List of usage examples for java.util ArrayList clear
public void clear()
From source file:com.rickendirk.rsgwijzigingen.ZoekService.java
private ArrayList<String> checkerClusters() { ArrayList<String> tempList = new ArrayList<>(); //String van klas halen uit SP String klasTextS = PreferenceManager.getDefaultSharedPreferences(getApplicationContext()) .getString("pref_klas", ""); String url = "http://www.rsgtrompmeesters.nl/roosters/roosterwijzigingen/Lijsterbesstraat/subst_001.htm"; SharedPreferences sp = PreferenceManager.getDefaultSharedPreferences(getApplicationContext()); //Clusters ophalen uit SP ArrayList<String> clusters = new ArrayList<>(); for (int a = 1; a < 15; a++) { //String initializen, anders kan hij hem niet toevoegen String clusterLowCase = ""; String cluster = sp.getString("pref_cluster" + a, ""); //If om nullpointer te voorkomen if (!cluster.equals("")) { clusterLowCase = cluster.substring(0, 1).toLowerCase() + cluster.substring(1); }/*from ww w .j av a2 s.c om*/ clusters.add(clusterLowCase); } //Lege clusters weghalen uit arraylist TODO: Kijken of singleton werkt/wat het is clusters.removeAll(Collections.singleton("")); //Er moeten wel clusters zijn ingevoerd: Zo nee, komt AlertDialog via onPostExecute if (clusters.isEmpty()) { tempList.add("geenClusters"); return tempList; } //Checken of klas niet leeg is if (klasTextS.equals("")) { tempList.add("geenKlas"); return tempList; } //Eerste teken klas mag geen letter zijn if (Character.isLetter(klasTextS.charAt(0))) { tempList.add("EersteTekenLetter"); return tempList; } //String opsplitsen in 2 delen, om naar hoofdletters te converteren char charcijfer = klasTextS.charAt(0); String klascijfer = String.valueOf(charcijfer); char charafdeling = klasTextS.charAt(1); String klasafdelingBig = String.valueOf(charafdeling).toUpperCase(); //Onderstaand voor hoofdlettercorrectie String klasCorrect; //KlasCorrect is klas na hoofdlettercorrectie switch (klasTextS.length()) { case 2: klasCorrect = klascijfer + klasafdelingBig; break; case 3: char klasabc = klasTextS.charAt(2); String klasabcSmall = String.valueOf(klasabc).toLowerCase(); klasCorrect = klascijfer + klasafdelingBig + klasabcSmall; break; case 4: char klasafdeling2 = klasTextS.charAt(2); String klasafdeling2Big = String.valueOf(klasafdeling2).toUpperCase(); klasabc = klasTextS.charAt(3); klasabcSmall = String.valueOf(klasabc).toLowerCase(); klasCorrect = klascijfer + klasafdelingBig + klasafdeling2Big + klasabcSmall; break; default: tempList.add("klasMeerDan4Tekens"); return tempList; } //Try en catch in het geval dat de internetverbinding mist try { Document doc = Jsoup.connect(url).get(); Elements tables = doc.select("table"); if (tables.size() < 1) { //Geen geschikte tabel aanwezig tempList.add("geenTabel"); return tempList; } Element table = tables.get(1); Elements rows = table.select("tr"); //Eerste loop is om 2e loop te herhalen voor iedere cluster, tweede loop //doorzoekt dan op zowel klas als cluster for (int b = 0; b < clusters.size(); b++) { for (int i = 2; i < rows.size(); i++) { Element row = rows.get(i); Elements cols = row.select("td"); if (cols.get(0).text().contains(klasCorrect) && cols.get(2).text().contains(clusters.get(b))) { String vakOud = Jsoup.parse(cols.get(2).toString()).text(); String docentOud = Jsoup.parse(cols.get(3).toString()).text(); String vakNieuw = Jsoup.parse(cols.get(4).toString()).text(); String docentNieuw = Jsoup.parse(cols.get(5).toString()).text(); //If in geval van uitval, else ingeval van wijziging if (Jsoup.parse(cols.get(6).toString()).text().contains("--")) { //2 opties: wordt verplaatst of valt uit if (Jsoup.parse(cols.get(8).toString()).text().contains("Uitval")) { String wijziging = Jsoup.parse(cols.get(1).toString()).text() + "e uur " + Jsoup.parse(cols.get(2).toString()).text() + " valt uit"; tempList.add(wijziging); } else { //Uur wordt verplaatst String wijziging = Jsoup.parse(cols.get(1).toString()).text() + "e uur " + "wordt verplaatst naar " + Jsoup.parse(cols.get(8).toString()).text(); tempList.add(wijziging); } } else if (vakOud.equals(vakNieuw) && docentOud.equals(docentNieuw)) { String wijziging = Jsoup.parse(cols.get(1).toString()).text() + "e uur " + vakOud + " wordt verplaatst naar " + Jsoup.parse(cols.get(6).toString()).text(); tempList.add(wijziging); } else { String wijzigingKaal = // Voegt alle kolommen samen tot 1 string // .text() zorgt voor leesbare text // Spaties voor leesbaarheid Jsoup.parse(cols.get(1).toString()).text() + "e uur " + Jsoup.parse(cols.get(2).toString()).text() + " " + Jsoup.parse(cols.get(3).toString()).text() + " wordt " + Jsoup.parse(cols.get(4).toString()).text() + " " + Jsoup.parse(cols.get(5).toString()).text() + " in " + Jsoup.parse(cols.get(6).toString()).text(); //ipv en naar bevatten een "/" ivm uren (ma 12-04 / 4) String ipv = ""; if (Jsoup.parse(cols.get(7).toString()).text().contains("/")) { ipv = "ipv " + Jsoup.parse(cols.get(7).toString()).text(); } String naar = ""; if (Jsoup.parse(cols.get(8).toString()).text().contains("/")) { naar = "naar " + Jsoup.parse(cols.get(8).toString()).text() + " "; } String vervangingsTekst = ""; // staat in lege cell, encoding enz, zie volgende link: // http://stackoverflow.com/questions/26837034/how-to-tell-if-a-html-table-has-an-empty-cell-nbsp-using-jsoup if (cols.size() > 9) { if (!Jsoup.parse(cols.get(9).toString()).text().equals("\u00a0")) { vervangingsTekst = "(" + Jsoup.parse(cols.get(9).toString()).text() + ")"; } } String wijziging = wijzigingKaal + " " + ipv + " " + naar + " " + vervangingsTekst; tempList.add(wijziging); } } //Geen wijzigingen pas bij laatste rij en de laatste cluster if (i == rows.size() - 1 && b == clusters.size() - 1) { //Checken of tempList leeg is, zo ja 1 ding toevoegen if (tempList.isEmpty()) { tempList.add("Er zijn geen wijzigingen"); } //Dag waarvoor wijzigingen zijn ophalen Element dag = doc.select("body > div > div:nth-child(2) > p > b > span").first(); //Compatibiliteit met andere opmaak, om NPE te voorkomen if (dag == null) { dag = doc.select("body > center:nth-child(2) > div").first(); } String dagStr = dag.text().toLowerCase(); // Woorden staan verkeerd om: omwisselen int indexVanSpatie = dagStr.indexOf(" "); String datum = dagStr.substring(0, indexVanSpatie); String rest = dagStr.substring(indexVanSpatie + 1); String dagGoed = rest + " " + datum; tempList.add(dagGoed); //Stand ophalen: staat in 1e tabel van HTML Element tableDate = doc.select("table").get(0); String dateFullText = tableDate.getElementsContainingOwnText("Stand:").text(); //Deel achter "Stand:" pakken String FullTextSplit[] = dateFullText.split("Stand:"); tempList.add(FullTextSplit[1]); return tempList; } } } } catch (java.io.IOException e) { //Error toevoegen aan tempList, dat wordt weergegeven in messagebox tempList.clear(); tempList.add("verbindFout"); return tempList; } //Zover hoort de method NOOIT te komen tempList.add("andereFout"); return tempList; }
From source file:base.BasePlayer.FileRead.java
void getVariantWindow(String chrom, int start, int end) { try {//from ww w . java 2s. c o m FileRead.lastpos = 0; removeNonListVariants(); removeBedLinks(); for (int i = 0; i < Control.controlData.fileArray.size(); i++) { Control.controlData.fileArray.get(i).controlled = false; } readFiles = true; head.putNext(null); current = head; cancelvarcount = false; cancelfileread = false; Main.drawCanvas.loadingtext = "Loading variants..."; for (int i = 0; i < Main.samples; i++) { if (cancelvarcount || cancelfileread) { cancelFileRead(); break; } if (Main.drawCanvas.sampleList.get(i).getTabixFile() == null || Main.drawCanvas.sampleList.get(i).multipart) { continue; } current = head; getVariants(chrom, start, end, Main.drawCanvas.sampleList.get(i)); } readFiles = false; annotate(); if (Control.controlData.controlsOn) { Control.applyControl(); } Main.bedCanvas.intersected = false; if (bigcalc) { Main.drawCanvas.calcClusters(FileRead.head); } else { Main.drawCanvas.calcClusters(FileRead.head, 1); } if (Main.bedCanvas.bedOn) { //VarNode current = FileRead.head.getNext(); /*while(current != null) { current.bedhit = true; current = current.getNext(); }*/ ArrayList<BedTrack> bigs = new ArrayList<BedTrack>(); int smalls = 0; for (int i = 0; i < Main.bedCanvas.bedTrack.size(); i++) { if (!Main.bedCanvas.bedTrack.get(i).small || Main.bedCanvas.bedTrack.get(i).getZoomlevel() != null) { if (Main.bedCanvas.bedTrack.get(i).intersect) { bigs.add(Main.bedCanvas.bedTrack.get(i)); Main.bedCanvas.bedTrack.get(i).intersect = false; } } else { if (Main.bedCanvas.bedTrack.get(i).intersect) { smalls++; } } } if (smalls == 0) { VarNode current = FileRead.head.getNext(); while (current != null) { current.bedhit = true; current = current.getNext(); } } for (int i = 0; i < Main.bedCanvas.bedTrack.size(); i++) { Main.bedCanvas.bedTrack.get(i).used = false; if (Main.bedCanvas.bedTrack.get(i).small && Main.bedCanvas.bedTrack.get(i).getZoomlevel() == null) { if (Main.bedCanvas.bedTrack.get(i).intersect && !Main.bedCanvas.bedTrack.get(i).loading) { Main.bedCanvas.annotate(Main.bedCanvas.bedTrack.get(i).getHead(), FileRead.head.getNext()); } else if (Main.bedCanvas.bedTrack.get(i).intersect && Main.bedCanvas.bedTrack.get(i).loading) { Main.bedCanvas.bedTrack.get(i).waiting = true; } } //else if(Main.bedCanvas.bedTrack.get(i).intersect) { /*BedCanvas.Annotator annotator = Main.bedCanvas.new Annotator(Main.bedCanvas.bedTrack.get(i)); annotator.annotateVars(); */ // } } if (bigs.size() > 0) { for (int i = 0; i < bigs.size(); i++) { bigs.get(i).intersect = true; BedCanvas.Annotator annotator = Main.bedCanvas.new Annotator(bigs.get(i)); annotator.annotateVars(); } bigs.clear(); } Main.bedCanvas.intersected = true; if (FileRead.bigcalc) { Main.drawCanvas.calcClusters(FileRead.head); } else { Main.drawCanvas.calcClusters(FileRead.head, 1); } } } catch (Exception e) { e.printStackTrace(); } }
From source file:pl.selvin.android.syncframework.content.BaseContentProvider.java
protected boolean Sync(String service, String scope, String params) { final Date start = new Date(); boolean hasError = false; if (params == null) params = ""; final SQLiteDatabase db = mDB.getWritableDatabase(); final ArrayList<TableInfo> notifyTableInfo = new ArrayList<TableInfo>(); final String download = String.format(contentHelper.DOWNLOAD_SERVICE_URI, service, scope, params); final String upload = String.format(contentHelper.UPLOAD_SERVICE_URI, service, scope, params); final String scopeServerBlob = String.format("%s.%s.%s", service, scope, _.serverBlob); String serverBlob = null;// w ww . java 2 s.c o m Cursor cur = db.query(BlobsTable.NAME, new String[] { BlobsTable.C_VALUE }, BlobsTable.C_NAME + "=?", new String[] { scopeServerBlob }, null, null, null); final String originalBlob; if (cur.moveToFirst()) { originalBlob = serverBlob = cur.getString(0); } else { originalBlob = null; } cur.close(); db.beginTransaction(); try { boolean nochanges = false; if (serverBlob != null) { nochanges = !contentHelper.hasDirtTable(db, scope); } boolean resolve = false; final Metadata meta = new Metadata(); final HashMap<String, Object> vals = new HashMap<String, Object>(); final ContentValues cv = new ContentValues(2); JsonFactory jsonFactory = new JsonFactory(); JsonToken current = null; String name = null; boolean moreChanges = false; boolean forceMoreChanges = false; do { final int requestMethod; final String serviceRequestUrl; final ContentProducer contentProducer; if (serverBlob != null) { requestMethod = HTTP_POST; if (nochanges) { serviceRequestUrl = download; } else { serviceRequestUrl = upload; forceMoreChanges = true; } contentProducer = new SyncContentProducer(jsonFactory, db, scope, serverBlob, !nochanges, notifyTableInfo, contentHelper); nochanges = true; } else { requestMethod = HTTP_GET; serviceRequestUrl = download; contentProducer = null; } if (moreChanges) { db.beginTransaction(); } Result result = executeRequest(requestMethod, serviceRequestUrl, contentProducer); if (result.getStatus() == HttpStatus.SC_OK) { final JsonParser jp = jsonFactory.createParser(result.getInputStream()); jp.nextToken(); // skip ("START_OBJECT(d) expected"); jp.nextToken(); // skip ("FIELD_NAME(d) expected"); if (jp.nextToken() != JsonToken.START_OBJECT) throw new Exception("START_OBJECT(d - object) expected"); while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); if (_.__sync.equals(name)) { current = jp.nextToken(); while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); current = jp.nextToken(); if (_.serverBlob.equals(name)) { serverBlob = jp.getText(); } else if (_.moreChangesAvailable.equals(name)) { moreChanges = jp.getBooleanValue() || forceMoreChanges; forceMoreChanges = false; } else if (_.resolveConflicts.equals(name)) { resolve = jp.getBooleanValue(); } } } else if (_.results.equals(name)) { if (jp.nextToken() != JsonToken.START_ARRAY) throw new Exception("START_ARRAY(results) expected"); while (jp.nextToken() != JsonToken.END_ARRAY) { meta.isDeleted = false; meta.tempId = null; vals.clear(); while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); current = jp.nextToken(); if (current == JsonToken.VALUE_STRING) { vals.put(name, jp.getText()); } else if (current == JsonToken.VALUE_NUMBER_INT) { vals.put(name, jp.getLongValue()); } else if (current == JsonToken.VALUE_NUMBER_FLOAT) { vals.put(name, jp.getDoubleValue()); } else if (current == JsonToken.VALUE_FALSE) { vals.put(name, 0L); } else if (current == JsonToken.VALUE_TRUE) { vals.put(name, 1L); } else if (current == JsonToken.VALUE_NULL) { vals.put(name, null); } else { if (current == JsonToken.START_OBJECT) { if (_.__metadata.equals(name)) { while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); jp.nextToken(); if (_.uri.equals(name)) { meta.uri = jp.getText(); } else if (_.type.equals(name)) { meta.type = jp.getText(); } else if (_.isDeleted.equals(name)) { meta.isDeleted = jp.getBooleanValue(); } else if (_.tempId.equals(name)) { meta.tempId = jp.getText(); } } } else if (_.__syncConflict.equals(name)) { while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); jp.nextToken(); if (_.isResolved.equals(name)) { } else if (_.conflictResolution.equals(name)) { } else if (_.conflictingChange.equals(name)) { while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); current = jp.nextToken(); if (current == JsonToken.START_OBJECT) { if (_.__metadata.equals(name)) { while (jp.nextToken() != JsonToken.END_OBJECT) { } } } } } } // resolve conf } else if (_.__syncError.equals(name)) { while (jp.nextToken() != JsonToken.END_OBJECT) { name = jp.getCurrentName(); jp.nextToken(); } } } } } TableInfo tab = contentHelper.getTableFromType(meta.type); if (meta.isDeleted) { tab.DeleteWithUri(meta.uri, db); } else { tab.SyncJSON(vals, meta, db); } if (!notifyTableInfo.contains(tab)) notifyTableInfo.add(tab); } } } jp.close(); if (!hasError) { cv.clear(); cv.put(BlobsTable.C_NAME, scopeServerBlob); cv.put(BlobsTable.C_VALUE, serverBlob); cv.put(BlobsTable.C_DATE, Calendar.getInstance().getTimeInMillis()); cv.put(BlobsTable.C_STATE, 0); db.replace(BlobsTable.NAME, null, cv); db.setTransactionSuccessful(); db.endTransaction(); if (DEBUG) { Log.d(TAG, "CP-Sync: commit changes"); } final ContentResolver cr = getContext().getContentResolver(); for (TableInfo t : notifyTableInfo) { final Uri nu = contentHelper.getDirUri(t.name, false); cr.notifyChange(nu, null, false); // false - do not force sync cause we are in sync if (DEBUG) { Log.d(TAG, "CP-Sync: notifyChange table: " + t.name + ", uri: " + nu); } for (String n : t.notifyUris) { cr.notifyChange(Uri.parse(n), null, false); if (DEBUG) { Log.d(TAG, "+uri: " + n); } } } notifyTableInfo.clear(); } } else { if (DEBUG) { Log.e(TAG, "Server error in fetching remote contacts: " + result.getStatus()); } hasError = true; break; } } while (moreChanges); } catch (final ConnectTimeoutException e) { hasError = true; if (DEBUG) { Log.e(TAG, "ConnectTimeoutException", e); } } catch (final IOException e) { hasError = true; if (DEBUG) { Log.e(TAG, Log.getStackTraceString(e)); } } catch (final ParseException e) { hasError = true; if (DEBUG) { Log.e(TAG, "ParseException", e); } } catch (final Exception e) { hasError = true; if (DEBUG) { Log.e(TAG, "ParseException", e); } } if (hasError) { db.endTransaction(); ContentValues cv = new ContentValues(); cv.put(BlobsTable.C_NAME, scopeServerBlob); cv.put(BlobsTable.C_VALUE, originalBlob); cv.put(BlobsTable.C_DATE, Calendar.getInstance().getTimeInMillis()); cv.put(BlobsTable.C_STATE, -1); db.replace(BlobsTable.NAME, null, cv); } /*-if (!hasError) { final ContentValues cv = new ContentValues(2); cv.put(BlobsTable.C_NAME, scopeServerBlob); cv.put(BlobsTable.C_VALUE, serverBlob); db.replace(BlobsTable.NAME, null, cv); db.setTransactionSuccessful(); } db.endTransaction(); if (!hasError) { for (String t : notifyTableInfo) { getContext().getContentResolver().notifyChange(getDirUri(t), null); } }*/ if (DEBUG) { Helpers.LogInfo(start); } return !hasError; }
From source file:com.sentaroh.android.SMBSync2.SyncTaskUtility.java
public void editDirFilterDlg(final SyncTaskItem sti, final String prof_master, final ArrayList<String> dir_filter, final NotifyEvent p_ntfy) { ArrayList<FilterListItem> filterList = new ArrayList<FilterListItem>(); final AdapterFilterList filterAdapter; // ??/*from ww w .j a va2 s . co m*/ final Dialog dialog = new Dialog(mContext); dialog.requestWindowFeature(Window.FEATURE_NO_TITLE); dialog.setCanceledOnTouchOutside(false); dialog.setContentView(R.layout.filter_list_dlg); LinearLayout ll_dlg_view = (LinearLayout) dialog.findViewById(R.id.filter_select_edit_view); ll_dlg_view.setBackgroundColor(mGp.themeColorList.dialog_msg_background_color); final LinearLayout title_view = (LinearLayout) dialog.findViewById(R.id.filter_select_edit_title_view); final TextView title = (TextView) dialog.findViewById(R.id.filter_select_edit_title); title_view.setBackgroundColor(mGp.themeColorList.dialog_title_background_color); title.setTextColor(mGp.themeColorList.text_color_dialog_title); filterAdapter = new AdapterFilterList(mContext, R.layout.filter_list_item_view, filterList); final ListView lv = (ListView) dialog.findViewById(R.id.filter_select_edit_listview); for (int i = 0; i < dir_filter.size(); i++) { String inc = dir_filter.get(i).substring(0, 1); String filter = dir_filter.get(i).substring(1, dir_filter.get(i).length()); boolean b_inc = false; if (inc.equals(SMBSYNC_PROF_FILTER_INCLUDE)) b_inc = true; filterAdapter.add(new FilterListItem(filter, b_inc)); } if (filterAdapter.getCount() == 0) filterAdapter.add(new FilterListItem(mContext.getString(R.string.msgs_filter_list_no_filter), false)); lv.setAdapter(filterAdapter); lv.setScrollingCacheEnabled(false); lv.setScrollbarFadingEnabled(false); title.setText(mContext.getString(R.string.msgs_filter_list_dlg_dir_filter)); final TextView dlg_msg = (TextView) dialog.findViewById(R.id.filter_select_edit_msg); final Button dirbtn = (Button) dialog.findViewById(R.id.filter_select_edit_dir_btn); CommonDialog.setDlgBoxSizeLimit(dialog, true); final EditText et_filter = (EditText) dialog.findViewById(R.id.filter_select_edit_new_filter); final Button addbtn = (Button) dialog.findViewById(R.id.filter_select_edit_add_btn); final Button btn_cancel = (Button) dialog.findViewById(R.id.filter_select_edit_cancel_btn); final Button btn_ok = (Button) dialog.findViewById(R.id.filter_select_edit_ok_btn); lv.setOnItemClickListener(new OnItemClickListener() { public void onItemClick(AdapterView<?> items, View view, int idx, long id) { FilterListItem fli = filterAdapter.getItem(idx); if (fli.getFilter().startsWith("---") || fli.isDeleted()) return; // ???????? editDirFilter(idx, filterAdapter, fli, fli.getFilter()); } }); // Add? et_filter.addTextChangedListener(new TextWatcher() { @Override public void afterTextChanged(Editable s) { if (s.length() != 0) { if (isFilterExists(s.toString().trim(), filterAdapter)) { String mtxt = mContext.getString(R.string.msgs_filter_list_duplicate_filter_specified); dlg_msg.setText(String.format(mtxt, s.toString().trim())); addbtn.setEnabled(false); dirbtn.setEnabled(true); btn_ok.setEnabled(true); } else { dlg_msg.setText(""); addbtn.setEnabled(true); dirbtn.setEnabled(false); btn_ok.setEnabled(false); } } else { addbtn.setEnabled(false); dirbtn.setEnabled(true); btn_ok.setEnabled(true); } // et_filter.setText(s); } @Override public void beforeTextChanged(CharSequence s, int start, int count, int after) { } @Override public void onTextChanged(CharSequence s, int start, int before, int count) { } }); addbtn.setEnabled(false); addbtn.setOnClickListener(new View.OnClickListener() { public void onClick(View v) { dlg_msg.setText(""); String newfilter = et_filter.getText().toString(); if (isFilterExists(newfilter, filterAdapter)) { String mtxt = mContext.getString(R.string.msgs_filter_list_duplicate_filter_specified); dlg_msg.setText(String.format(mtxt, newfilter)); return; } dlg_msg.setText(""); et_filter.setText(""); if (filterAdapter.getItem(0).getFilter().startsWith("---")) filterAdapter.remove(filterAdapter.getItem(0)); filterAdapter.add(new FilterListItem(newfilter, true)); filterAdapter.setNotifyOnChange(true); filterAdapter.sort(new Comparator<FilterListItem>() { @Override public int compare(FilterListItem lhs, FilterListItem rhs) { return lhs.getFilter().compareToIgnoreCase(rhs.getFilter()); }; }); dirbtn.setEnabled(true); btn_ok.setEnabled(true); } }); // Directory? // if (getProfileType(prof_master,prof_dapter).equals("L")) { // if (!mGp.externalStorageIsMounted) dirbtn.setEnabled(false); // } else if (getProfileType(prof_master,prof_dapter).equals("R")) { // if (util.isRemoteDisable()) dirbtn.setEnabled(false); // } else dirbtn.setEnabled(false); dirbtn.setOnClickListener(new View.OnClickListener() { public void onClick(View v) { NotifyEvent ntfy = new NotifyEvent(mContext); //Listen setRemoteShare response ntfy.setListener(new NotifyEventListener() { @Override public void positiveResponse(Context arg0, Object[] arg1) { dlg_msg.setText(""); } @Override public void negativeResponse(Context arg0, Object[] arg1) { if (arg1 != null) dlg_msg.setText((String) arg1[0]); else dlg_msg.setText(""); } }); listDirFilter(sti, prof_master, dir_filter, filterAdapter, ntfy); } }); // CANCEL? btn_cancel.setOnClickListener(new View.OnClickListener() { public void onClick(View v) { dialog.dismiss(); // glblParms.profileListView.setSelectionFromTop(currentViewPosX,currentViewPosY); } }); // Cancel? dialog.setOnCancelListener(new Dialog.OnCancelListener() { @Override public void onCancel(DialogInterface arg0) { btn_cancel.performClick(); } }); // OK? btn_ok.setOnClickListener(new View.OnClickListener() { public void onClick(View v) { dialog.dismiss(); dir_filter.clear(); if (filterAdapter.getCount() > 0) { for (int i = 0; i < filterAdapter.getCount(); i++) { if (!filterAdapter.getItem(i).isDeleted() && !filterAdapter.getItem(i).getFilter().startsWith("---")) { String inc = SMBSYNC_PROF_FILTER_EXCLUDE; if (filterAdapter.getItem(i).getInc()) inc = SMBSYNC_PROF_FILTER_INCLUDE; dir_filter.add(inc + filterAdapter.getItem(i).getFilter()); } } } p_ntfy.notifyToListener(true, null); } }); // dialog.setOnKeyListener(new DialogOnKeyListener(context)); // dialog.setCancelable(false); dialog.show(); }
From source file:com.krawler.spring.hrms.common.hrmsCommonController.java
public ModelAndView exportUserInfo(HttpServletRequest request, HttpServletResponse response) { KwlReturnObject kmsg = null;/*from w w w.j av a2 s . c o m*/ JSONObject jobj = new JSONObject(); JSONArray jarr = new JSONArray(); JSONObject countobj = new JSONObject(); JSONObject jobj1 = new JSONObject(); try { String Searchjson = request.getParameter("searchJson"); String appendCase = "and"; String companyid = sessionHandlerImplObj.getCompanyid(request); String lid = StringUtil.checkForNull(request.getParameter("lid")); HashMap<String, Object> requestParams = new HashMap<String, Object>(); ArrayList filter_names = new ArrayList( Arrays.asList("ua.user.company.companyID", "ua.user.deleteflag")); ArrayList filter_values = new ArrayList(Arrays.asList(companyid, 0)); requestParams.put("ss", StringUtil.checkForNull(request.getParameter("ss"))); requestParams.put("allflag", true); requestParams.put("searchcol", new String[] { "u.firstName", "u.lastName", "ua.department.value", "ua.designationid.value", "ua.role.name", "u.emailID" }); if (request.getParameter("combo") != null) { requestParams.put("combo", request.getParameter("combo")); } else { requestParams.put("combo", ""); } StringUtil.checkpaging(requestParams, request); SimpleDateFormat df = new SimpleDateFormat("yyyy/MM/dd"); if (!StringUtil.isNullOrEmpty(request.getParameter("stdate"))) { filter_names.add(">=emp.joindate"); filter_values.add(new Date(df.format(new Date(request.getParameter("stdate"))))); filter_names.add("<=emp.joindate"); filter_values.add(new Date(df.format(new Date(request.getParameter("enddate"))))); } if (!StringUtil.isNullOrEmpty(Searchjson)) { getMyAdvanceSearchparams(Searchjson, filter_names); insertParamAdvanceSearchString(filter_values, Searchjson); } requestParams.put("filter_names", filter_names); requestParams.put("filter_values", filter_values); kmsg = hrmsCommonDAOObj.getUserDetailsHrms(requestParams); List lst = kmsg.getEntityList(); jarr = kwlCommonTablesDAOObj.getDetailsJson(lst, 0, "com.krawler.common.admin.User"); int count = 0; for (int ctr = 0; ctr < jarr.length(); ctr++) { jobj = jarr.getJSONObject(ctr); Object[] row = (Object[]) lst.get(ctr); User u = (User) jobj.get("instance"); Useraccount ua = (Useraccount) kwlCommonTablesDAOObj .getObject("com.krawler.common.admin.Useraccount", row[0].toString()); if (row[1] != null) { Empprofile e = (Empprofile) kwlCommonTablesDAOObj.getObject("com.krawler.hrms.ess.Empprofile", row[1].toString()); if (!StringUtil.isNullOrEmpty(e.getStatus())) { jobj.put("status", messageSource.getMessage("hrms.administration." + e.getStatus(), null, e.getStatus(), RequestContextUtils.getLocale(request))); } else { jobj.put("status", messageSource.getMessage("hrms.administration.Pending", null, "Pending", RequestContextUtils.getLocale(request))); } jobj.put("dob", e.getDoB() == null ? "" : e.getDoB()); jobj.put("gender", e.getGender() == null ? "" : e.getGender()); jobj.put("bloodgrp", e.getBloodgrp() == null ? "" : e.getBloodgrp()); jobj.put("fathername", e.getFathername() == null ? "" : e.getFathername()); jobj.put("mothername", e.getMothername() == null ? "" : e.getMothername()); jobj.put("passportno", e.getPassportno() == null ? "" : e.getPassportno()); jobj.put("joindate", e.getJoindate() == null ? "" : e.getJoindate()); jobj.put("confirmdate", e.getConfirmdate() == null ? "" : e.getConfirmdate()); jobj.put("middlename", e.getMiddlename() == null ? "" : e.getMiddlename()); jobj.put("keyskills", e.getKeyskills() == null ? "" : e.getKeyskills()); jobj.put("wkstarttime", e.getWkstarttime() == null ? "" : e.getWkstarttime()); jobj.put("wkendtime", e.getWkendtime() == null ? "" : e.getWkendtime()); jobj.put("weekoff", e.getWeekoff() == null ? "" : e.getWeekoff()); jobj.put("pannumber", e.getPanno() == null ? "" : e.getPanno()); jobj.put("updatedon", e.getUpdated_on() == null ? "" : e.getUpdated_on()); } else { jobj.put("status", messageSource.getMessage("hrms.recruitment.InComplete", null, "Incomplete", RequestContextUtils.getLocale(request))); jobj.put("dob", ""); jobj.put("gender", ""); jobj.put("bloodgrp", ""); jobj.put("fathername", ""); jobj.put("mothername", ""); jobj.put("passportno", ""); jobj.put("joindate", ""); jobj.put("confirmdate", ""); jobj.put("middlename", ""); jobj.put("keyskills", ""); jobj.put("wkstarttime", ""); jobj.put("wkendtime", ""); jobj.put("weekoff", ""); } jobj.put("department", (ua.getDepartment() == null ? "" : ua.getDepartment().getId())); jobj.put("departmentname", (ua.getDepartment() == null ? "" : ua.getDepartment().getValue())); jobj.put("role", (ua.getRole() == null ? "" : ua.getRole().getID())); String name = ""; if (ua.getRole() != null && ua.getRole().getCompany() != null) { name = ua.getRole().getName(); } else { name = messageSource.getMessage("hrms.common.role." + ua.getRole().getID(), null, ua.getRole().getName(), RequestContextUtils.getLocale(request)); } jobj.put("rolename", (ua.getRole() == null ? "" : name)); jobj.put("username", u.getUserLogin().getUserName()); jobj.put("fullname", u.getFirstName() + " " + (u.getLastName() == null ? "" : u.getLastName())); jobj.put("lastlogin", (u.getUserLogin().getLastActivityDate() == null ? "" : sessionHandlerImplObj.getDateFormatter(request) .format(u.getUserLogin().getLastActivityDate()))); jobj.put("designation", ua.getDesignationid() == null ? "" : ua.getDesignationid().getValue()); jobj.put("designationid", ua.getDesignationid() == null ? "" : ua.getDesignationid().getId()); jobj.put("templateid", ua.getTemplateid() != null ? ua.getTemplateid() : ""); jobj.put("salary", ua.getSalary() != null ? ua.getSalary() : ""); jobj.put("accno", ua.getAccno() != null ? ua.getAccno() : ""); jobj.put("createdon", ua.getUser().getCreatedon() != null ? ua.getUser().getCreatedon() : ""); requestParams.clear(); requestParams.put("companyid", sessionHandlerImplObj.getCompanyid(request)); requestParams.put("empid", ua.getEmployeeid()); KwlReturnObject result; // KwlReturnObject result = profileHandlerDAOObj.getEmpidFormatEdit(requestParams); if (ua.getEmployeeIdFormat() == null) { jobj.put("employeeid", ua.getEmployeeid() == null ? "" : profileHandlerDAOObj.getEmpidFormatEdit(requestParams).getEntityList().get(0)); } else { requestParams.put("standardEmpId", profileHandlerDAOObj.getEmpidFormatEdit(requestParams) .getEntityList().get(0).toString()); requestParams.put("employeeIdFormat", ua.getEmployeeIdFormat()); jobj.put("employeeid", profileHandlerDAOObj.getNewEmployeeIdFormat(requestParams)); } requestParams.clear(); filter_names.add("assignemp.userID"); filter_values.add(u.getUserID()); filter_names.add("managerstatus"); filter_values.add(1); requestParams.put("filter_names", Arrays.asList("assignemp.userID", "managerstatus", "assignman.deleteflag")); requestParams.put("filter_values", Arrays.asList(u.getUserID(), 1, 0)); result = hrmsCommonDAOObj.getAssignmanager(requestParams); List lst1 = result.getEntityList(); Iterator itr1 = lst1.iterator(); if (itr1.hasNext()) { String manager = ""; while (itr1.hasNext()) { Assignmanager asm = (Assignmanager) itr1.next(); if (asm.getAssignman() != null) { jobj.append("managerid", asm.getAssignman().getUserID()); manager += asm.getAssignman().getFirstName() + " " + asm.getAssignman().getLastName() + ","; } } jobj.put("manager", manager.substring(0, manager.length() - 1)); } else { jobj.put("manager", " "); jobj.put("managerid", " "); } requestParams.clear(); filter_names.clear(); filter_values.clear(); filter_names.add("employee.userID"); filter_values.add(u.getUserID()); filter_names.add("reviewer.deleteflag"); filter_values.add(0); filter_names.add("reviewerstatus"); filter_values.add(1); requestParams.put("filter_names", filter_names); requestParams.put("filter_values", filter_values); result = hrmsCommonDAOObj.getAssignreviewer(requestParams); lst1 = result.getEntityList(); itr1 = lst1.iterator(); if (itr1.hasNext()) { String reviewer = ""; while (itr1.hasNext()) { Assignreviewer rev = (Assignreviewer) itr1.next(); if (rev.getReviewer() != null) { jobj.append("reviewerid", rev.getReviewer().getUserID()); reviewer += rev.getReviewer().getFirstName() + " " + rev.getReviewer().getLastName() + ","; } } jobj.put("reviewer", reviewer.substring(0, reviewer.length() - 1)); } else { jobj.put("reviewer", " "); jobj.put("reviewerid", " "); } jarr.put(ctr, jobj); count++; } countobj.put("data", jarr); countobj.put("count", kmsg.getRecordTotalCount()); exportDAOImplObj.processRequest(request, response, countobj); } catch (Exception e) { e.printStackTrace(); } return new ModelAndView("jsonView", "model", jobj.toString()); }
From source file:com.datatorrent.stram.engine.GenericNode.java
/** * Originally this method was defined in an attempt to implement the interface Runnable. * * Note that activate does not return as long as there is useful workload for the node. *//*from ww w .ja v a2 s.co m*/ @Override @SuppressWarnings({ "SleepWhileInLoop", "UseSpecificCatch", "BroadCatchBlock", "TooBroadCatch" }) public final void run() { doCheckpoint = false; final long maxSpinMillis = context.getValue(OperatorContext.SPIN_MILLIS); long spinMillis = 0; final boolean handleIdleTime = operator instanceof IdleTimeHandler; int totalQueues = inputs.size(); int regularQueues = totalQueues; // regularQueues is the number of queues that are not connected to a DelayOperator for (String portName : inputs.keySet()) { if (isInputPortConnectedToDelayOperator(portName)) { regularQueues--; } } ArrayList<Map.Entry<String, SweepableReservoir>> activeQueues = new ArrayList<>(); activeQueues.addAll(inputs.entrySet()); int expectingBeginWindow = activeQueues.size(); int receivedEndWindow = 0; long firstWindowId = -1; calculateNextCheckpointWindow(); TupleTracker tracker; LinkedList<TupleTracker> resetTupleTracker = new LinkedList<TupleTracker>(); try { do { Iterator<Map.Entry<String, SweepableReservoir>> buffers = activeQueues.iterator(); activequeue: while (buffers.hasNext()) { Map.Entry<String, SweepableReservoir> activePortEntry = buffers.next(); SweepableReservoir activePort = activePortEntry.getValue(); Tuple t = activePort.sweep(); if (t != null) { spinMillis = 0; boolean delay = (operator instanceof Operator.DelayOperator); long windowAhead = 0; if (delay) { windowAhead = WindowGenerator.getAheadWindowId(t.getWindowId(), firstWindowMillis, windowWidthMillis, 1); } switch (t.getType()) { case BEGIN_WINDOW: if (expectingBeginWindow == totalQueues) { // This is the first begin window tuple among all ports if (isInputPortConnectedToDelayOperator(activePortEntry.getKey())) { // We need to wait for the first BEGIN_WINDOW from a port not connected to DelayOperator before // we can do anything with it, because otherwise if a CHECKPOINT tuple arrives from // upstream after the BEGIN_WINDOW tuple for the next window from the delay operator, it would end // up checkpointing in the middle of the window. This code is assuming we have at least one // input port that is not connected to a DelayOperator, and we might have to change this later. // In the future, this condition will not be needed if we get rid of the CHECKPOINT tuple. continue; } activePort.remove(); expectingBeginWindow--; receivedEndWindow = 0; currentWindowId = t.getWindowId(); if (delay) { if (WindowGenerator.getBaseSecondsFromWindowId(windowAhead) > t .getBaseSeconds()) { // Buffer server code strips out the base seconds from BEGIN_WINDOW and END_WINDOW tuples for // serialization optimization. That's why we need a reset window here to tell the buffer // server we are having a new baseSeconds now. Tuple resetWindowTuple = new ResetWindowTuple(windowAhead); for (int s = sinks.length; s-- > 0;) { sinks[s].put(resetWindowTuple); } controlTupleCount++; } t.setWindowId(windowAhead); } for (int s = sinks.length; s-- > 0;) { sinks[s].put(t); } controlTupleCount++; context.setWindowsFromCheckpoint(nextCheckpointWindowCount--); if (applicationWindowCount == 0) { insideWindow = true; operator.beginWindow(currentWindowId); } } else if (t.getWindowId() == currentWindowId) { activePort.remove(); expectingBeginWindow--; } else { buffers.remove(); String port = activePortEntry.getKey(); if (PROCESSING_MODE == ProcessingMode.AT_MOST_ONCE) { if (t.getWindowId() < currentWindowId) { /* * we need to fast forward this stream till we find the current * window or the window which is bigger than the current window. */ /* lets move the current reservoir in the background */ Sink<Object> sink = activePort.setSink(Sink.BLACKHOLE); deferredInputConnections.add(0, new DeferredInputConnection(port, activePort)); /* replace it with the reservoir which blocks the tuples in the past */ WindowIdActivatedReservoir wiar = new WindowIdActivatedReservoir(port, activePort, currentWindowId); wiar.setSink(sink); inputs.put(port, wiar); activeQueues.add(new AbstractMap.SimpleEntry<String, SweepableReservoir>( port, wiar)); break activequeue; } else { expectingBeginWindow--; if (++receivedEndWindow == totalQueues) { processEndWindow(null); activeQueues.addAll(inputs.entrySet()); expectingBeginWindow = activeQueues.size(); break activequeue; } } } else { logger.error( "Catastrophic Error: Out of sequence {} tuple {} on port {} while expecting {}", t.getType(), Codec.getStringWindowId(t.getWindowId()), port, Codec.getStringWindowId(currentWindowId)); System.exit(2); } } break; case END_WINDOW: buffers.remove(); if (t.getWindowId() == currentWindowId) { activePort.remove(); endWindowDequeueTimes.put(activePort, System.currentTimeMillis()); if (++receivedEndWindow == totalQueues) { assert (activeQueues.isEmpty()); if (delay) { t.setWindowId(windowAhead); } processEndWindow(t); activeQueues.addAll(inputs.entrySet()); expectingBeginWindow = activeQueues.size(); break activequeue; } } break; case CHECKPOINT: activePort.remove(); long checkpointWindow = t.getWindowId(); if (lastCheckpointWindowId < checkpointWindow) { dagCheckpointOffsetCount = 0; if (PROCESSING_MODE == ProcessingMode.EXACTLY_ONCE) { lastCheckpointWindowId = checkpointWindow; } else if (!doCheckpoint) { if (checkpointWindowCount == 0) { checkpoint(checkpointWindow); lastCheckpointWindowId = checkpointWindow; } else { doCheckpoint = true; } } if (!delay) { for (int s = sinks.length; s-- > 0;) { sinks[s].put(t); } controlTupleCount++; } } break; case RESET_WINDOW: /** * we will receive tuples which are equal to the number of input streams. */ activePort.remove(); if (isInputPortConnectedToDelayOperator(activePortEntry.getKey())) { break; // breaking out of the switch/case } buffers.remove(); int baseSeconds = t.getBaseSeconds(); tracker = null; for (Iterator<TupleTracker> trackerIterator = resetTupleTracker .iterator(); trackerIterator.hasNext();) { tracker = trackerIterator.next(); if (tracker.tuple.getBaseSeconds() == baseSeconds) { break; } } if (tracker == null) { tracker = new TupleTracker(t, regularQueues); resetTupleTracker.add(tracker); } int trackerIndex = 0; while (trackerIndex < tracker.ports.length) { if (tracker.ports[trackerIndex] == null) { tracker.ports[trackerIndex++] = activePort; break; } else if (tracker.ports[trackerIndex] == activePort) { break; } trackerIndex++; } if (trackerIndex == regularQueues) { Iterator<TupleTracker> trackerIterator = resetTupleTracker.iterator(); while (trackerIterator.hasNext()) { if (trackerIterator.next().tuple.getBaseSeconds() <= baseSeconds) { trackerIterator.remove(); } } if (!delay) { for (int s = sinks.length; s-- > 0;) { sinks[s].put(t); } controlTupleCount++; } if (!activeQueues.isEmpty()) { // make sure they are all queues from DelayOperator for (Map.Entry<String, SweepableReservoir> entry : activeQueues) { if (!isInputPortConnectedToDelayOperator(entry.getKey())) { assert (false); } } activeQueues.clear(); } activeQueues.addAll(inputs.entrySet()); expectingBeginWindow = activeQueues.size(); if (firstWindowId == -1) { if (delay) { for (int s = sinks.length; s-- > 0;) { sinks[s].put(t); } controlTupleCount++; // if it's a DelayOperator and this is the first RESET_WINDOW (start) or END_STREAM // (recovery), fabricate the first window fabricateFirstWindow((Operator.DelayOperator) operator, windowAhead); } firstWindowId = t.getWindowId(); } break activequeue; } break; case END_STREAM: activePort.remove(); buffers.remove(); if (firstWindowId == -1) { // this is for recovery from a checkpoint for DelayOperator if (delay) { // if it's a DelayOperator and this is the first RESET_WINDOW (start) or END_STREAM (recovery), // fabricate the first window fabricateFirstWindow((Operator.DelayOperator) operator, windowAhead); } firstWindowId = t.getWindowId(); } for (Iterator<Entry<String, SweepableReservoir>> it = inputs.entrySet().iterator(); it .hasNext();) { Entry<String, SweepableReservoir> e = it.next(); if (e.getValue() == activePort) { if (!descriptor.inputPorts.isEmpty()) { descriptor.inputPorts.get(e.getKey()).component.setConnected(false); } it.remove(); /* check the deferred connection list for any new port that should be connected here */ Iterator<DeferredInputConnection> dici = deferredInputConnections.iterator(); while (dici.hasNext()) { DeferredInputConnection dic = dici.next(); if (e.getKey().equals(dic.portname)) { connectInputPort(dic.portname, dic.reservoir); dici.remove(); activeQueues.add( new AbstractMap.SimpleEntry<>(dic.portname, dic.reservoir)); break activequeue; } } break; } } /** * We are not going to receive begin window on this ever! */ expectingBeginWindow--; /** * Since one of the operators we care about it gone, we should relook at our ports. * We need to make sure that the END_STREAM comes outside of the window. */ regularQueues--; totalQueues--; boolean break_activequeue = false; if (regularQueues == 0) { alive = false; break_activequeue = true; } else if (activeQueues.isEmpty()) { assert (!inputs.isEmpty()); processEndWindow(null); activeQueues.addAll(inputs.entrySet()); expectingBeginWindow = activeQueues.size(); break_activequeue = true; } /** * also make sure that we update the reset tuple tracker if this stream had delivered any reset tuples. * Check all the reset buffers to see if current input port has already delivered reset tuple. If it has * then we are waiting for something else to deliver the reset tuple, so just clear current reservoir * from the list of tracked reservoirs. If the current input port has not delivered the reset tuple, and * it's the only one which has not, then we consider it delivered and release the reset tuple downstream. */ Tuple tuple = null; for (Iterator<TupleTracker> trackerIterator = resetTupleTracker .iterator(); trackerIterator.hasNext();) { tracker = trackerIterator.next(); trackerIndex = 0; while (trackerIndex < tracker.ports.length) { if (tracker.ports[trackerIndex] == activePort) { SweepableReservoir[] ports = new SweepableReservoir[regularQueues]; System.arraycopy(tracker.ports, 0, ports, 0, trackerIndex); if (trackerIndex < regularQueues) { System.arraycopy(tracker.ports, trackerIndex + 1, ports, trackerIndex, tracker.ports.length - trackerIndex - 1); } tracker.ports = ports; break; } else if (tracker.ports[trackerIndex] == null) { if (trackerIndex == regularQueues) { /* regularQueues is already adjusted above */ if (tuple == null || tuple.getBaseSeconds() < tracker.tuple.getBaseSeconds()) { tuple = tracker.tuple; } trackerIterator.remove(); } break; } else { tracker.ports = Arrays.copyOf(tracker.ports, regularQueues); } trackerIndex++; } } /* * Since we were waiting for a reset tuple on this stream, we should not any longer. */ if (tuple != null && !delay) { for (int s = sinks.length; s-- > 0;) { sinks[s].put(tuple); } controlTupleCount++; } if (break_activequeue) { break activequeue; } break; default: throw new UnhandledException("Unrecognized Control Tuple", new IllegalArgumentException(t.toString())); } } } if (activeQueues.isEmpty() && alive) { logger.error("Catastrophic Error: Invalid State - the operator blocked forever!"); System.exit(2); } else { boolean need2sleep = true; for (Map.Entry<String, SweepableReservoir> cb : activeQueues) { need2sleep = cb.getValue().isEmpty(); if (!need2sleep) { spinMillis = 0; break; } } if (need2sleep) { if (handleIdleTime && insideWindow) { ((IdleTimeHandler) operator).handleIdleTime(); } else { Thread.sleep(spinMillis); spinMillis = Math.min(maxSpinMillis, spinMillis + 1); } } } } while (alive); } catch (ShutdownException se) { logger.debug("Shutdown requested by the operator when alive = {}.", alive); alive = false; } catch (Throwable cause) { synchronized (this) { if (alive) { DTThrowable.rethrow(cause); } } Throwable rootCause = cause; while (rootCause != null) { if (rootCause instanceof InterruptedException) { break; } rootCause = rootCause.getCause(); } if (rootCause == null) { DTThrowable.rethrow(cause); } else { logger.debug("Ignoring InterruptedException after shutdown", cause); } } /** * TODO: If shutdown and inside window provide alternate way of notifying the operator in such ways * TODO: as using a listener callback */ if (insideWindow && !shutdown) { operator.endWindow(); endWindowEmitTime = System.currentTimeMillis(); if (++applicationWindowCount == APPLICATION_WINDOW_COUNT) { applicationWindowCount = 0; } if (++checkpointWindowCount == CHECKPOINT_WINDOW_COUNT) { checkpointWindowCount = 0; if (doCheckpoint || PROCESSING_MODE == ProcessingMode.EXACTLY_ONCE) { checkpoint(currentWindowId); } } ContainerStats.OperatorStats stats = new ContainerStats.OperatorStats(); fixEndWindowDequeueTimesBeforeDeactivate(); reportStats(stats, currentWindowId); stats.metrics = collectMetrics(); handleRequests(currentWindowId); } }
From source file:edu.mit.mobile.android.locast.sync.SyncEngine.java
/** * @param toSync// w ww . j a va2 s . c om * @param account * @param extras * @param provider * @param syncResult * @return true if the item was sync'd successfully. Soft errors will cause this to return * false. * @throws RemoteException * @throws SyncException * @throws JSONException * @throws IOException * @throws NetworkProtocolException * @throws NoPublicPath * @throws OperationApplicationException * @throws InterruptedException */ public boolean sync(Uri toSync, Account account, Bundle extras, ContentProviderClient provider, SyncResult syncResult) throws RemoteException, SyncException, JSONException, IOException, NetworkProtocolException, NoPublicPath, OperationApplicationException, InterruptedException { String pubPath = null; // // Handle http or https uris separately. These require the // destination uri. // if ("http".equals(toSync.getScheme()) || "https".equals(toSync.getScheme())) { pubPath = toSync.toString(); if (!extras.containsKey(EXTRA_DESTINATION_URI)) { throw new IllegalArgumentException("missing EXTRA_DESTINATION_URI when syncing HTTP URIs"); } toSync = Uri.parse(extras.getString(EXTRA_DESTINATION_URI)); } final String type = provider.getType(toSync); final boolean isDir = type.startsWith(CONTENT_TYPE_PREFIX_DIR); final boolean manualSync = extras.getBoolean(ContentResolver.SYNC_EXTRAS_MANUAL, false); // skip any items already sync'd if (!manualSync && mLastUpdated.isUpdatedRecently(toSync)) { if (DEBUG) { Log.d(TAG, "not syncing " + toSync + " as it's been updated recently"); } syncResult.stats.numSkippedEntries++; return false; } // the sync map will convert the json data to ContentValues final SyncMap syncMap = MediaProvider.getSyncMap(provider, toSync); final Uri toSyncWithoutQuerystring = toSync.buildUpon().query(null).build(); final HashMap<String, SyncStatus> syncStatuses = new HashMap<String, SyncEngine.SyncStatus>(); final ArrayList<ContentProviderOperation> cpo = new ArrayList<ContentProviderOperation>(); final LinkedList<String> cpoPubUris = new LinkedList<String>(); // // first things first, upload any content that needs to be // uploaded. // try { uploadUnpublished(toSync, account, provider, syncMap, syncStatuses, syncResult); if (Thread.interrupted()) { throw new InterruptedException(); } // this should ensure that all items have a pubPath when we // query it below. if (pubPath == null) { // we should avoid calling this too much as it // can be expensive pubPath = MediaProvider.getPublicPath(mContext, toSync); } } catch (final NoPublicPath e) { // TODO this is a special case and this is probably not the best place to handle this. // Ideally, this should be done in such a way as to reduce any extra DB queries - // perhaps by doing a join with the parent. if (syncMap.isFlagSet(SyncMap.FLAG_PARENT_MUST_SYNC_FIRST)) { if (DEBUG) { Log.d(TAG, "skipping " + toSync + " whose parent hasn't been sync'd first"); } syncResult.stats.numSkippedEntries++; return false; } // if it's an item, we can handle it. if (isDir) { throw e; } } if (pubPath == null) { // this should have been updated already by the initial // upload, so something must be wrong throw new SyncException("never got a public path for " + toSync); } if (DEBUG) { Log.d(TAG, "sync(toSync=" + toSync + ", account=" + account + ", extras=" + extras + ", manualSync=" + manualSync + ",...)"); Log.d(TAG, "pubPath: " + pubPath); } final long request_time = System.currentTimeMillis(); HttpResponse hr = mNetworkClient.get(pubPath); final long response_time = System.currentTimeMillis(); // the time compensation below allows a time-based synchronization to function even if the // local clock is entirely wrong. The server's time is extracted using the Date header and // all are compared relative to the respective clock reference. Any data that's stored on // the mobile should be stored relative to the local clock and the server will respect the // same. long serverTime; try { serverTime = getServerTime(hr); } catch (final DateParseException e) { Log.w(TAG, "could not retrieve date from server. Using local time, which may be incorrect.", e); serverTime = System.currentTimeMillis(); } // TODO check out // http://www.w3.org/Protocols/rfc2616/rfc2616-sec13.html final long response_delay = response_time - request_time; if (DEBUG) { Log.d(TAG, "request took " + response_delay + "ms"); } final long localTime = request_time; // add this to the server time to get the local time final long localOffset = (localTime - serverTime); if (Math.abs(localOffset) > 30 * 60 * 1000) { Log.w(TAG, "local clock is off by " + localOffset + "ms"); } if (Thread.interrupted()) { throw new InterruptedException(); } final HttpEntity ent = hr.getEntity(); String selection; String selectionInverse; String[] selectionArgs; if (isDir) { final JSONArray ja = new JSONArray(StreamUtils.inputStreamToString(ent.getContent())); ent.consumeContent(); final int len = ja.length(); selectionArgs = new String[len]; // build the query to see which items are already in the // database final StringBuilder sb = new StringBuilder(); sb.append("("); for (int i = 0; i < len; i++) { if (Thread.interrupted()) { throw new InterruptedException(); } final SyncStatus syncStatus = loadItemFromJsonObject(ja.getJSONObject(i), syncMap, serverTime); syncStatuses.put(syncStatus.remote, syncStatus); selectionArgs[i] = syncStatus.remote; // add in a placeholder for the query sb.append('?'); if (i != (len - 1)) { sb.append(','); } } sb.append(")"); final String placeholders = sb.toString(); selection = JsonSyncableItem._PUBLIC_URI + " IN " + placeholders; selectionInverse = JsonSyncableItem._PUBLIC_URI + " NOT IN " + placeholders; } else { final JSONObject jo = new JSONObject(StreamUtils.inputStreamToString(ent.getContent())); ent.consumeContent(); final SyncStatus syncStatus = loadItemFromJsonObject(jo, syncMap, serverTime); syncStatuses.put(syncStatus.remote, syncStatus); selection = JsonSyncableItem._PUBLIC_URI + "=?"; selectionInverse = JsonSyncableItem._PUBLIC_URI + "!=?"; selectionArgs = new String[] { syncStatus.remote }; } // first check without the querystring. This will ensure that we // properly mark things that we already have in the database. final Cursor check = provider.query(toSyncWithoutQuerystring, SYNC_PROJECTION, selection, selectionArgs, null); // these items are on both sides try { final int pubUriCol = check.getColumnIndex(JsonSyncableItem._PUBLIC_URI); final int idCol = check.getColumnIndex(JsonSyncableItem._ID); // All the items in this cursor should be found on both // the client and the server. for (check.moveToFirst(); !check.isAfterLast(); check.moveToNext()) { if (Thread.interrupted()) { throw new InterruptedException(); } final long id = check.getLong(idCol); final Uri localUri = ContentUris.withAppendedId(toSync, id); final String pubUri = check.getString(pubUriCol); final SyncStatus itemStatus = syncStatuses.get(pubUri); itemStatus.state = SyncState.BOTH_UNKNOWN; itemStatus.local = localUri; // make the status searchable by both remote and // local uri syncStatuses.put(localUri.toString(), itemStatus); } } finally { check.close(); } Cursor c = provider.query(toSync, SYNC_PROJECTION, selection, selectionArgs, null); // these items are on both sides try { final int pubUriCol = c.getColumnIndex(JsonSyncableItem._PUBLIC_URI); final int localModifiedCol = c.getColumnIndex(JsonSyncableItem._MODIFIED_DATE); final int serverModifiedCol = c.getColumnIndex(JsonSyncableItem._SERVER_MODIFIED_DATE); final int idCol = c.getColumnIndex(JsonSyncableItem._ID); // All the items in this cursor should be found on both // the client and the server. for (c.moveToFirst(); !c.isAfterLast(); c.moveToNext()) { if (Thread.interrupted()) { throw new InterruptedException(); } final long id = c.getLong(idCol); final Uri localUri = ContentUris.withAppendedId(toSync, id); final String pubUri = c.getString(pubUriCol); final SyncStatus itemStatus = syncStatuses.get(pubUri); if (itemStatus.state == SyncState.ALREADY_UP_TO_DATE || itemStatus.state == SyncState.NOW_UP_TO_DATE) { if (DEBUG) { Log.d(TAG, localUri + "(" + pubUri + ")" + " is already up to date."); } continue; } itemStatus.local = localUri; // make the status searchable by both remote and local uri syncStatuses.put(localUri.toString(), itemStatus); // last modified as stored in the DB, in phone time final long itemLocalModified = c.getLong(localModifiedCol); // last modified as stored in the DB, in server time final long itemServerModified = c.getLong(serverModifiedCol); final long localAge = localTime - itemLocalModified; final long remoteAge = serverTime - itemStatus.remoteModifiedTime; final long ageDifference = Math.abs(localAge - remoteAge); // up to date, as far remote -> local goes if (itemServerModified == itemStatus.remoteModifiedTime) { itemStatus.state = SyncState.ALREADY_UP_TO_DATE; if (DEBUG) { Log.d(TAG, pubUri + " is up to date."); } // need to download } else if (localAge > remoteAge) { if (DEBUG) { final long serverModified = itemStatus.remoteModifiedTime; Log.d(TAG, pubUri + " : local is " + ageDifference + "ms older (" + android.text.format.DateUtils.formatDateTime(mContext, itemLocalModified, FORMAT_ARGS_DEBUG) + ") than remote (" + android.text.format.DateUtils.formatDateTime(mContext, serverModified, FORMAT_ARGS_DEBUG) + "); updating local copy..."); } itemStatus.state = SyncState.REMOTE_DIRTY; final ContentProviderOperation.Builder b = ContentProviderOperation.newUpdate(localUri); // update this so it's in the local timescale correctServerOffset(itemStatus.remoteCVs, JsonSyncableItem._CREATED_DATE, JsonSyncableItem._CREATED_DATE, localOffset); correctServerOffset(itemStatus.remoteCVs, JsonSyncableItem._SERVER_MODIFIED_DATE, JsonSyncableItem._MODIFIED_DATE, localOffset); b.withValues(itemStatus.remoteCVs); b.withExpectedCount(1); cpo.add(b.build()); cpoPubUris.add(pubUri); syncResult.stats.numUpdates++; // need to upload } else if (localAge < remoteAge) { if (DEBUG) { final long serverModified = itemStatus.remoteModifiedTime; Log.d(TAG, pubUri + " : local is " + ageDifference + "ms newer (" + android.text.format.DateUtils.formatDateTime(mContext, itemLocalModified, FORMAT_ARGS_DEBUG) + ") than remote (" + android.text.format.DateUtils.formatDateTime(mContext, serverModified, FORMAT_ARGS_DEBUG) + "); publishing to server..."); } itemStatus.state = SyncState.LOCAL_DIRTY; mNetworkClient.putJson(pubPath, JsonSyncableItem.toJSON(mContext, localUri, c, syncMap)); } mLastUpdated.markUpdated(localUri); syncResult.stats.numEntries++; } // end for } finally { c.close(); } /* * Apply updates in bulk */ if (cpo.size() > 0) { if (DEBUG) { Log.d(TAG, "applying " + cpo.size() + " bulk updates..."); } final ContentProviderResult[] r = provider.applyBatch(cpo); if (DEBUG) { Log.d(TAG, "Done applying updates. Running postSync handler..."); } for (int i = 0; i < r.length; i++) { final ContentProviderResult res = r[i]; final SyncStatus ss = syncStatuses.get(cpoPubUris.get(i)); if (ss == null) { Log.e(TAG, "can't get sync status for " + res.uri); continue; } syncMap.onPostSyncItem(mContext, account, ss.local, ss.remoteJson, res.count != null ? res.count == 1 : true); ss.state = SyncState.NOW_UP_TO_DATE; } if (DEBUG) { Log.d(TAG, "done running postSync handler."); } cpo.clear(); cpoPubUris.clear(); } if (Thread.interrupted()) { throw new InterruptedException(); } /* * Look through the SyncState.state values and find ones that need to be stored. */ for (final Map.Entry<String, SyncStatus> entry : syncStatuses.entrySet()) { if (Thread.interrupted()) { throw new InterruptedException(); } final String pubUri = entry.getKey(); final SyncStatus status = entry.getValue(); if (status.state == SyncState.REMOTE_ONLY) { if (DEBUG) { Log.d(TAG, pubUri + " is not yet stored locally, adding..."); } // update this so it's in the local timescale correctServerOffset(status.remoteCVs, JsonSyncableItem._CREATED_DATE, JsonSyncableItem._CREATED_DATE, localOffset); correctServerOffset(status.remoteCVs, JsonSyncableItem._SERVER_MODIFIED_DATE, JsonSyncableItem._MODIFIED_DATE, localOffset); final ContentProviderOperation.Builder b = ContentProviderOperation.newInsert(toSync); b.withValues(status.remoteCVs); cpo.add(b.build()); cpoPubUris.add(pubUri); syncResult.stats.numInserts++; } } /* * Execute the content provider operations in bulk. */ if (cpo.size() > 0) { if (DEBUG) { Log.d(TAG, "bulk inserting " + cpo.size() + " items..."); } final ContentProviderResult[] r = provider.applyBatch(cpo); if (DEBUG) { Log.d(TAG, "applyBatch completed. Processing results..."); } int successful = 0; for (int i = 0; i < r.length; i++) { final ContentProviderResult res = r[i]; if (res.uri == null) { syncResult.stats.numSkippedEntries++; Log.e(TAG, "result from content provider bulk operation returned null"); continue; } final String pubUri = cpoPubUris.get(i); final SyncStatus ss = syncStatuses.get(pubUri); if (ss == null) { syncResult.stats.numSkippedEntries++; Log.e(TAG, "could not find sync status for " + cpoPubUris.get(i)); continue; } ss.local = res.uri; if (DEBUG) { Log.d(TAG, "onPostSyncItem(" + res.uri + ", ...); pubUri: " + pubUri); } syncMap.onPostSyncItem(mContext, account, res.uri, ss.remoteJson, res.count != null ? res.count == 1 : true); ss.state = SyncState.NOW_UP_TO_DATE; successful++; } if (DEBUG) { Log.d(TAG, successful + " batch inserts successfully applied."); } } else { if (DEBUG) { Log.d(TAG, "no updates to perform."); } } /** * Look through all the items that we didn't already find on the server side, but which * still have a public uri. They should be checked to make sure they're not deleted. */ c = provider.query(toSync, SYNC_PROJECTION, ProviderUtils.addExtraWhere(selectionInverse, JsonSyncableItem._PUBLIC_URI + " NOT NULL"), selectionArgs, null); try { final int idCol = c.getColumnIndex(JsonSyncableItem._ID); final int pubUriCol = c.getColumnIndex(JsonSyncableItem._PUBLIC_URI); cpo.clear(); for (c.moveToFirst(); !c.isAfterLast(); c.moveToNext()) { final String pubUri = c.getString(pubUriCol); SyncStatus ss = syncStatuses.get(pubUri); final Uri item = isDir ? ContentUris.withAppendedId(toSyncWithoutQuerystring, c.getLong(idCol)) : toSync; if (ss == null) { ss = syncStatuses.get(item.toString()); } if (DEBUG) { Log.d(TAG, item + " was not found in the main list of items on the server (" + pubPath + "), but appears to be a child of " + toSync); if (ss != null) { Log.d(TAG, "found sync status for " + item + ": " + ss); } } if (ss != null) { switch (ss.state) { case ALREADY_UP_TO_DATE: case NOW_UP_TO_DATE: if (DEBUG) { Log.d(TAG, item + " is already up to date. No need to see if it was deleted."); } continue; case BOTH_UNKNOWN: if (DEBUG) { Log.d(TAG, item + " was found on both sides, but has an unknown sync status. Skipping..."); } continue; default: Log.w(TAG, "got an unexpected state for " + item + ": " + ss); } } else { ss = new SyncStatus(pubUri, SyncState.LOCAL_ONLY); ss.local = item; hr = mNetworkClient.head(pubUri); switch (hr.getStatusLine().getStatusCode()) { case 200: if (DEBUG) { Log.d(TAG, "HEAD " + pubUri + " returned 200"); } ss.state = SyncState.BOTH_UNKNOWN; break; case 404: if (DEBUG) { Log.d(TAG, "HEAD " + pubUri + " returned 404. Deleting locally..."); } ss.state = SyncState.DELETED_REMOTELY; final ContentProviderOperation deleteOp = ContentProviderOperation .newDelete(ContentUris.withAppendedId(toSyncWithoutQuerystring, c.getLong(idCol))) .build(); cpo.add(deleteOp); break; default: syncResult.stats.numIoExceptions++; Log.w(TAG, "HEAD " + pubUri + " got unhandled result: " + hr.getStatusLine()); } } syncStatuses.put(pubUri, ss); } // for cursor if (cpo.size() > 0) { final ContentProviderResult[] results = provider.applyBatch(cpo); for (final ContentProviderResult result : results) { if (result.count != 1) { throw new SyncException("Error deleting item"); } } } } finally { c.close(); } syncStatuses.clear(); mLastUpdated.markUpdated(toSync); return true; }
From source file:base.BasePlayer.FileRead.java
public void changeChrom(String chrom) { try {//from www.j av a 2s . c o m nobeds = false; cancelfileread = false; if (!search) { FileRead.novars = false; } try { Main.drawCanvas.loading("Loading annotation..."); Main.drawCanvas.splits.get(0).setGenes(getExons(chrom)); Main.chromDraw.updateExons = true; Main.chromDraw.repaint(); } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } Main.drawCanvas.ready("Loading annotation..."); ArrayList<BedTrack> bigs = new ArrayList<BedTrack>(); if (Main.bedCanvas.bedTrack.size() > 0) { Main.drawCanvas.loading("Loading BED-files..."); Main.bedCanvas.bedOn = true; boolean ison = false; for (int i = 0; i < Main.bedCanvas.bedTrack.size(); i++) { if (Main.bedCanvas.bedTrack.get(i).intersect) { ison = true; break; } } if (!ison) { Main.bedCanvas.bedOn = false; } //if(search) { for (int i = 0; i < Main.bedCanvas.bedTrack.size(); i++) { Main.bedCanvas.bedTrack.get(i).used = false; if (Main.bedCanvas.bedTrack.get(i).small && Main.bedCanvas.bedTrack.get(i).getBBfileReader() == null) { Main.bedCanvas.getBEDfeatures(Main.bedCanvas.bedTrack.get(i), 1, Main.drawCanvas.splits.get(0).chromEnd); } else { if (search && searchEnd - searchStart < Settings.windowSize) { Main.bedCanvas.getBEDfeatures(Main.bedCanvas.bedTrack.get(i), searchStart, searchEnd); } else { if (Main.bedCanvas.bedTrack.get(i).small) { Main.bedCanvas.getBEDfeatures(Main.bedCanvas.bedTrack.get(i), 1, Main.drawCanvas.splits.get(0).chromEnd); } } } if (Main.bedCanvas.bedTrack.get(i).intersect && (!Main.bedCanvas.bedTrack.get(i).small || Main.bedCanvas.bedTrack.get(i).getBBfileReader() != null)) { Main.bedCanvas.bedTrack.get(i).intersect = false; bigs.add(Main.bedCanvas.bedTrack.get(i)); } if (nobeds) { Main.drawCanvas.ready("Loading BED-files..."); return; } } } /* } else { for(int i = 0; i< Main.bedCanvas.bedTrack.size(); i++) { Main.bedCanvas.bedTrack.get(i).used = false; if(Main.bedCanvas.bedTrack.get(i).small && Main.bedCanvas.bedTrack.get(i).getBBfileReader() == null) { Main.bedCanvas.getBEDfeatures(Main.bedCanvas.bedTrack.get(i), 1, Main.drawCanvas.splits.get(0).chromEnd); } else { Main.bedCanvas.getBEDfeatures(Main.bedCanvas.bedTrack.get(i), 1, Main.drawCanvas.splits.get(0).chromEnd); } if(Main.bedCanvas.bedTrack.get(i).intersect && (!Main.bedCanvas.bedTrack.get(i).small || Main.bedCanvas.bedTrack.get(i).getBBfileReader() != null)) { Main.bedCanvas.bedTrack.get(i).intersect = false; bigs.add(Main.bedCanvas.bedTrack.get(i)); } if(nobeds) { Main.drawCanvas.ready("Loading BED-files..."); return; } } } */ //} Main.drawCanvas.ready("Loading BED-files..."); if (novars) { Main.drawCanvas.variantsStart = 0; Main.drawCanvas.variantsEnd = 0; } else { changing = true; } if (Main.varsamples > 0 && !novars && !bigcalc) { removeNonListVariants(); removeBedLinks(); Main.drawCanvas.loading("Loading variants..."); head.putNext(null); current = FileRead.head; if (FileRead.head.getPosition() > 0) { FileRead.head = new VarNode(0, (byte) 0, "N", 0, 0, false, (float) 0, (float) 0, null, null, null, null, null); } Main.drawCanvas.current = head; Main.chromDraw.varnode = null; Main.chromDraw.vardraw = null; for (int i = 0; i < Main.samples; i++) { if (nobeds) { return; } if (cancelfileread || !Main.drawCanvas.loading) { cancelFileRead(); break; } if (Main.drawCanvas.sampleList.get(i).getTabixFile() == null || Main.drawCanvas.sampleList.get(i).multipart) { continue; } if (search) { getVariants(chrom, FileRead.searchStart, FileRead.searchEnd, Main.drawCanvas.sampleList.get(i)); } else { getVariants(chrom, 0, Main.drawCanvas.splits.get(0).chromEnd, Main.drawCanvas.sampleList.get(i)); } } annotate(); if (Main.drawCanvas.annotationOn) { SampleDialog.checkAnnotation(); } Main.drawCanvas.loading("Applying controls..."); if (Control.controlData.controlsOn) { Control.applyControl(); } Main.drawCanvas.ready("Applying controls..."); readFiles = false; Main.bedCanvas.intersected = false; if (bigcalc) { Main.drawCanvas.calcClusters(FileRead.head); } else { Main.drawCanvas.calcClusters(FileRead.head); } if (Main.bedCanvas.bedOn) { Main.drawCanvas.loadingtext = "Annotating variants"; int smalls = 0; for (int i = 0; i < Main.bedCanvas.bedTrack.size(); i++) { if (Main.bedCanvas.bedTrack.get(i).small && Main.bedCanvas.bedTrack.get(i).getBBfileReader() == null) { if (Main.bedCanvas.bedTrack.get(i).intersect && !Main.bedCanvas.bedTrack.get(i).loading) { smalls++; Main.bedCanvas.annotate(Main.bedCanvas.bedTrack.get(i).getHead(), FileRead.head.getNext()); Main.bedCanvas.intersected = true; } else if (Main.bedCanvas.bedTrack.get(i).intersect && Main.bedCanvas.bedTrack.get(i).loading) { Main.bedCanvas.bedTrack.get(i).waiting = true; } } //else if(Main.bedCanvas.bedTrack.get(i).intersect) { //bigs.add(Main.bedCanvas.bedTrack.get(i)); /*BedCanvas.Annotator annotator = Main.bedCanvas.new Annotator(Main.bedCanvas.bedTrack.get(i)); annotator.annotateVars(); Main.bedCanvas.intersected = true; */ //} } if (smalls == 0) { VarNode current = FileRead.head.getNext(); while (current != null) { current.bedhit = true; current = current.getNext(); } } for (int i = 0; i < bigs.size(); i++) { bigs.get(i).intersect = true; BedCanvas.Annotator annotator = Main.bedCanvas.new Annotator(bigs.get(i)); annotator.annotateVars(); Main.bedCanvas.intersected = true; } bigs.clear(); } if (FileRead.bigcalc) { Main.drawCanvas.calcClusters(FileRead.head); } else { Main.drawCanvas.calcClusters(FileRead.head); } } Draw.updatevars = true; Main.drawCanvas.ready("Loading variants..."); if (!Main.drawCanvas.loading) { Draw.calculateVars = true; } if (novars) { Main.drawCanvas.variantsStart = 0; Main.drawCanvas.variantsEnd = Main.drawCanvas.splits.get(0).chromEnd; } search = false; changing = false; current = null; Main.chromDraw.updateExons = true; Main.chromDraw.repaint(); } catch (Exception e) { e.printStackTrace(); ErrorLog.addError(e.getStackTrace()); changing = false; } Main.drawCanvas.loadbarAll = 0; Main.drawCanvas.loadBarSample = 0; Main.drawCanvas.repaint(); }
From source file:base.BasePlayer.FileRead.java
java.util.ArrayList<java.util.Map.Entry<Integer, Byte>> getMismatches(SAMRecord samRecord, Reads readClass,
double[][] coverageArray, SplitClass split) {
if (readClass == null) {
sample.resetreadHash();/*from www .j a v a 2s. co m*/
}
java.util.ArrayList<java.util.Map.Entry<Integer, Byte>> mismatches = null;
String MD = samRecord.getStringAttribute("MD");
String SA = samRecord.getStringAttribute("SA");
if (samRecord.getReadBases().length == 0) {
return null;
}
try {
if (MD == null) {
if (readClass.sample.MD) {
readClass.sample.MD = false;
}
}
if ((readClass.sample.MD || MD != null) && (samRecord.getCigarString().contains("S")
&& Settings.softClips == 0)/* && ((!samRecord.getCigarString().contains("S") && SA == null) || SA !=null)*/) {
if (!readClass.sample.MD) {
readClass.sample.MD = true;
}
java.util.ArrayList<java.util.Map.Entry<Integer, Integer>> insertions = null;
int softstart = 0;
if (samRecord.getCigarLength() > 1) {
readstart = samRecord.getUnclippedStart();
if (readClass.getCoverageStart() > readstart) {
return null;
}
readpos = 0;
for (int i = 0; i < samRecord.getCigarLength(); i++) {
element = samRecord.getCigar().getCigarElement(i);
if (element.getOperator().compareTo(CigarOperator.MATCH_OR_MISMATCH) == 0) {
for (int r = readpos; r < readpos + element.getLength(); r++) {
try {
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]++;
} catch (Exception e) {
//TODO
}
try {
if (coverageArray[((readstart + r)
- readClass.getCoverageStart())][0] > readClass.getMaxcoverage()) {
readClass.setMaxcoverage(
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]);
}
} catch (Exception e) {
//TODO
}
mispos++;
}
readpos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.DELETION) == 0) {
for (int d = 0; d < element.getLength(); d++) {
readClass.getCoverages()[(readstart + readpos + d)
- readClass.getCoverageStart()][Main.baseMap.get((byte) 'D')]++;
}
readpos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.INSERTION) == 0) {
if (insertions == null) {
insertions = new java.util.ArrayList<java.util.Map.Entry<Integer, Integer>>();
}
java.util.Map.Entry<Integer, Integer> ins = new java.util.AbstractMap.SimpleEntry<>(
readpos, element.getLength());
insertions.add(ins);
readClass.getCoverages()[(readstart + readpos)
- readClass.getCoverageStart()][Main.baseMap.get((byte) 'I')]++;
mispos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.SOFT_CLIP) == 0) {
if (i == 0 && SA == null) {
softstart = element.getLength();
}
if (Settings.softClips == 1) {
for (int r = readpos; r < readpos + element.getLength(); r++) {
if (SA == null) {
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]++;
}
mispos++;
}
readpos += element.getLength();
} else {
if (i == 0) {
readstart = samRecord.getAlignmentStart();
mispos += element.getLength();
}
}
} else if (element.getOperator().compareTo(CigarOperator.HARD_CLIP) == 0) {
if (i == 0) {
readstart = samRecord.getAlignmentStart();
}
} else if (element.getOperator().compareTo(CigarOperator.SKIPPED_REGION) == 0) {
readpos += element.getLength();
}
}
} else {
readstart = samRecord.getUnclippedStart();
for (int i = 0; i < samRecord.getReadLength(); i++) {
try {
if (readClass.getCoverageStart() > readstart) {
break;
}
coverageArray[(readstart + i) - readClass.getCoverageStart()][0]++;
if (coverageArray[(samRecord.getUnclippedStart() - readClass.getCoverageStart())
+ i][0] > readClass.getMaxcoverage()) {
readClass.setMaxcoverage(
coverageArray[(samRecord.getUnclippedStart() - readClass.getCoverageStart())
+ i][0]);
}
} catch (Exception e) {
ErrorLog.addError(e.getStackTrace());
e.printStackTrace();
FileRead.cancelreadread = true;
break;
}
}
}
if (MD != null) {
try {
Integer.parseInt(MD);
return null;
} catch (Exception ex) {
readstart = samRecord.getAlignmentStart() - softstart;
char[] chars = MD.toCharArray();
String bases = samRecord.getReadString();
String qualities = samRecord.getBaseQualityString();
if (SA == null) {
softstart = 0;
}
int readpos = softstart;
int mispos = softstart;
int add = 0;
int digitpointer = 0, insertionpointer = 0;
boolean first = true;
for (int i = 0; i < chars.length; i++) {
try {
if (insertions != null) {
if (insertionpointer < insertions.size()
&& insertions.get(insertionpointer).getKey() <= readpos) {
while (insertionpointer < insertions.size()
&& insertions.get(insertionpointer).getKey() <= readpos) {
mispos += insertions.get(insertionpointer).getValue();
insertionpointer++;
}
}
}
if (Character.isDigit(chars[i])) {
digitpointer = i + 1;
while (digitpointer < chars.length && Character.isDigit(chars[digitpointer])) {
digitpointer++;
}
if (digitpointer == chars.length) {
if ((mispos + Integer.parseInt(MD.substring(i, digitpointer))) > samRecord
.getReadLength()) {
if (!first) {
break;
}
first = false;
readpos = 0;
mispos = 0;
i = -1;
digitpointer = 0;
insertionpointer = 0;
mismatches.clear();
continue;
}
break;
} else {
add = Integer.parseInt(MD.substring(i, digitpointer));
readpos += add;
mispos += add;
}
i = digitpointer - 1;
} else if (chars[i] != '^') {
if (mismatches == null) {
mismatches = new java.util.ArrayList<java.util.Map.Entry<Integer, Byte>>();
}
readClass.getCoverages()[(readstart + readpos)
- readClass.getCoverageStart()][Main.baseMap
.get((byte) bases.charAt(mispos))]++;
if (samRecord.getBaseQualityString().length() != 1
&& (int) qualities.charAt(mispos)
- readClass.sample.phred < Settings.baseQ) {
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
readpos, (byte) Character.toLowerCase(bases.charAt(mispos)));
mismatches.add(mismatch);
} else {
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
readpos, (byte) bases.charAt(mispos));
mismatches.add(mismatch);
}
mispos++;
readpos++;
} else {
digitpointer = i + 1;
while (!Character.isDigit(chars[digitpointer])) {
digitpointer++;
readpos++;
}
i = digitpointer - 1;
}
} catch (Exception exc) {
if (!first) {
break;
}
first = false;
readpos = 0;
mispos = 0;
i = -1;
digitpointer = 0;
insertionpointer = 0;
mismatches.clear();
}
}
}
}
} else {
/*if(split.getReference() == null) {
readClass.setReference(new ReferenceSeq(splitIndex.chrom,start-500, end+500, Main.referenceFile));
}*/
//timecounter = 0;
/*while(splitIndex.getReadReference() == null) {
Thread.sleep(100);
timecounter++;
if(timecounter > 20) {
break;
}
}
Thread.sleep(0);
*/
// if(splitIndex.getReadReference() == null) {
//splitIndex.setReference(new ReferenceSeq(splitIndex.chrom,startpos-searchwindow-1, endpos+searchwindow +200, Main.referenceFile));
// return null;
//}
if (samRecord.getCigarLength() > 1) {
readstart = samRecord.getUnclippedStart();
readpos = 0;
mispos = 0;
/*if(readClass.getCoverageStart()>readstart) {
return null;
}*/
if (mismatches == null) {
mismatches = new java.util.ArrayList<java.util.Map.Entry<Integer, Byte>>();
}
for (int i = 0; i < samRecord.getCigarLength(); i++) {
element = samRecord.getCigar().getCigarElement(i);
if (element.getOperator().compareTo(CigarOperator.MATCH_OR_MISMATCH) == 0) {
for (int r = readpos; r < readpos + element.getLength(); r++) {
if (((readstart + r) - split.getReadReference().getStartPos()
- 1) > split.getReadReference().getSeq().length - 1) {
split.getReadReference().append(samRecord.getUnclippedEnd() + 1000);
}
if (((readstart + r) - split.getReadReference().getStartPos() - 1) < 0) {
split.getReadReference().appendToStart(samRecord.getUnclippedStart() - 1000);
}
try {
if (samRecord.getReadBases()[mispos] != split.getReadReference()
.getSeq()[((readstart + r) - split.getReadReference().getStartPos()
- 1)]) {
readClass.getCoverages()[(readstart + r)
- readClass.getCoverageStart()][Main.baseMap
.get((byte) samRecord.getReadBases()[mispos])]++;
if (samRecord.getBaseQualityString().length() != 1
&& (int) samRecord.getBaseQualityString().charAt(mispos)
- readClass.sample.phred < Settings.baseQ) {
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
r, (byte) Character
.toLowerCase((char) samRecord.getReadBases()[mispos]));
mismatches.add(mismatch);
} else {
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
r, samRecord.getReadBases()[mispos]);
mismatches.add(mismatch);
}
}
} catch (Exception e) {
System.out.println(samRecord.getReadBases().length);
e.printStackTrace();
}
try {
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]++;
if (coverageArray[((readstart + r)
- readClass.getCoverageStart())][0] > readClass.getMaxcoverage()) {
readClass.setMaxcoverage(
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]);
}
} catch (Exception e) {
//TODO
}
mispos++;
}
readpos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.DELETION) == 0) {
// readWidth+=element.getLength();
for (int d = 0; d < element.getLength(); d++) {
readClass.getCoverages()[(readstart + readpos + d)
- readClass.getCoverageStart()][Main.baseMap.get((byte) 'D')]++;
}
readpos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.INSERTION) == 0) {
readClass.getCoverages()[(readstart + readpos)
- readClass.getCoverageStart()][Main.baseMap.get((byte) 'I')]++;
mispos += element.getLength();
} else if (element.getOperator().compareTo(CigarOperator.SOFT_CLIP) == 0) {
if (Settings.softClips == 1) {
for (int r = readpos; r < readpos + element.getLength(); r++) {
if (((readstart + r) - split.getReadReference().getStartPos()
- 1) > split.getReadReference().getSeq().length - 1) {
split.getReadReference().append(samRecord.getUnclippedEnd() + 1000);
}
if (((readstart + r) - splitIndex.getReadReference().getStartPos() - 1) < 0) {
split.getReadReference()
.appendToStart(samRecord.getUnclippedStart() - 1000);
}
/* if(((readstart+r)-readClass.reference.getStartPos()-1) < 0) {
continue;
}*/
if (samRecord.getReadBases()[mispos] != split.getReadReference()
.getSeq()[((readstart + r) - split.getReadReference().getStartPos()
- 1)]) {
if (SA == null) {
readClass.getCoverages()[(readstart + r)
- readClass.getCoverageStart()][Main.baseMap
.get(samRecord.getReadBases()[mispos])]++;
}
if (mismatches == null) {
mismatches = new java.util.ArrayList<java.util.Map.Entry<Integer, Byte>>();
}
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
r, samRecord.getReadBases()[mispos]);
mismatches.add(mismatch);
}
if (SA == null) {
coverageArray[((readstart + r) - readClass.getCoverageStart())][0]++;
}
mispos++;
}
readpos += element.getLength();
} else {
if (i == 0) {
readpos += element.getLength();
mispos += element.getLength();
}
}
} else if (element.getOperator().compareTo(CigarOperator.HARD_CLIP) == 0) {
if (i == 0) {
readstart = samRecord.getAlignmentStart();
}
} else if (element.getOperator().compareTo(CigarOperator.SKIPPED_REGION) == 0) {
readpos += element.getLength();
// this.readWidth+=element.getLength();
}
}
} else {
readstart = samRecord.getUnclippedStart();
/*if(readClass.getCoverageStart()>readstart) {
return null;
}*/
if ((samRecord.getUnclippedEnd() - split.getReadReference().getStartPos()
- 1) > split.getReadReference().getSeq().length - 1) {
split.getReadReference().append(samRecord.getUnclippedEnd() + 100);
}
if ((samRecord.getUnclippedStart() - split.getReadReference().getStartPos() - 1) < 0) {
split.getReadReference().appendToStart(samRecord.getUnclippedStart() - 100);
}
for (int r = 0; r < samRecord.getReadLength(); r++) {
try {
if (samRecord.getReadBases()[r] != split.getReadReference()
.getSeq()[((readstart + r) - split.getReadReference().getStartPos() - 1)]) {
if ((readstart + r) - readClass.getCoverageStart() < readClass.getCoverages().length
- 1) {
readClass.getCoverages()[(readstart + r)
- readClass.getCoverageStart()][Main.baseMap
.get(samRecord.getReadBases()[r])]++;
if (mismatches == null) {
mismatches = new java.util.ArrayList<java.util.Map.Entry<Integer, Byte>>();
}
java.util.Map.Entry<Integer, Byte> mismatch = new java.util.AbstractMap.SimpleEntry<>(
r, samRecord.getReadBases()[r]);
mismatches.add(mismatch);
}
}
try {
coverageArray[(readstart + r) - readClass.getCoverageStart()][0]++;
} catch (Exception e) {
//TODO
//e.printStackTrace();
continue;
}
if (coverageArray[(samRecord.getUnclippedStart() - readClass.getCoverageStart())
+ r][0] > readClass.getMaxcoverage()) {
readClass.setMaxcoverage(
coverageArray[(samRecord.getUnclippedStart() - readClass.getCoverageStart())
+ r][0]);
}
} catch (Exception e) {
ErrorLog.addError(e.getStackTrace());
e.printStackTrace();
return mismatches;
}
}
}
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
return mismatches;
}