfo for the original input operator.
 * @param origInputAlias
 *          The alias associated with the original input operator.
 * @param unionoutRR
 *          The union's output row resolver.
 * @param unionalias
 *          The alias of the union.
 * @return
 * @throws SemanticException
 */
private Operator<? extends OperatorDesc> genInputSelectForUnion(Operator<? extends OperatorDesc> origInputOp,
        Map<String, ColumnInfo> origInputFieldMap, String origInputAlias, RowResolver unionoutRR,
        String unionalias) throws SemanticException {

    HashMap<String, ColumnInfo> fieldMap = unionoutRR.getFieldMap(unionalias);

    Iterator<ColumnInfo> oIter = origInputFieldMap.values().iterator();
    Iterator<ColumnInfo> uIter = fieldMap.values().iterator();

    List<ExprNodeDesc> columns = new ArrayList<ExprNodeDesc>();
    boolean needsCast = false;
    while (oIter.hasNext()) {
        ColumnInfo oInfo = oIter.next();
        ColumnInfo uInfo = uIter.next();
        ExprNodeDesc column = new ExprNodeColumnDesc(oInfo.getType(), oInfo.getInternalName(),
                oInfo.getTabAlias(), oInfo.getIsVirtualCol(), oInfo.isSkewedCol());
        if (!oInfo.getType().equals(uInfo.getType())) {
            needsCast = true;
            column = ParseUtils.createConversionCast(column, (PrimitiveTypeInfo) uInfo.getType());
        }
        columns.add(column);
    }

    // If none of the columns need to be cast there's no need for an additional select operator
    if (!needsCast) {
        return origInputOp;
    }

    RowResolver rowResolver = new RowResolver();
    Map<String, ExprNodeDesc> columnExprMap = new HashMap<String, ExprNodeDesc>();

    List<String> colName = new ArrayList<String>();
    for (int i = 0; i < columns.size(); i++) {
        String name = getColumnInternalName(i);
        ColumnInfo col = new ColumnInfo(name, columns.get(i).getTypeInfo(), "", false);
        rowResolver.put(origInputAlias, name, col);
        colName.add(name);
        columnExprMap.put(name, columns.get(i));
    }

    Operator<SelectDesc> newInputOp = OperatorFactory.getAndMakeChild(new SelectDesc(columns, colName),
            new RowSchema(rowResolver.getColumnInfos()), columnExprMap, origInputOp);
    return putOpInsertMap(newInputOp, rowResolver);
}

---

From source file:com.nbplus.iotlib.IoTInterface.java

private void handleDeviceListNotification(Bundle b) {
    mEmergencyDeviceList.clear();/*from w  w  w  .  j  a v  a  2  s. c  om*/
    HashMap<String, IoTDevice> scannedDevices = new HashMap<>();
    if (b == null) {
        Log.w(TAG, "bundle data is null");
        //return; // ?  ?     .
    } else {
        b.setClassLoader(IoTDevice.class.getClassLoader());
        scannedDevices = (HashMap<String, IoTDevice>) b.getSerializable(IoTServiceCommand.KEY_DATA);
        if (scannedDevices == null) {
            scannedDevices = new HashMap<>();
        }
    }

    if (scannedDevices == null || scannedDevices.size() == 0) {
        Log.w(TAG, "empty device list");
        //return; // ?  ?     .
    }

    boolean changed = false;
    Iterator<String> iter = scannedDevices.keySet().iterator();
    Log.d(TAG, "IoTServiceCommand.GET_DEVICE_LIST added size = " + scannedDevices.size());
    while (iter.hasNext()) {
        String key = iter.next();
        IoTDevice bondedDevice = mBondedWithServerList.get(key);

        IoTDevice scannedDevice = scannedDevices.get(key);
        Log.d(TAG, "check " + key + " is exist or new...");
        // ? ?? ? ?? ? ?  ? ?.
        if (bondedDevice == null) {
            continue;
        }

        //            if (bondedDevice != null) {           // already exist
        if (scannedDevice.getUuids() == null || scannedDevice.getUuids().size() == 0) {
            Log.e(TAG, ">>> xx device name " + bondedDevice.getDeviceName() + " has no uuid advertisement");
            continue;
        }
        ArrayList<String> deviceUuids = bondedDevice.getUuids();
        if (deviceUuids == null || deviceUuids.size() == 0) {
            if (bondedDevice.getDeviceTypeId() == IoTDevice.DEVICE_TYPE_ID_BT) {
                bondedDevice.setAdRecordHashMap(scannedDevice.getAdRecordHashMap());
                bondedDevice.setUuids(scannedDevice.getUuids());
                bondedDevice.setUuidLen(scannedDevice.getUuidLen());
            }
            bondedDevice.setIsKnownDevice(isKnownScenarioDevice(bondedDevice.getDeviceTypeId(),
                    bondedDevice.getUuids(), bondedDevice.getUuidLen()));
            mBondedWithServerList.put(key, bondedDevice);
            changed = true;
        } else {
            if (!scannedDevice.getUuids().equals(deviceUuids)) {
                if (bondedDevice.getDeviceTypeId() == IoTDevice.DEVICE_TYPE_ID_BT) {
                    bondedDevice.setAdRecordHashMap(scannedDevice.getAdRecordHashMap());
                    bondedDevice.setUuids(scannedDevice.getUuids());
                    bondedDevice.setUuidLen(scannedDevice.getUuidLen());
                }
                bondedDevice.setIsKnownDevice(isKnownScenarioDevice(bondedDevice.getDeviceTypeId(),
                        bondedDevice.getUuids(), bondedDevice.getUuidLen()));
                mBondedWithServerList.put(key, bondedDevice);
                changed = true;
            }
        }
        // do nothing...
        // ? ?? ? ?? ? ?  ? ?.
        //            } else {
        //                ArrayList<String> uuids = DataParser.getUuids(scannedDevice.getAdRecordHashMap());
        //                if (uuids == null || uuids.size() == 0) {
        //                    Log.e(TAG, ">>> device name " + scannedDevice.getDeviceName() + " has no uuid advertisement");
        //                    continue;
        //                }
        //                scannedDevice.setUuids(uuids);
        //                scannedDevice.setUuidLen(DataParser.getUuidLength(scannedDevice.getAdRecordHashMap()));
        //                scannedDevice.setIsKnownDevice(isKnownScenarioDevice(scannedDevice.getDeviceTypeId(), scannedDevice.getUuids(), scannedDevice.getUuidLen()));
        //
        //                bondedDevice = scannedDevice;
        //                mBondedWithServerList.put(bondedDevice.getDeviceId(), bondedDevice);
        //                changed = true;
        //            }

        // ??  ?? .
        if (bondedDevice.isBondedWithServer() && isEmergencyCallDevice(bondedDevice.getDeviceTypeId(),
                bondedDevice.getUuids(), bondedDevice.getUuidLen())) {
            Log.d(TAG, "Emergency call device broadcast received : " + bondedDevice.getDeviceId());

            mEmergencyDeviceList.add(bondedDevice);
        }

        //   ? ?  ?? Notification  ?.
        if (bondedDevice.isBondedWithServer() && isKeepAliveDevice(bondedDevice)) {
            Log.d(TAG, "Smart sensor device found device ID = " + bondedDevice.getDeviceId());

            if (!mKeepAliveDeviceList.containsKey(bondedDevice.getDeviceId())) {
                // ? ? ?  3 .
                if (mKeepAliveDeviceList.size() >= MAX_KEEP_ALIVE_CONNECTED_DEVICE_SIZE) {
                    Log.d(TAG, "MAX_KEEP_ALIVE_CONNECTED_DEVICE_SIZE reached....");
                    // do nothing.
                } else {
                    mKeepAliveDeviceList.put(bondedDevice.getDeviceId(), bondedDevice);
                    Bundle extras = new Bundle();
                    IoTHandleData data = new IoTHandleData();
                    data.setDeviceId(bondedDevice.getDeviceId());
                    data.setDeviceTypeId(bondedDevice.getDeviceTypeId());
                    data.setIsKeepAliveDevice(true);

                    extras.putParcelable(IoTServiceCommand.KEY_DATA, data);
                    sendMessageToService(IoTServiceCommand.DEVICE_CONNECT, extras);
                }
            } else {
                Log.d(TAG, "This device already connected. and collecting data... ");
            }
        }
    }

    if (changed) {
        // save to preference.
        String json = mGson.toJson(mBondedWithServerList);
        if (json != null) {
            IoTServicePreference.setIoTDevicesList(mCtx, json);
        }
    }
    Log.d(TAG, "Current device size = " + mBondedWithServerList.size());
    if (mEmergencyDeviceList.size() > 0) {
        // ??  ?  
        long currTimeMs = System.currentTimeMillis();
        //if (currTimeMs - mLastEmergencyDeviceFoundTimeMs > 1 * 60 * 1000) {
        mIsEmergencyDataCollecting = true;

        //   ?  ?? ? .
        Bundle extras = new Bundle();
        extras.putBoolean(IoTServiceCommand.KEY_DATA, false);
        sendMessageToService(IoTServiceCommand.SCANNING_STOP, extras);

        mHandler.removeMessages(HANDLER_RETRIEVE_IOT_DEVICES);
        sendMessageToService(IoTServiceCommand.DEVICE_DISCONNECT_ALL, null);
        //            } else {
        //                Log.d(TAG, ">>> Already emergency device retrive.. before = " + (currTimeMs - mLastEmergencyDeviceFoundTimeMs));
        //                mIsEmergencyDataCollecting = false;
        //                mEmergencyDeviceList.clear();
        //            }
    }

    if (mForceRescanCallback == null) {
        return;
    }

    final IoTServiceStatusNotification responseCallback = mForceRescanCallback.get();
    if (responseCallback != null) {
        Bundle extras = new Bundle();
        ArrayList<IoTDevice> devicesList = null;
        // 2015.12.09
        // ?? ? BT  .
        // ? ?? ? ???  ?  .

        //if (mBondedWithServerList != null && mBondedWithServerList.size() > 0) {
        //    devicesList = new ArrayList<>(mBondedWithServerList.values());
        //} else {
        //    devicesList = new ArrayList<>();
        //}
        if (mKeepAliveDeviceList != null && mKeepAliveDeviceList.size() > 0) {
            devicesList = new ArrayList<>(mKeepAliveDeviceList.values());
        } else {
            devicesList = new ArrayList<>();
        }

        // 
        ArrayList<String> deviceIdList = new ArrayList<>();
        for (int i = 0; i < devicesList.size(); i++) {
            deviceIdList.add(devicesList.get(i).getDeviceId());
        }

        ArrayList<IoTDevice> scannedDevicesList = new ArrayList<>(scannedDevices.values());
        for (int i = 0; i < scannedDevicesList.size(); i++) {
            if (deviceIdList.contains(scannedDevicesList.get(i).getDeviceId())) {
                Log.d(TAG, "mForceRescanCallback device id " + scannedDevicesList.get(i).getDeviceId()
                        + " is already added.");
                continue;
            }
            devicesList.add(scannedDevicesList.get(i));
        }
        extras.putParcelableArrayList(IoTServiceCommand.KEY_DATA, devicesList);
        responseCallback.onResult(IoTServiceCommand.GET_DEVICE_LIST, mServiceStatus, mErrorCodes, extras);
    }
    mForceRescanCallback = null;
    // TODO : log
    if (BuildConfig.DEBUG) {
        iter = mBondedWithServerList.keySet().iterator();
        while (iter.hasNext()) {
            String key = iter.next();
            IoTDevice device = mBondedWithServerList.get(key);

            printScanDeviceInformation(device);
        }
    }

}

---

From source file:edu.isi.wings.catalog.component.api.impl.kb.ComponentReasoningKB.java

/**
 * Helper function which does the actual data requirement checking
 * //from   ww w  .j  av  a  2 s. c o  m
 * @param details
 * @param specialize
 * @param useRules
 * @return
 */
public ArrayList<ComponentPacket> findDataDetails(ComponentPacket details, boolean specialize,
        boolean useRules) {
    ArrayList<ComponentPacket> list = new ArrayList<ComponentPacket>();

    HashMap<String, KBObject> omap = this.objPropMap;
    HashMap<String, KBObject> dmap = this.dataPropMap;

    // Extract info from details object
    ComponentVariable c = details.getComponent();
    HashMap<String, Variable> roleMaps = details.getStringRoleMaps();
    HashMap<String, Role> varMaps = details.getStringVariableMap();
    ArrayList<KBTriple> redbox = details.getRequirements();

    // Get All component bindings
    String incompid = c.getID();
    Binding cb = c.getBinding();
    ArrayList<String> cbindings = new ArrayList<String>();
    if (!cb.isSet())
        cbindings.add(cb.getID());
    else {
        for (WingsSet s : cb) {
            cbindings.add(((Binding) s).getID());
        }
    }

    // Get List of all concrete components
    ArrayList<Component> ccomps = new ArrayList<Component>();
    for (String cbid : cbindings) {
        Component comp = this.getCachedComponent(cbid);
        if (comp == null) {
            logger.debug(cbid + " is not a valid component");
            details.addExplanations(cbid + " is not a valid component");
            details.setInvalidFlag(true);
            list.add(details);
            return list;
        }
        boolean isConcrete = (comp.getType() == Component.CONCRETE);
        if (!specialize) {
            // If no specialization required, add component as is
            ccomps.add(comp);
        } else if (isConcrete) {
            // If specialization required, but component is already concrete,
            // add as is
            ccomps.add(comp);
        } else {
            /* If the component is abstract, then get all it's concrete
             * components. Example of how components are structured in ontology:
             * absClass 
             * - [abs (isConcrete: false)] 
             * - conc1Class 
             *    - [conc1 (isConcrete: true)] 
             * - conc2Class 
             *    - [conc2 (isConcrete: true)] 
             * Note: Only 1 Component Instance per Class
             */
            ArrayList<String> concreteids = this.getConcreteComponentsForAbstract(comp.getID());
            for (String concreteid : concreteids) {
                Component instcomp = this.getCachedComponent(concreteid);
                if (instcomp != null && instcomp.getType() == Component.CONCRETE) {
                    ccomps.add(instcomp);
                }
            }
        }
    }

    logger.debug("Available components to check validity: " + ccomps);

    // For All concrete components :
    // - Get mapping of specialized arguments to variables
    // - Transfer "relevant" output variable properties to input variables
    // - Pass back the specialized component + specialized mappings +
    // modified red-box
    // - Handle *NEW* Arguments as well -> Create *NEW* DataVariables

    // Get Metrics property hierarchy triples for adding into the temporary
    // kb

    for (Component ccomp : ccomps) {
        HashMap<Role, Variable> sRoleMap = new HashMap<Role, Variable>();
        ArrayList<String> varids = new ArrayList<String>();

        // Create a new temporary kb
        KBAPI tkb = this.ontologyFactory.getKB(OntSpec.PLAIN);

        // Add the redbox (i.e. datavariable constraints) to the temporary
        // kb, along with domain knowledge about the data catalog
        tkb.addTriples(redbox);
        tkb.addTriples(domainKnowledge);

        KBObject ccompobj = this.kb.getIndividual(ccomp.getID());
        // Create a copy of the specialized component in the temporary kb
        KBObject tcomp = this.copyObjectIntoKB(incompid, ccompobj, tkb, this.pcdomns, null, false);

        boolean typesOk = true;

        // For all argument roles of the specialized component :
        ArrayList<ComponentRole> allArgs = new ArrayList<ComponentRole>(ccomp.getInputs());
        allArgs.addAll(ccomp.getOutputs());

        HashSet<String> explanations = new HashSet<String>();
        ComponentPacket cmr;
        ComponentVariable concreteComponent = new ComponentVariable(incompid);
        concreteComponent.setBinding(new Binding(ccomp.getID()));
        if (specialize)
            concreteComponent.setConcrete(true);
        else
            concreteComponent.setConcrete(c.isConcrete());

        ArrayList<String> inputRoles = new ArrayList<String>();

        for (ComponentRole arg : allArgs) {
            // Get the argument ID for the specialized argument
            String argid = arg.getRoleName();

            Variable var = roleMaps.get(argid);
            String varid = null;
            String roleid = null;
            if (var == null) {
                // Create a new Variable for role if none exists currently
                // varid = arg.getID()+"_"+ccomp.getName()+"_Variable";
                varid = ccomp.getNamespace() + argid;
                roleid = ccomp.getID() + "_" + argid + "_role";

                short type = 0;
                if (arg.isParam())
                    type = VariableType.PARAM;
                else
                    type = VariableType.DATA;
                var = new Variable(varid, type);
            } else {
                varid = var.getID();
                roleid = varMaps.get(var.getID()).getID();
                // Make sure that the variable has a type that is either
                // subsumed by the argument type, or that the argument type
                // is subsumed by the variable type
                if (!checkTypeCompatibility(tkb, varid, arg.getID())) {
                    logger.debug(arg.getID() + " is not type compatible with variable: " + varid);
                    explanations.add("INFO " + ccomp + " is not selectable because " + arg.getID()
                            + " is not type compatible with variable: " + varid);
                    typesOk = false;
                    break;
                }
            }

            // Copy over the argument's classes to the variable
            KBObject argobj = this.kb.getIndividual(arg.getID());
            KBObject varobj = this.copyObjectClassesIntoKB(varid, argobj, tkb, this.dcdomns, null, false);

            // create hasArgumentID property for the variable
            tkb.addTriple(varobj, dmap.get("hasArgumentID"), tkb.createLiteral(argid));

            Role r = new Role(roleid);
            r.setRoleId(argid);
            r.setDimensionality(arg.getDimensionality());

            // Set variable data binding
            if (var.isDataVariable() && var.getBinding() != null && var.getBinding().getName() != null) {
                tkb.addTriple(varobj, dmap.get("hasBindingID"), tkb.createLiteral(var.getBinding().getName()));
            } else {
                tkb.addTriple(varobj, dmap.get("hasBindingID"), tkb.createLiteral(""));
            }

            // Set variable parameter binding (default if none set)
            if (var.isParameterVariable()) {
                KBObject arg_value = null;
                ValueBinding parambinding = (ValueBinding) var.getBinding();
                if (parambinding != null && parambinding.getValue() != null) {
                    arg_value = tkb.createXSDLiteral(parambinding.getValueAsString(),
                            parambinding.getDatatype());
                } else if (arg.getParamDefaultalue() != null) {
                    arg_value = tkb.createLiteral(arg.getParamDefaultalue());
                }
                if (arg_value != null) {
                    tkb.setPropertyValue(varobj, dmap.get("hasValue"), arg_value);
                }
            }

            // assign this variable as an input or output to the component
            if (ccomp.getInputs().contains(arg)) {
                inputRoles.add(r.getRoleId());
                tkb.addTriple(tcomp, omap.get("hasInput"), varobj);
            } else {
                tkb.addTriple(tcomp, omap.get("hasOutput"), varobj);
            }
            sRoleMap.put(r, var);
            varids.add(var.getID());
        }

        // Empty triple list returned if errors encountered below
        ArrayList<KBTriple> empty = new ArrayList<KBTriple>();

        // Return if there was some problem with types
        if (!typesOk) {
            logger.debug(ccomp + " is not selectable ");
            explanations.add("INFO " + ccomp + " is not selectable ");
            cmr = new ComponentPacket(concreteComponent, sRoleMap, empty);
            cmr.setInputRoles(inputRoles);
            cmr.addExplanations(explanations);
            cmr.setInvalidFlag(true);
            list.add(cmr);
            continue;
        }

        // ** Run Rules **
        if (useRules && ccomp.hasRules()) {
            // Redirect output to a byte stream
            ByteArrayOutputStream bost = new ByteArrayOutputStream();
            PrintStream oldout = System.out;
            System.setOut(new PrintStream(bost, true));

            // Run propagation rules on the temporary kb
            tkb.setRulePrefixes(this.rulePrefixes);
            tkb.applyRules(this.getCachedComponentRules(ccomp));
            //tkb.applyRulesFromString(allrules);

            // Get printouts from Rules and store as Explanations
            if (!bost.toString().equals("")) {
                for (String exp : bost.toString().split("\\n")) {
                    explanations.add(exp);
                }
            }
            // Set output back to original System.out
            System.setOut(oldout);
        }

        // Checking for invalidity
        KBObject invalidProp = tkb.getProperty(this.pcns + "isInvalid");
        KBObject isInvalid = tkb.getPropertyValue(tcomp, invalidProp);
        if (isInvalid != null && (Boolean) isInvalid.getValue()) {
            logger.debug(ccomp + " is not selectable ");
            explanations.add("INFO " + ccomp + " is not selectable ");
            cmr = new ComponentPacket(concreteComponent, sRoleMap, empty);
            cmr.setInputRoles(inputRoles);
            cmr.addExplanations(explanations);
            cmr.setInvalidFlag(true);
            list.add(cmr);
            continue;
        }

        // Set parameter values (if any)
        for (Variable var : roleMaps.values()) {
            if (var.isParameterVariable() && var.getBinding() == null) {
                KBObject varobj = tkb.getResource(var.getID());
                KBObject val = tkb.getPropertyValue(varobj, dmap.get("hasValue"));
                if (val != null && val.getValue() != null) {
                    tkb.addTriple(varobj, tkb.getResource(this.wflowns + "hasParameterValue"), val);
                    var.setBinding(new ValueBinding(val.getValue(), val.getDataType()));
                }
            }
        }

        // Create a constraint engine and get Relevant Constraints here
        ConstraintEngine cons = new ConstraintEngineKB(tkb, "");
        cons.addWhitelistedNamespace(this.dcdomns);
        cons.addWhitelistedNamespace(this.dcns);
        cons.addWhitelistedNamespace(this.wflowns);
        ArrayList<String> blacklistedIds = new ArrayList<String>();
        blacklistedIds.add(dmap.get("hasArgumentID").getID());
        blacklistedIds.add(dmap.get("hasBindingID").getID());
        blacklistedIds.add(this.dcns + "hasMetrics");
        blacklistedIds.add(this.dcns + "hasDataMetrics");
        blacklistedIds.add(this.pcns + "hasValue");

        for (String id : blacklistedIds)
            cons.addBlacklistedId(id);
        ArrayList<KBTriple> constraints = cons.getConstraints(varids);
        for (String id : blacklistedIds)
            cons.removeBlacklistedId(id);

        cmr = new ComponentPacket(concreteComponent, sRoleMap, constraints);
        cmr.setInputRoles(inputRoles);
        cmr.addExplanations(explanations);
        list.add(cmr);
    }
    return list;
}

---

From source file:com.conferenceengineer.android.iosched.io.SessionsHandler.java

private ArrayList<ContentProviderOperation> buildContentProviderOperations(SessionsResponse sessions,
        SessionsResponse starredSessions, TracksResponse tracks) {

    // If there was no starred sessions response (e.g. there was an auth issue,
    // or this is a local sync), keep all the locally starred sessions.
    boolean retainLocallyStarredSessions = (starredSessions == null);

    final ArrayList<ContentProviderOperation> batch = Lists.newArrayList();

    // Build lookup table for starredSessions mappings
    HashSet<String> starredSessionsMap = new HashSet<String>();
    if (starredSessions != null) {
        List<SessionResponse> starredSessionList = starredSessions.getSessions();
        if (starredSessionList != null) {
            for (SessionResponse session : starredSessionList) {
                String sessionId = session.getId();
                starredSessionsMap.add(sessionId);
            }/*from   w  w w.j a  va  2 s .c o  m*/
        }
    }

    // Build lookup table for track mappings
    // Assumes that sessions can only have one track. Not guarenteed by the Conference API,
    // but is being enforced by conference organizer policy.
    HashMap<String, TrackResponse> trackMap = new HashMap<String, TrackResponse>();
    if (tracks != null) {
        for (TrackResponse track : tracks.getTracks()) {
            List<String> sessionIds = track.getSessions();
            if (sessionIds != null) {
                for (String sessionId : sessionIds) {
                    trackMap.put(sessionId, track);
                }
            }
        }
    }

    if (sessions != null) {
        List<SessionResponse> sessionList = sessions.getSessions();
        int numSessions = sessionList.size();

        if (numSessions > 0) {
            LOGI(TAG, "Updating sessions data");

            Set<String> starredSessionIds = new HashSet<String>();
            if (retainLocallyStarredSessions) {
                Cursor starredSessionsCursor = mContext.getContentResolver().query(Sessions.CONTENT_STARRED_URI,
                        new String[] { ScheduleContract.Sessions.SESSION_ID }, null, null, null);
                while (starredSessionsCursor.moveToNext()) {
                    starredSessionIds.add(starredSessionsCursor.getString(0));
                }
                starredSessionsCursor.close();
            }

            // Clear out existing sessions
            batch.add(ContentProviderOperation
                    .newDelete(ScheduleContract.addCallerIsSyncAdapterParameter(Sessions.CONTENT_URI)).build());

            // Maintain a list of created session block IDs
            Set<String> blockIds = new HashSet<String>();

            // Maintain a map of insert operations for sandbox-only blocks
            HashMap<String, ContentProviderOperation> sandboxBlocks = new HashMap<String, ContentProviderOperation>();

            for (SessionResponse session : sessionList) {
                int flags = 0;
                String sessionId = session.getId();
                if (retainLocallyStarredSessions) {
                    flags = (starredSessionIds.contains(sessionId) ? PARSE_FLAG_FORCE_SCHEDULE_ADD
                            : PARSE_FLAG_FORCE_SCHEDULE_REMOVE);
                }
                if (session.getFlags() != 0) {
                    // Allow data set flags to override locally
                    // set ones (e.g. single talk slot additions).
                    flags = session.getFlags();
                }

                if (TextUtils.isEmpty(sessionId)) {
                    LOGW(TAG, "Found session with empty ID in API response.");
                    continue;
                }

                // Session title
                String sessionTitle = session.getTitle();
                String sessionSubtype = session.getSubtype();
                if (EVENT_TYPE_CODELAB.equals(sessionSubtype)) {
                    sessionTitle = mContext.getString(R.string.codelab_title_template, sessionTitle);
                }

                // Whether or not it's in the schedule
                boolean inSchedule = starredSessionsMap.contains(sessionId);
                if ((flags & PARSE_FLAG_FORCE_SCHEDULE_ADD) != 0
                        || (flags & PARSE_FLAG_FORCE_SCHEDULE_REMOVE) != 0) {
                    inSchedule = (flags & PARSE_FLAG_FORCE_SCHEDULE_ADD) != 0;
                }

                if (EVENT_TYPE_KEYNOTE.equals(sessionSubtype)) {
                    // Keynotes are always in your schedule.
                    inSchedule = true;
                }

                // Clean up session abstract
                String sessionAbstract = session.getDescription();
                if (sessionAbstract != null) {
                    sessionAbstract = sessionAbstract.replace('\r', '\n');
                }

                // Hashtags
                TrackResponse track = trackMap.get(sessionId);
                String hashtag = null;
                if (track != null) {
                    hashtag = ParserUtils.sanitizeId(track.getTitle());
                }

                // Get block id
                long sessionStartTime = session.getStartTimestamp().longValue() * 1000;
                long sessionEndTime = session.getEndTimestamp().longValue() * 1000;
                String blockId = ScheduleContract.Blocks.generateBlockId(sessionStartTime, sessionEndTime);

                if (!blockIds.contains(blockId) && !EVENT_TYPE_SANDBOX.equals(sessionSubtype)) {
                    // New non-sandbox block
                    if (sandboxBlocks.containsKey(blockId)) {
                        sandboxBlocks.remove(blockId);
                    }
                    String blockType;
                    String blockTitle;
                    if (EVENT_TYPE_KEYNOTE.equals(sessionSubtype)) {
                        blockType = ScheduleContract.Blocks.BLOCK_TYPE_KEYNOTE;
                        blockTitle = mContext.getString(R.string.schedule_block_title_keynote);
                    } else if (EVENT_TYPE_CODELAB.equals(sessionSubtype)) {
                        blockType = ScheduleContract.Blocks.BLOCK_TYPE_CODELAB;
                        blockTitle = mContext.getString(R.string.schedule_block_title_code_labs);
                    } else if (EVENT_TYPE_OFFICE_HOURS.equals(sessionSubtype)) {
                        blockType = ScheduleContract.Blocks.BLOCK_TYPE_OFFICE_HOURS;
                        blockTitle = mContext.getString(R.string.schedule_block_title_office_hours);
                    } else {
                        blockType = ScheduleContract.Blocks.BLOCK_TYPE_SESSION;
                        blockTitle = mContext.getString(R.string.schedule_block_title_sessions);
                    }

                    batch.add(ContentProviderOperation.newInsert(ScheduleContract.Blocks.CONTENT_URI)
                            .withValue(ScheduleContract.Blocks.BLOCK_ID, blockId)
                            .withValue(ScheduleContract.Blocks.BLOCK_TYPE, blockType)
                            .withValue(ScheduleContract.Blocks.BLOCK_TITLE, blockTitle)
                            .withValue(ScheduleContract.Blocks.BLOCK_START, sessionStartTime)
                            .withValue(ScheduleContract.Blocks.BLOCK_END, sessionEndTime).build());
                    blockIds.add(blockId);

                } else if (!sandboxBlocks.containsKey(blockId) && !blockIds.contains(blockId)
                        && EVENT_TYPE_SANDBOX.equals(sessionSubtype)) {
                    // New sandbox-only block, add insert operation to map
                    String blockType = ScheduleContract.Blocks.BLOCK_TYPE_SANDBOX;
                    String blockTitle = mContext.getString(R.string.schedule_block_title_sandbox);
                    sandboxBlocks.put(blockId,
                            ContentProviderOperation.newInsert(ScheduleContract.Blocks.CONTENT_URI)
                                    .withValue(ScheduleContract.Blocks.BLOCK_ID, blockId)
                                    .withValue(ScheduleContract.Blocks.BLOCK_TYPE, blockType)
                                    .withValue(ScheduleContract.Blocks.BLOCK_TITLE, blockTitle)
                                    .withValue(ScheduleContract.Blocks.BLOCK_START, sessionStartTime)
                                    .withValue(ScheduleContract.Blocks.BLOCK_END, sessionEndTime).build());

                }

                // Insert session info
                final ContentProviderOperation.Builder builder;
                if (EVENT_TYPE_SANDBOX.equals(sessionSubtype)) {
                    // Sandbox companies go in the special sandbox table

                    builder = ContentProviderOperation
                            .newInsert(ScheduleContract
                                    .addCallerIsSyncAdapterParameter(ScheduleContract.Sandbox.CONTENT_URI))
                            .withValue(SyncColumns.UPDATED, System.currentTimeMillis())
                            .withValue(ScheduleContract.Sandbox.COMPANY_ID, sessionId)
                            .withValue(ScheduleContract.Sandbox.COMPANY_NAME, sessionTitle)
                            .withValue(ScheduleContract.Sandbox.COMPANY_DESC, sessionAbstract)
                            .withValue(ScheduleContract.Sandbox.COMPANY_URL, session.getWebLink())
                            .withValue(ScheduleContract.Sandbox.COMPANY_LOGO_URL, session.getIconUrl())
                            .withValue(ScheduleContract.Sandbox.ROOM_ID, sanitizeId(session.getLocation()))
                            .withValue(ScheduleContract.Sandbox.TRACK_ID,
                                    (track != null ? track.getId() : null))
                            .withValue(ScheduleContract.Sandbox.BLOCK_ID, blockId);
                    batch.add(builder.build());

                } else {
                    // All other fields go in the normal sessions table
                    builder = ContentProviderOperation
                            .newInsert(ScheduleContract.addCallerIsSyncAdapterParameter(Sessions.CONTENT_URI))
                            .withValue(SyncColumns.UPDATED, System.currentTimeMillis())
                            .withValue(Sessions.SESSION_ID, sessionId)
                            .withValue(Sessions.SESSION_TYPE, sessionSubtype)
                            .withValue(Sessions.SESSION_LEVEL, null) // Not available
                            .withValue(Sessions.SESSION_TITLE, sessionTitle)
                            .withValue(Sessions.SESSION_ABSTRACT, sessionAbstract)
                            .withValue(Sessions.SESSION_HASHTAGS, hashtag)
                            .withValue(Sessions.SESSION_TAGS, null) // Not available
                            .withValue(Sessions.SESSION_URL, session.getWebLink())
                            .withValue(Sessions.SESSION_MODERATOR_URL, null) // Not available
                            .withValue(Sessions.SESSION_REQUIREMENTS, null) // Not available
                            .withValue(Sessions.SESSION_STARRED, inSchedule)
                            .withValue(Sessions.SESSION_YOUTUBE_URL, null) // Not available
                            .withValue(Sessions.SESSION_PDF_URL, null) // Not available
                            .withValue(Sessions.SESSION_NOTES_URL, null) // Not available
                            .withValue(Sessions.ROOM_ID, sanitizeId(session.getLocation()))
                            .withValue(Sessions.BLOCK_ID, blockId);

                    batch.add(builder.build());
                }

                // Replace all session speakers
                final Uri sessionSpeakersUri = Sessions.buildSpeakersDirUri(sessionId);
                batch.add(ContentProviderOperation
                        .newDelete(ScheduleContract.addCallerIsSyncAdapterParameter(sessionSpeakersUri))
                        .build());

                List<String> presenterIds = session.getPresenterIds();
                if (presenterIds != null) {
                    for (String presenterId : presenterIds) {
                        batch.add(ContentProviderOperation.newInsert(sessionSpeakersUri)
                                .withValue(SessionsSpeakers.SESSION_ID, sessionId)
                                .withValue(SessionsSpeakers.SPEAKER_ID, presenterId).build());
                    }
                }

                // Add track mapping
                if (track != null) {
                    String trackId = track.getId();
                    if (trackId != null) {
                        final Uri sessionTracksUri = ScheduleContract.addCallerIsSyncAdapterParameter(
                                ScheduleContract.Sessions.buildTracksDirUri(sessionId));
                        batch.add(ContentProviderOperation.newInsert(sessionTracksUri)
                                .withValue(ScheduleDatabase.SessionsTracks.SESSION_ID, sessionId)
                                .withValue(ScheduleDatabase.SessionsTracks.TRACK_ID, trackId).build());
                    }
                }

                // Codelabs: Add mapping to codelab table
                if (EVENT_TYPE_CODELAB.equals(sessionSubtype)) {
                    final Uri sessionTracksUri = ScheduleContract.addCallerIsSyncAdapterParameter(
                            ScheduleContract.Sessions.buildTracksDirUri(sessionId));
                    batch.add(ContentProviderOperation.newInsert(sessionTracksUri)
                            .withValue(ScheduleDatabase.SessionsTracks.SESSION_ID, sessionId)
                            .withValue(ScheduleDatabase.SessionsTracks.TRACK_ID, "CODE_LABS").build());
                }
            }

            // Insert sandbox-only blocks
            batch.addAll(sandboxBlocks.values());
        }
    }

    return batch;
}

---

From source file:ffx.potential.parsers.BiojavaFilter.java

/**
 * Assign force field atoms types to common chemistries using "biotype"
 * records.//from  ww w .j a  v  a2s .c  o m
 */
public void assignAtomTypes() {
    /**
     * Create a new List to store bonds determined based on PDB atom names.
     */
    bondList = new ArrayList<>();

    /**
     * To Do: Look for cyclic peptides and disulfides.
     */
    Polymer[] polymers = activeMolecularAssembly.getChains();

    /**
     * Loop over chains.
     */
    if (polymers != null) {
        logger.info(format("\n Assigning atom types for %d chains.", polymers.length));
        for (Polymer polymer : polymers) {
            List<Residue> residues = polymer.getResidues();
            int numberOfResidues = residues.size();
            /**
             * Check if all residues are known amino acids.
             */
            boolean isProtein = true;
            if (!residues.isEmpty()) {
                //renameNTerminusHydrogens(residues.get(0)); Not safe to use until it distinguishes between true N-termini and N-terminal residues in general.
            }
            for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
                Residue residue = residues.get(residueNumber);
                String name = residue.getName().toUpperCase();
                boolean aa = false;
                for (AminoAcid3 amino : aminoAcidList) {
                    if (amino.toString().equalsIgnoreCase(name)) {
                        aa = true;
                        renameNonstandardHydrogens(residue);
                        break;
                    }
                }
                // Check for a patch.
                if (!aa) {
                    HashMap<String, AtomType> types = forceField.getAtomTypes(name);
                    if (types.isEmpty()) {
                        isProtein = false;
                        break;
                    } else {
                        logger.info(" Patch found for non-standard amino acid " + name);
                    }
                }
            }

            /**
             * If all the residues in this chain have known amino acids
             * names, then attempt to assign atom types.
             */
            if (isProtein) {
                try {
                    logger.info(format(" Amino acid chain %s", polymer.getName()));
                    double dist = properties.getDouble("chainbreak", 3.0);
                    // Detect main chain breaks!
                    List<List<Residue>> subChains = findChainBreaks(residues, dist);
                    for (List<Residue> subChain : subChains) {
                        assignAminoAcidAtomTypes(subChain);
                    }
                } catch (MissingHeavyAtomException missingHeavyAtomException) {
                    logger.severe(missingHeavyAtomException.toString());
                } catch (MissingAtomTypeException missingAtomTypeException) {
                    logger.severe(missingAtomTypeException.toString());
                }
                continue;
            }

            /**
             * Check if all residues have known nucleic acids names.
             */
            boolean isNucleicAcid = true;
            for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
                Residue residue = residues.get(residueNumber);
                String name = residue.getName().toUpperCase();
                /**
                 * Convert 1 and 2-character nucleic acid names to
                 * 3-character names.
                 */
                if (name.length() == 1) {
                    if (name.equals("A")) {
                        name = NucleicAcid3.ADE.toString();
                    } else if (name.equals("C")) {
                        name = NucleicAcid3.CYT.toString();
                    } else if (name.equals("G")) {
                        name = NucleicAcid3.GUA.toString();
                    } else if (name.equals("T")) {
                        name = NucleicAcid3.THY.toString();
                    } else if (name.equals("U")) {
                        name = NucleicAcid3.URI.toString();
                    }
                } else if (name.length() == 2) {
                    if (name.equals("YG")) {
                        name = NucleicAcid3.YYG.toString();
                    }
                }
                residue.setName(name);
                NucleicAcid3 nucleicAcid = null;
                for (NucleicAcid3 nucleic : nucleicAcidList) {
                    String nuc3 = nucleic.toString();
                    nuc3 = nuc3.substring(nuc3.length() - 3);
                    if (nuc3.equalsIgnoreCase(name)) {
                        nucleicAcid = nucleic;
                        break;
                    }
                }
                if (nucleicAcid == null) {
                    logger.info(format("Nucleic acid was not recognized %s.", name));
                    isNucleicAcid = false;
                    break;
                }
            }

            /**
             * If all the residues in this chain have known nucleic acids
             * names, then attempt to assign atom types.
             */
            if (isNucleicAcid) {
                try {
                    logger.info(format(" Nucleic acid chain %s", polymer.getName()));
                    assignNucleicAcidAtomTypes(residues);
                } catch (MissingHeavyAtomException missingHeavyAtomException) {
                    logger.severe(missingHeavyAtomException.toString());
                } catch (MissingAtomTypeException missingAtomTypeException) {
                    logger.severe(missingAtomTypeException.toString());
                }
            }
        }
    }

    // Assign ion atom types.
    ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
    if (ions != null && ions.size() > 0) {
        logger.info(format(" Assigning atom types for %d ions.", ions.size()));
        for (MSNode m : ions) {
            Molecule ion = (Molecule) m;
            String name = ion.getResidueName().toUpperCase();
            HetAtoms hetatm = HetAtoms.valueOf(name);
            Atom atom = ion.getAtomList().get(0);
            if (ion.getAtomList().size() != 1) {
                logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
            }
            try {
                switch (hetatm) {
                case NA:
                    atom.setAtomType(findAtomType(2003));
                    break;
                case K:
                    atom.setAtomType(findAtomType(2004));
                    break;
                case MG:
                case MG2:
                    atom.setAtomType(findAtomType(2005));
                    break;
                case CA:
                case CA2:
                    atom.setAtomType(findAtomType(2006));
                    break;
                case CL:
                    atom.setAtomType(findAtomType(2007));
                    break;
                case ZN:
                case ZN2:
                    atom.setAtomType(findAtomType(2008));
                    break;
                case BR:
                    atom.setAtomType(findAtomType(2009));
                    break;
                default:
                    logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
                }
            } catch (Exception e) {
                String message = "Error assigning atom types.";
                logger.log(Level.SEVERE, message, e);
            }
        }
    }
    // Assign water atom types.
    ArrayList<MSNode> water = activeMolecularAssembly.getWaters();
    if (water != null && water.size() > 0) {
        logger.info(format(" Assigning atom types for %d waters.", water.size()));
        for (MSNode m : water) {
            Molecule wat = (Molecule) m;
            try {
                Atom O = buildHeavy(wat, "O", null, 2001);
                Atom H1 = buildHydrogen(wat, "H1", O, 0.96e0, null, 109.5e0, null, 120.0e0, 0, 2002);
                H1.setHetero(true);
                Atom H2 = buildHydrogen(wat, "H2", O, 0.96e0, H1, 109.5e0, null, 120.0e0, 0, 2002);
                H2.setHetero(true);
            } catch (Exception e) {
                String message = "Error assigning atom types to a water.";
                logger.log(Level.SEVERE, message, e);
            }
        }
    }

    // Assign small molecule atom types.
    ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
    for (MSNode m : molecules) {
        Molecule molecule = (Molecule) m;
        String moleculeName = molecule.getResidueName();
        logger.info(" Attempting to patch " + moleculeName);
        ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
        boolean patched = true;
        HashMap<String, AtomType> types = forceField.getAtomTypes(moleculeName);
        /**
         * Assign atom types for all known atoms.
         */
        for (Atom atom : moleculeAtoms) {
            String atomName = atom.getName().toUpperCase();
            AtomType atomType = types.get(atomName);
            if (atomType == null) {
                logger.info(" No atom type was found for " + atomName + " of " + moleculeName + ".");
                patched = false;
                break;
            } else {
                atom.setAtomType(atomType);
                types.remove(atomName);
            }
        }
        /**
         * Create missing hydrogen atoms. Check for missing heavy atoms.
         */
        if (patched && !types.isEmpty()) {
            for (AtomType type : types.values()) {
                if (type.atomicNumber != 1) {
                    logger.info(" Missing heavy atom " + type.name);
                    patched = false;
                    break;
                }
            }
        }
        // Create bonds between known atoms.
        if (patched) {
            for (Atom atom : moleculeAtoms) {
                String atomName = atom.getName();
                String bonds[] = forceField.getBonds(moleculeName, atomName);
                if (bonds != null) {
                    for (String name : bonds) {
                        Atom atom2 = molecule.getAtom(name);
                        if (atom2 != null && !atom.isBonded(atom2)) {
                            buildBond(atom, atom2);
                        }
                    }
                }
            }
        }
        // Create missing hydrogen atoms.
        if (patched && !types.isEmpty()) {
            // Create a hashmap of the molecule's atoms
            HashMap<String, Atom> atomMap = new HashMap<String, Atom>();
            for (Atom atom : moleculeAtoms) {
                atomMap.put(atom.getName().toUpperCase(), atom);
            }
            for (String atomName : types.keySet()) {
                AtomType type = types.get(atomName);
                String bonds[] = forceField.getBonds(moleculeName, atomName.toUpperCase());
                if (bonds == null || bonds.length != 1) {
                    patched = false;
                    logger.info(" Check biotype for hydrogen " + type.name + ".");
                    break;
                }
                // Get the heavy atom the hydrogen is bonded to.
                Atom ia = atomMap.get(bonds[0].toUpperCase());
                Atom hydrogen = new Atom(0, atomName, ia.getAltLoc(), new double[3], ia.getResidueName(),
                        ia.getResidueNumber(), ia.getChainID(), ia.getOccupancy(), ia.getTempFactor(),
                        ia.getSegID());
                logger.fine(" Created hydrogen " + atomName + ".");
                hydrogen.setAtomType(type);
                hydrogen.setHetero(true);
                molecule.addMSNode(hydrogen);
                int valence = ia.getAtomType().valence;
                List<Bond> aBonds = ia.getBonds();
                int numBonds = aBonds.size();
                /**
                 * Try to find the following configuration: ib-ia-ic
                 */
                Atom ib = null;
                Atom ic = null;
                Atom id = null;
                if (numBonds > 0) {
                    Bond bond = aBonds.get(0);
                    ib = bond.get1_2(ia);
                }
                if (numBonds > 1) {
                    Bond bond = aBonds.get(1);
                    ic = bond.get1_2(ia);
                }
                if (numBonds > 2) {
                    Bond bond = aBonds.get(2);
                    id = bond.get1_2(ia);
                }

                /**
                 * Building the hydrogens depends on hybridization and the
                 * locations of other bonded atoms.
                 */
                logger.fine(" Bonding " + atomName + " to " + ia.getName() + " (" + numBonds + " of " + valence
                        + ").");
                switch (valence) {
                case 4:
                    switch (numBonds) {
                    case 3:
                        // Find the average coordinates of atoms ib, ic and id.
                        double b[] = ib.getXYZ(null);
                        double c[] = ib.getXYZ(null);
                        double d[] = ib.getXYZ(null);
                        double a[] = new double[3];
                        a[0] = (b[0] + c[0] + d[0]) / 3.0;
                        a[1] = (b[1] + c[1] + d[1]) / 3.0;
                        a[2] = (b[2] + c[2] + d[2]) / 3.0;
                        // Place the hydrogen at chiral position #1.
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 1);
                        double e1[] = new double[3];
                        hydrogen.getXYZ(e1);
                        double ret[] = new double[3];
                        diff(a, e1, ret);
                        double l1 = r(ret);
                        // Place the hydrogen at chiral position #2.
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, -1);
                        double e2[] = new double[3];
                        hydrogen.getXYZ(e2);
                        diff(a, e2, ret);
                        double l2 = r(ret);
                        // Revert to #1 if it is farther from the average.
                        if (l1 > l2) {
                            hydrogen.setXYZ(e1);
                        }
                        break;
                    case 2:
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 0);
                        break;
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 3:
                    switch (numBonds) {
                    case 2:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, ic, 0.0, 0);
                        break;
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 2:
                    switch (numBonds) {
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 1:
                    switch (numBonds) {
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                default:
                    logger.info(" Check biotype for hydrogen " + atomName + ".");
                    patched = false;
                }
                if (!patched) {
                    break;
                } else {
                    buildBond(ia, hydrogen);
                }
            }
        }
        if (!patched) {
            logger.log(Level.WARNING, format(" Deleting unrecognized molecule %s.", m.toString()));
            activeMolecularAssembly.deleteMolecule((Molecule) m);
        } else {
            logger.info(" Patch for " + moleculeName + " succeeded.");
        }
    }
}

---

From source file:ffx.potential.parsers.PDBFilter.java

/**
 * Assign force field atoms types to common chemistries using "biotype"
 * records.//w  w  w.j  a  va  2  s .com
 */
private void assignAtomTypes() {
    /**
     * Create a list to store bonds defined by PDB atom names.
     */
    bondList = new ArrayList<>();

    /**
     * To Do: Look for cyclic peptides and disulfides.
     */
    Polymer[] polymers = activeMolecularAssembly.getChains();

    /**
     * Loop over chains.
     */
    if (polymers != null) {
        logger.info(format("\n Assigning atom types for %d chains.", polymers.length));
        for (Polymer polymer : polymers) {
            List<Residue> residues = polymer.getResidues();
            int numberOfResidues = residues.size();
            /**
             * Check if all residues are known amino acids.
             */
            boolean isProtein = true;
            for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
                Residue residue = residues.get(residueNumber);
                String name = residue.getName().toUpperCase();
                boolean aa = false;
                for (AminoAcid3 amino : aminoAcidList) {
                    if (amino.toString().equalsIgnoreCase(name)) {
                        aa = true;
                        checkHydrogenAtomNames(residue);
                        break;
                    }
                }
                // Check for a patch.
                if (!aa) {
                    logger.info(" Checking for non-standard amino acid patch " + name);
                    HashMap<String, AtomType> types = forceField.getAtomTypes(name);
                    if (types.isEmpty()) {
                        isProtein = false;
                        break;
                    } else {
                        logger.info(" Patch found for non-standard amino acid " + name);
                    }
                }
            }

            /**
             * If all the residues in this chain have known amino acids
             * names, then attempt to assign atom types.
             */
            if (isProtein) {
                try {
                    logger.info(format(" Amino acid chain %s", polymer.getName()));
                    double dist = properties.getDouble("chainbreak", 3.0);
                    // Detect main chain breaks!
                    List<List<Residue>> subChains = findChainBreaks(residues, dist);
                    for (List<Residue> subChain : subChains) {
                        assignAminoAcidAtomTypes(subChain);
                    }
                } catch (MissingHeavyAtomException missingHeavyAtomException) {
                    logger.severe(missingHeavyAtomException.toString());
                } catch (MissingAtomTypeException missingAtomTypeException) {
                    logger.severe(missingAtomTypeException.toString());
                }
                continue;
            }

            /**
             * Check if all residues have known nucleic acids names.
             */
            boolean isNucleicAcid = true;
            for (int residueNumber = 0; residueNumber < numberOfResidues; residueNumber++) {
                Residue residue = residues.get(residueNumber);
                String name = residue.getName().toUpperCase();
                /**
                 * Convert 1 and 2-character nucleic acid names to
                 * 3-character names.
                 */
                if (name.length() == 1) {
                    if (name.equals("A")) {
                        name = NucleicAcid3.ADE.toString();
                    } else if (name.equals("C")) {
                        name = NucleicAcid3.CYT.toString();
                    } else if (name.equals("G")) {
                        name = NucleicAcid3.GUA.toString();
                    } else if (name.equals("T")) {
                        name = NucleicAcid3.THY.toString();
                    } else if (name.equals("U")) {
                        name = NucleicAcid3.URI.toString();
                    }
                } else if (name.length() == 2) {
                    if (name.equals("YG")) {
                        name = NucleicAcid3.YYG.toString();
                    }
                }
                residue.setName(name);
                NucleicAcid3 nucleicAcid = null;
                for (NucleicAcid3 nucleic : nucleicAcidList) {
                    String nuc3 = nucleic.toString();
                    nuc3 = nuc3.substring(nuc3.length() - 3);
                    if (nuc3.equalsIgnoreCase(name)) {
                        nucleicAcid = nucleic;
                        break;
                    }
                }
                if (nucleicAcid == null) {
                    logger.info(format("Nucleic acid was not recognized %s.", name));
                    isNucleicAcid = false;
                    break;
                }
            }

            /**
             * If all the residues in this chain have known nucleic acids
             * names, then attempt to assign atom types.
             */
            if (isNucleicAcid) {
                try {
                    logger.info(format(" Nucleic acid chain %s", polymer.getName()));
                    assignNucleicAcidAtomTypes(residues, forceField, bondList);
                } catch (MissingHeavyAtomException | MissingAtomTypeException e) {
                    logger.severe(e.toString());
                }
            }
        }
    }

    // Assign ion atom types.
    ArrayList<MSNode> ions = activeMolecularAssembly.getIons();
    if (ions != null && ions.size() > 0) {
        logger.info(format(" Assigning atom types for %d ions.", ions.size()));
        for (MSNode m : ions) {
            Molecule ion = (Molecule) m;
            String name = ion.getResidueName().toUpperCase();
            HetAtoms hetatm = HetAtoms.valueOf(name);
            Atom atom = ion.getAtomList().get(0);
            if (ion.getAtomList().size() != 1) {
                logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
            }
            try {
                switch (hetatm) {
                case NA:
                    atom.setAtomType(findAtomType(2003));
                    break;
                case K:
                    atom.setAtomType(findAtomType(2004));
                    break;
                case MG:
                case MG2:
                    atom.setAtomType(findAtomType(2005));
                    break;
                case CA:
                case CA2:
                    atom.setAtomType(findAtomType(2006));
                    break;
                case CL:
                    atom.setAtomType(findAtomType(2007));
                    break;
                case ZN:
                case ZN2:
                    atom.setAtomType(findAtomType(2008));
                    break;
                case BR:
                    atom.setAtomType(findAtomType(2009));
                    break;
                default:
                    logger.severe(format(" Check residue %s of chain %s.", ion.toString(), ion.getChainID()));
                }
            } catch (Exception e) {
                String message = "Error assigning atom types.";
                logger.log(Level.SEVERE, message, e);
            }
        }
    }
    // Assign water atom types.
    ArrayList<MSNode> water = activeMolecularAssembly.getWaters();
    if (water != null && water.size() > 0) {
        logger.info(format(" Assigning atom types for %d waters.", water.size()));
        for (MSNode m : water) {
            Molecule wat = (Molecule) m;
            try {
                Atom O = buildHeavy(wat, "O", null, 2001);
                Atom H1 = buildHydrogen(wat, "H1", O, 0.96e0, null, 109.5e0, null, 120.0e0, 0, 2002);
                H1.setHetero(true);
                Atom H2 = buildHydrogen(wat, "H2", O, 0.96e0, H1, 109.5e0, null, 120.0e0, 0, 2002);
                H2.setHetero(true);
            } catch (Exception e) {
                String message = "Error assigning atom types to a water.";
                logger.log(Level.SEVERE, message, e);
            }
        }
    }

    // Assign small molecule atom types.
    ArrayList<Molecule> molecules = activeMolecularAssembly.getMolecules();
    for (MSNode m : molecules) {
        Molecule molecule = (Molecule) m;
        String moleculeName = molecule.getResidueName();
        logger.info(" Attempting to patch " + moleculeName);
        ArrayList<Atom> moleculeAtoms = molecule.getAtomList();
        boolean patched = true;
        HashMap<String, AtomType> types = forceField.getAtomTypes(moleculeName);
        /**
         * Assign atom types for all known atoms.
         */
        for (Atom atom : moleculeAtoms) {
            String atomName = atom.getName().toUpperCase();
            AtomType atomType = types.get(atomName);
            if (atomType == null) {
                logger.info(" No atom type was found for " + atomName + " of " + moleculeName + ".");
                patched = false;
                break;
            } else {
                logger.fine(" " + atom.toString() + " -> " + atomType.toString());
                atom.setAtomType(atomType);
                types.remove(atomName);
            }
        }
        /**
         * Create missing hydrogen atoms. Check for missing heavy atoms.
         */
        if (patched && !types.isEmpty()) {
            for (AtomType type : types.values()) {
                if (type.atomicNumber != 1) {
                    logger.info(" Missing heavy atom " + type.name);
                    patched = false;
                    break;
                }
            }
        }
        // Create bonds between known atoms.
        if (patched) {
            for (Atom atom : moleculeAtoms) {
                String atomName = atom.getName();
                String bonds[] = forceField.getBonds(moleculeName, atomName);
                if (bonds != null) {
                    for (String name : bonds) {
                        Atom atom2 = molecule.getAtom(name);
                        if (atom2 != null && !atom.isBonded(atom2)) {
                            buildBond(atom, atom2);
                        }
                    }
                }
            }
        }
        // Create missing hydrogen atoms.
        if (patched && !types.isEmpty()) {
            // Create a hashmap of the molecule's atoms
            HashMap<String, Atom> atomMap = new HashMap<String, Atom>();
            for (Atom atom : moleculeAtoms) {
                atomMap.put(atom.getName().toUpperCase(), atom);
            }
            for (String atomName : types.keySet()) {
                AtomType type = types.get(atomName);
                String bonds[] = forceField.getBonds(moleculeName, atomName.toUpperCase());
                if (bonds == null || bonds.length != 1) {
                    patched = false;
                    logger.info(" Check biotype for hydrogen " + type.name + ".");
                    break;
                }
                // Get the heavy atom the hydrogen is bonded to.
                Atom ia = atomMap.get(bonds[0].toUpperCase());
                Atom hydrogen = new Atom(0, atomName, ia.getAltLoc(), new double[3], ia.getResidueName(),
                        ia.getResidueNumber(), ia.getChainID(), ia.getOccupancy(), ia.getTempFactor(),
                        ia.getSegID());
                logger.fine(" Created hydrogen " + atomName + ".");
                hydrogen.setAtomType(type);
                hydrogen.setHetero(true);
                molecule.addMSNode(hydrogen);
                int valence = ia.getAtomType().valence;
                List<Bond> aBonds = ia.getBonds();
                int numBonds = aBonds.size();
                /**
                 * Try to find the following configuration: ib-ia-ic
                 */
                Atom ib = null;
                Atom ic = null;
                Atom id = null;
                if (numBonds > 0) {
                    Bond bond = aBonds.get(0);
                    ib = bond.get1_2(ia);
                }
                if (numBonds > 1) {
                    Bond bond = aBonds.get(1);
                    ic = bond.get1_2(ia);
                }
                if (numBonds > 2) {
                    Bond bond = aBonds.get(2);
                    id = bond.get1_2(ia);
                }

                /**
                 * Building the hydrogens depends on hybridization and the
                 * locations of other bonded atoms.
                 */
                logger.fine(" Bonding " + atomName + " to " + ia.getName() + " (" + numBonds + " of " + valence
                        + ").");
                switch (valence) {
                case 4:
                    switch (numBonds) {
                    case 3:
                        // Find the average coordinates of atoms ib, ic and id.
                        double b[] = ib.getXYZ(null);
                        double c[] = ib.getXYZ(null);
                        double d[] = ib.getXYZ(null);
                        double a[] = new double[3];
                        a[0] = (b[0] + c[0] + d[0]) / 3.0;
                        a[1] = (b[1] + c[1] + d[1]) / 3.0;
                        a[2] = (b[2] + c[2] + d[2]) / 3.0;
                        // Place the hydrogen at chiral position #1.
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 1);
                        double e1[] = new double[3];
                        hydrogen.getXYZ(e1);
                        double ret[] = new double[3];
                        diff(a, e1, ret);
                        double l1 = r(ret);
                        // Place the hydrogen at chiral position #2.
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, -1);
                        double e2[] = new double[3];
                        hydrogen.getXYZ(e2);
                        diff(a, e2, ret);
                        double l2 = r(ret);
                        // Revert to #1 if it is farther from the average.
                        if (l1 > l2) {
                            hydrogen.setXYZ(e1);
                        }
                        break;
                    case 2:
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, ic, 109.5, 0);
                        break;
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 109.5, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 3:
                    switch (numBonds) {
                    case 2:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, ic, 0.0, 0);
                        break;
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 2:
                    switch (numBonds) {
                    case 1:
                        intxyz(hydrogen, ia, 1.0, ib, 120.0, null, 0.0, 0);
                        break;
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                case 1:
                    switch (numBonds) {
                    case 0:
                        intxyz(hydrogen, ia, 1.0, null, 0.0, null, 0.0, 0);
                        break;
                    default:
                        logger.info(" Check biotype for hydrogen " + atomName + ".");
                        patched = false;
                    }
                    break;
                default:
                    logger.info(" Check biotype for hydrogen " + atomName + ".");
                    patched = false;
                }
                if (!patched) {
                    break;
                } else {
                    buildBond(ia, hydrogen);
                }
            }
        }
        if (!patched) {
            logger.log(Level.WARNING, format(" Deleting unrecognized molecule %s.", m.toString()));
            activeMolecularAssembly.deleteMolecule((Molecule) m);
        } else {
            logger.info(" Patch for " + moleculeName + " succeeded.");
        }
    }
}

---

From source file:it.iit.genomics.cru.igb.bundles.mi.business.MIWorker.java

@Override
public ArrayList<MIResult> doInBackground() {

    // Display the log tab
    MIView.getInstance().getResultsTabbedPan().setSelectedIndex(0);

    UniprotkbUtils uniprotUtil = UniprotkbUtils.getInstance(query.getTaxid());

    // Create a new Symmetry manager for each query
    symManager = new MISymManager(this.trackId);

    Collection<SeqSymmetry> selectedSyms = query.getSelectedSymmetries();

    // Initialize progress property.
    progressBar.setIndeterminate(false);
    ProgressManager progressManager = new ProgressManager(5);

    setProgress(progressManager.getProgress());

    Set<String> queryUniprotAcs = new HashSet<>();
    Set<String> targetUniprotAcs = new HashSet<>();

    // interactions
    MapOfMap<String, String> uniprotAc2uniprotAcs;

    // Interaction found
    ArrayList<MIResult> resultsInBackground = new ArrayList<>();

    logAndPublish("map selection to genome and proteins..");

    // Step 1// w  w  w.j a  va  2 s .  c  om
    progressManager.nextMajorStep(selectedSyms.size());
    // Get gene Symmetries covered by query symmetries
    // don't create container at the moment: many genes syms for a single
    // gene may be present

    // Order list of syms
    SymListOrderer list = new SymListOrderer();

    for (SeqSymmetry querySym : selectedSyms) {
        list.addSymmetry(querySym);
    }

    for (BioSeq chr : list.getSequences()) {
        ArrayList<SeqSymmetry> querySyms = list.getSymmetries(chr);
        getGenes(querySyms, chr, true);
        // for (MIGene gene : getGenes(querySyms, chr, true)) {
        // // load exons (we only need this for the selected ones)
        // miGene2selectedSyms.add(gene, querySym);
        // }
        progressManager.nextStep();
        setProgress(progressManager.getProgress());
    }

    // Step 2
    progressManager.nextMajorStep(miGene2selectedSyms.keySet().size());
    // Associate selected residues
    for (MIGene gene : miGene2selectedSyms.keySet()) {

        logAndPublish("Associate residues to " + gene.getID());

        MoleculeEntry protein = gene.getProtein();

        if (protein != null) {
            queryUniprotAcs.add(protein.getUniprotAc());

            MISymContainer container = symManager.getByProtein(protein);
            symManager.addGeneSymmetry(container, gene);

            symManager.addSelectedSymmetry(container, gene);
        } else {
            igbLogger.getLogger().warn("No protein for {0}", gene.getID());
        }
        progressManager.nextStep();
        setProgress(progressManager.getProgress());
    }

    // Step 3
    progressManager.nextMajorStep(queryUniprotAcs.size());

    // Get interactors
    uniprotAc2uniprotAcs = new MapOfMap<>(queryUniprotAcs);

    logAndPublish("get interactions");

    HashMap<String, MoleculeEntry> targetUniprotEntries = new HashMap<>();

    InteractionManager interactors = new InteractionManager();

    for (String ac : queryUniprotAcs) {

        logAndPublish("Get interactions for " + ac);

        if (ac == null) {
            continue;
        }

        try {
            if (false == PsicquicInitWorker.nullServer.equals(query.getPsiquicServer())
                    && null != query.getPsiquicServer()) {
                for (Interaction interaction : PsicquicUtils.getInstance()
                        .getInteractors(query.getPsiquicServer(), ac)) {
                    interactors.merge(interaction);
                }
            }
        } catch (BridgesRemoteAccessException be) {
            igbLogger.severe("Cannot access PSICQUIC server!");
            break;
        }

        //         // Add interactors from User structures?
        //         if (null != query.getUserStructuresPath() && query.searchUserStructures()) {
        //            Interactome3DLocalRepository userStructures = UserStructuresManager.getInstance()
        //                  .getUserRepository(query.getUserStructuresPath());
        //            for (String interactorAc : userStructures.getInteractors(ac)) {
        //               interactors.getOrCreateInteraction(ac, interactorAc).addType(INTERACTION_TYPE_I3D);
        //               uniprotNeedMapping.add(interactorAc);
        //            }
        //         }

        // Add interactors from I3D?
        if (query.searchInteractome3D() || query.searchDSysMap()) {
            // Check or download I3D interaction file

            // get it from local repository?
            Interactome3DLocalRepository userStructures;
            //            System.out.println("I3D cache: " +  MIBundleConfiguration.getInstance().getI3DStructuresDirectory());
            if (null != MIBundleConfiguration.getInstance().getI3DStructuresDirectory()) {
                userStructures = UserStructuresManager.getInstance()
                        .getUserRepository(MIBundleConfiguration.getInstance().getI3DStructuresDirectory());
            } else {
                I3DDownload download = new I3DDownload(MIBundleConfiguration.getInstance().getCachePath());

                if (false == download.isDatDownloaded(query.getTaxid())) {
                    logAndPublish("download interactions from Interactome3D");
                    download.downloadDat(query.getTaxid());
                }

                // get interactions
                userStructures = UserStructuresManager.getInstance()
                        .getUserRepository(download.getI3DdatPath(query.getTaxid()));
            }

            for (String interactorAc : userStructures.getInteractors(ac)) {
                interactors.getOrCreateInteraction(ac, interactorAc)
                        .addType("direct interaction (Interactome3D)");
                uniprotNeedMapping.add(interactorAc);
            }
        }

        // add interactors from PDB structures
        if (query.searchPDB() || query.searchPDBLocal() || query.searchEPPIC()) {
            MoleculeEntry entry = symManager.getByProteinAc(ac).getEntry();

            PDBWSClient client = new PDBWSClient();
            // Do only 10 by 10
            List<String> pdbs = new ArrayList<>();
            pdbs.addAll(entry.getPdbs());

            while (false == pdbs.isEmpty()) {
                List<String> subset = pdbs.subList(0, Math.min(10, pdbs.size()));
                pdbs = pdbs.subList(Math.min(10, pdbs.size()), pdbs.size());

                if (query.searchPPI() || query.searchNucleicAcid()) {

                    MoleculeDescription molDesc;
                    try {
                        molDesc = client.getDescription(subset);
                    } catch (BridgesRemoteAccessException be) {
                        igbLogger.severe("Cannot access PDB!");
                        break;
                    }

                    if (molDesc != null) {
                        for (StructureID structureId : molDesc.getStructureId()) {

                            for (Polymer polymer : structureId.getPolymers()) {
                                if (polymer.getPolymerDescription() == null) {
                                    igbLogger.severe("No description for " + structureId.getId());
                                }
                                if (null != polymer.getType()) {
                                    switch (polymer.getType()) {
                                    case "protein":
                                        if (query.searchPPI() && null != polymer.getMacromolecule()) {
                                            String proteinAc = polymer.getMacromolecule().getAccession().get(0);

                                            if (false == proteinAc.equals(entry.getUniprotAc())
                                                    || polymer.getChains().size() > 1) {

                                                interactors.getOrCreateInteraction(ac, proteinAc)
                                                        .addType(INTERACTION_TYPE_PDB);
                                                uniprotNeedMapping.add(ac);
                                            }
                                        }
                                        break;
                                    case "dna":
                                        if (false == query.searchNucleicAcid()) {
                                            break;
                                        }
                                        // Merge all DNA entries, use "DNA
                                        // as name rather that the
                                        // desciption
                                        MISymContainer dnaSym = symManager
                                                .getByProteinAc(MoleculeEntry.TAXID_DNA);
                                        uniprotNeedMapping.add(ac);

                                        interactors.getOrCreateInteraction(ac, MoleculeEntry.TAXID_DNA)
                                                .addType(INTERACTION_TYPE_PDB);

                                        if (dnaSym == null) {
                                            MoleculeEntry dnaEntry = new MoleculeEntry(MoleculeEntry.TAXID_DNA);
                                            dnaEntry.setSequence("");
                                            dnaEntry.setTaxid(MoleculeEntry.TAXID_DNA);

                                            targetUniprotEntries.put(MoleculeEntry.TAXID_DNA, dnaEntry);
                                            dnaEntry.addGeneName(MoleculeEntry.TAXID_DNA);

                                            dnaSym = symManager.getByProtein(dnaEntry);
                                        }

                                        MoleculeEntry dnaEntry = dnaSym.getEntry();

                                        for (Chain chain : polymer.getChains()) {
                                            ChainMapping chainMapping = new ChainMapping(structureId.getId(),
                                                    chain.getId(), 0, 0);
                                            dnaEntry.addChain(structureId.getId(), chainMapping, "unspecified");
                                        }

                                        break;

                                    case "rna":
                                        if (false == query.searchNucleicAcid()) {
                                            break;
                                        }
                                        uniprotNeedMapping.add(ac);
                                        // Merge all RNA entries, use "RNA
                                        // as name rather that the
                                        // desciption
                                        MISymContainer rnaSym = symManager
                                                .getByProteinAc(MoleculeEntry.TAXID_RNA);

                                        interactors.getOrCreateInteraction(ac, MoleculeEntry.TAXID_RNA)
                                                .addType(INTERACTION_TYPE_PDB);

                                        if (rnaSym == null) {
                                            MoleculeEntry rnaEntry = new MoleculeEntry(MoleculeEntry.TAXID_RNA);
                                            rnaEntry.setSequence("");
                                            rnaEntry.setTaxid(MoleculeEntry.TAXID_RNA);

                                            targetUniprotEntries.put(MoleculeEntry.TAXID_RNA, rnaEntry);
                                            rnaEntry.addGeneName(MoleculeEntry.TAXID_RNA);

                                            rnaSym = symManager.getByProtein(rnaEntry);
                                        }

                                        MoleculeEntry rnaEntry = rnaSym.getEntry();

                                        for (Chain chain : polymer.getChains()) {
                                            ChainMapping chainMapping = new ChainMapping(structureId.getId(),
                                                    chain.getId(), 0, 0);
                                            rnaEntry.addChain(structureId.getId(), chainMapping, "unspecified");
                                        }

                                        break;
                                    }
                                }
                            }
                        }
                    }
                }
                if (query.searchLigands() && false == query.searchEPPIC()) {
                    try {
                        for (Ligand ligand : client.getLigands(subset)) {

                            /**
                             * Only non polymer ligands
                             */
                            if (false == ligand.isNonPolymer()) {
                                continue;
                            }

                            int numAtoms = 0;

                            for (String atom : ligand.getFormula().split(" ")) {

                                String num = atom.replaceAll("\\D+", "").trim();
                                if ("".equals(num)) {
                                    numAtoms++;
                                } else {
                                    numAtoms += Integer.parseInt(num);
                                }
                            }

                            if (numAtoms <= 10) {
                                igbLogger.info("Skip ligand: " + ligand.getFormula());
                                continue;
                            }
                            uniprotNeedMapping.add(ac);
                            MISymContainer misym = symManager.getByProteinAc(ligand.getChemicalName());

                            interactors.getOrCreateInteraction(ac, ligand.getChemicalName())
                                    .addType(INTERACTION_TYPE_PDB);

                            if (misym == null) {
                                MoleculeEntry ligandEntry = new MoleculeEntry(ligand.getChemicalName());
                                ligandEntry.setSequence("");
                                ligandEntry.setTaxid(MoleculeEntry.TAXID_LIGAND);

                                ligandEntry.addGeneName(ligand.getChemicalId());
                                targetUniprotEntries.put(ligand.getChemicalName(), ligandEntry);

                                misym = symManager.getByProtein(ligandEntry);
                            }

                            MoleculeEntry ligandEntry = misym.getEntry();

                            ChainMapping chainMapping = new ChainMapping(ligand.getStructureId(), "ligand", 0,
                                    0);
                            ligandEntry.addChain(ligand.getStructureId(), chainMapping, "unspecified");

                        }
                    } catch (BridgesRemoteAccessException be) {
                        igbLogger.severe("Cannot access PDB!");
                        break;
                    }
                }
            }

        }

        if (query.searchModifications()) {
            MoleculeEntry entry = symManager.getByProteinAc(ac).getEntry();

            for (ModifiedResidue modification : entry.getModifications()) {
                MISymContainer misym = symManager.getByProteinAc(modification.getDescription());

                uniprotNeedMapping.add(ac);
                if (misym == null) {

                    interactors.getOrCreateInteraction(ac, modification.getDescription())
                            .addType("direct interaction (Uniprot)");
                    // interactors.add(modification.getDescription(),
                    // "association");
                    MoleculeEntry ligandEntry = new MoleculeEntry(modification.getDescription());
                    ligandEntry.setSequence("");
                    ligandEntry.setTaxid(MoleculeEntry.TAXID_MODIFICATION);

                    ligandEntry.addGeneName(modification.getDescription());
                    targetUniprotEntries.put(modification.getDescription(), ligandEntry);

                    symManager.getByProtein(ligandEntry);
                }

            }

        }

        Collection<String> interactorUniprotAcs = interactors.getInteractors();

        for (String interactorUniprotAc : interactorUniprotAcs) {
            // Skip interaction if we the type of query is INTRA (i.e. only
            // interactions between selected genes)
            // and one of the protein was not selected
            if (QueryType.EXTRA.equals(query.getQueryType()) || queryUniprotAcs.contains(interactorUniprotAc)) {
                uniprotAc2uniprotAcs.add(ac, interactorUniprotAc);
                targetUniprotAcs.add(interactorUniprotAc);

                // String key = ac + "#" + interactorUniprotAc;
                // interactionTypes.addAll(key,
                // interactors.get(interactorUniprotAc));
                // At this point we may not have created the symmetry
            }
        }

        progressManager.nextStep();
        setProgress(progressManager.getProgress());
    }

    // Only look for uniprot Acs for which we don't have an entry yet
    HashSet<String> uniprotAcToSearch = new HashSet<>();

    uniprotAcToSearch.addAll(targetUniprotAcs);

    uniprotAcToSearch.removeAll(symManager.getProteinAcs());

    // Allow proteins from other species
    try {
        targetUniprotEntries
                .putAll(uniprotUtil.getUniprotEntriesFromUniprotAccessions(uniprotAcToSearch, false));
    } catch (BridgesRemoteAccessException be) {
        igbLogger.severe("Cannot access Uniprot!");

        return resultsInBackground;
    }

    for (MoleculeEntry entry : targetUniprotEntries.values()) {
        MISymContainer container = symManager.getByProtein(entry);
        if (container == null) {
        }
    }

    // missing ones?
    Collection<String> missingUniprotAcs = new ArrayList<>();

    missingUniprotAcs.addAll(uniprotAcToSearch);

    missingUniprotAcs.removeAll(targetUniprotEntries.keySet());

    for (String missingAc : missingUniprotAcs) {
        MICommons.getInstance().addProteinToBlackList(missingAc);
    }

    for (MISymContainer container : symManager.getQueryContainers()) {
        if (null != container.getEntry()) {
            targetUniprotEntries.put(container.getEntry().getUniprotAc(), container.getEntry());
        }
    }

    // Do I need it if I don't need symmetries?
    // Step 4
    progressManager.nextMajorStep(targetUniprotEntries.values().size());
    for (MoleculeEntry uniprotEntry : targetUniprotEntries.values()) {

        logAndPublish("create symmetry for " + uniprotEntry.getUniprotAc());

        // Get symmetry, it has not been necessarily created
        MISymContainer container = symManager.getByProtein(uniprotEntry);

        Collection<String> geneIds;

        // Check if we are using Ensembl web service or QuickLoad.
        if (EnsemblGeneManager.class.isInstance(geneManager)) {
            geneIds = uniprotEntry.getEnsemblGenes();
        } else {
            geneIds = new HashSet<>();
            geneIds.addAll(uniprotEntry.getGeneNames());
            geneIds.addAll(uniprotEntry.getRefseqs());
            geneIds.addAll(uniprotEntry.getEnsemblGenes());
        }

        SimpleSymWithProps overlappingSym = new SimpleSymWithProps();
        overlappingSym.setProperty(TrackLineParser.ITEM_RGB, Color.RED);

        overlappingSym.setID(this.trackId + "-" + uniprotEntry.getGeneName());

        for (String geneId : geneIds) {

            Collection<MIGene> genes = geneManager.getByID(geneId);

            // For each gene create a "result symmetry", which will be
            // displayed in the interaction track
            if (genes.isEmpty()) {
                continue;
            }

            RangeMerger merger = new RangeMerger();

            for (MIGene gene : genes) {

                if (null == gene) {
                    continue;
                }

                if (null != uniprotEntry.getVarSpliceAC(gene.getID())) {

                    gene.getUniprotAcs().add(uniprotEntry.getUniprotAc());
                    gene.setProtein(uniprotEntry);
                    symManager.addGeneSymmetry(container, gene);

                    BioSeq chromosome = geneManager.getSequence(gene.getChromosomeName());

                    if (chromosome == null) {
                        igbLogger.severe("Unavailable sequence: " + gene.getChromosomeName()
                                + ", there may be a network problem.");
                        continue;
                    }

                    merger.addRange(chromosome.getId(), new Range(gene.getMin(), gene.getMax()));
                }
            }

            for (String seq : merger.getSequences()) {
                BioSeq chromosome = geneManager.getSequence(seq);

                if (chromosome == null) {
                    igbLogger.severe("No sequence for chromosome: " + seq);
                }
                for (Range range : merger.getRanges(seq)) {
                    SeqSpan span = new SimpleSeqSpan(range.getMin(), range.getMax(), chromosome);

                    // Check if it has already this span
                    boolean hasSpan = false;
                    for (int i = 0; i < overlappingSym.getSpanCount(); i++) {
                        SeqSpan otherSpan = overlappingSym.getSpan(i);
                        if (otherSpan.getMin() == span.getMin() && otherSpan.getMax() == span.getMax()) {
                            hasSpan = true;
                            break;
                        }
                    }

                    if (false == hasSpan) {
                        overlappingSym.addSpan(span);
                    }
                }
            }

            if (false == genes.isEmpty()) {
                // we found it
                break;
            }
        }

        symManager.setResultSym(container, overlappingSym);

        progressManager.nextStep();
        setProgress(progressManager.getProgress());

    }

    for (String ac : uniprotNeedMapping) {
        MISymContainer proteinContainer = symManager.getByProteinAc(ac);
        for (MIGene gene : proteinContainer.getMiGenes()) {

            if (false == miGene2selectedSyms.containsKey(gene)) {
                continue;
            }
            for (SeqSymmetry selectedSym : miGene2selectedSyms.get(gene)) {
                logAndPublish("Load residues for " + gene.getID());
                geneManager.loadTranscriptSequence(selectedSym.getSpanSeq(0), gene);

                // Maybe the protein was already assigned to the gene.
                // In order to be sure we are working on the right one,
                // Don't use the protein variable, but get it fromthe gene
                ArrayList<AAPosition> aaPositions = new ArrayList<>();

                // symmetry are 0-based exclusive,
                // use max -1 to have inclusive coordinates
                Collection<AAPosition> positions = AAPositionManager.getAAPositionManager(query.getLabel())
                        .getAAPositions(gene, selectedSym.getSpan(0).getMin(),
                                selectedSym.getSpan(0).getMax() - 1);
                aaPositions.addAll(positions);

                for (AAPosition aa : aaPositions) {
                    gene2pos.add(gene, aa);
                }
                symManager.addSelectedResidues(gene.getProtein(), aaPositions);
            }
        }
    }

    // Step 5
    // don't add twice the same interaction
    HashSet<String> interactionsDone = new HashSet<>();

    progressManager.nextMajorStep(symManager.getQueryContainers().size());

    for (MISymContainer container : symManager.getQueryContainers()) {

        logAndPublish(container.getEntry().getGeneName());

        if (null == container.getEntry()) {
            continue;
        }

        if (null == container.getResultSym()) {
            continue;
        }

        String queryUniprotAc = container.getEntry().getUniprotAc();

        if (null == uniprotAc2uniprotAcs.get(queryUniprotAc)) {
            continue;
        }

        if (MICommons.getInstance().isBlackListed(queryUniprotAc)) {
            continue;
        }

        for (String targetUniprotAc : uniprotAc2uniprotAcs.get(queryUniprotAc)) {

            if (MICommons.getInstance().isBlackListed(targetUniprotAc)) {
                continue;
            }

            // An interaction may be slected twice, as A-B and B-A,
            // avoid this.
            if (interactionsDone.contains(targetUniprotAc + "#" + queryUniprotAc)
                    || interactionsDone.contains(queryUniprotAc + "#" + targetUniprotAc)) {
                continue;
            }
            interactionsDone.add(queryUniprotAc + "#" + targetUniprotAc);

            MISymContainer targetContainer = symManager.getByProteinAc(targetUniprotAc);

            if (targetContainer == null) {
                continue;
            }

            if (targetContainer.getEntry() == null) {
                continue;
            }

            if (targetContainer.getResultSym() == null) {
                continue;
            }

            MIResult result = new MIResult(trackId, container, targetContainer,
                    interactors.getOrCreateInteraction(container.getEntry().getUniprotAc(),
                            targetContainer.getEntry().getUniprotAc()),
                    query, symManager);

            resultsInBackground.add(result);
            miSymmetries.add(targetContainer.getResultSym());
        }

        progressManager.nextStep();

        setProgress(progressManager.getProgress());
    }

    AAPositionManager.removeManager(query.getLabel());

    return resultsInBackground;

}

---

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