List of usage examples for java.lang NumberFormatException printStackTrace
public void printStackTrace()
From source file:massbank.BatchJobWorker.java
/** * Ytt@C???iHTML`?j/*from w w w .j a va 2s.c om*/ * @param time NGXg * @param resultFile t@C * @param htmlFile YtpHTMLt@C */ private void createHtmlFile(String time, File resultFile, File htmlFile) { NumberFormat nf = NumberFormat.getNumberInstance(); LineNumberReader in = null; PrintWriter out = null; try { in = new LineNumberReader(new FileReader(resultFile)); out = new PrintWriter(new BufferedWriter(new FileWriter(htmlFile))); // wb_?[?o String reqIonStr = "Both"; try { if (Integer.parseInt(this.ion) > 0) { reqIonStr = "Positive"; } else if (Integer.parseInt(this.ion) < 0) { reqIonStr = "Negative"; } } catch (NumberFormatException nfe) { nfe.printStackTrace(); } out.println("<html>"); out.println("<head><title>MassBank Batch Service Results</title></head>"); out.println("<body>"); out.println( "<h1><a href=\"http://www.massbank.jp/\" target=\"_blank\">MassBank</a> Batch Service Results</h1>"); out.println("<hr>"); out.println("<h2>Request Date : " + time + "<h2>"); out.println("Instrument Type : " + this.inst + "<br>"); out.println("Ion Mode : " + reqIonStr + "<br>"); out.println("<br><hr>"); // ?o String line; long queryCnt = 0; boolean readName = false; boolean readHit = false; boolean readNum = false; while ((line = in.readLine()) != null) { if (in.getLineNumber() < 4) { continue; } if (!readName) { queryCnt++; out.println("<h2>Query " + nf.format(queryCnt) + "</h2><br>"); out.println("Name: " + line.trim() + "<br>"); readName = true; } else if (!readHit) { out.println("Hit: " + nf.format(Integer.parseInt(line.trim())) + "<br>"); readHit = true; } else if (!readNum) { out.println("<table border=\"1\">"); out.println("<tr><td colspan=\"6\">Top " + line.trim() + " List</td></tr>"); out.println( "<tr><th>Accession</th><th>Title</th><th>Formula</th><th>Ion</th><th>Score</th><th>Hit</th></tr>"); readNum = true; } else { if (!line.trim().equals("")) { String[] data = formatLine(line); String acc = data[0]; String title = data[1]; String formula = data[2]; String ion = data[3]; String score = data[4]; String hit = data[5]; out.println("<tr>"); out.println("<td><a href=\"http://www.massbank.jp/jsp/FwdRecord.jsp?id=" + acc + "\" target=\"_blank\">" + acc + "</td>"); out.println("<td>" + title + "</td>"); out.println("<td>" + formula + "</td>"); out.println("<td>" + ion + "</td>"); out.println("<td>" + score + "</td>"); out.println("<td align=\"right\">" + hit + "</td>"); out.println("</tr>"); } else { out.println("</table>"); out.println("<hr>"); readName = false; readHit = false; readNum = false; } } } } catch (Exception e) { e.printStackTrace(); } finally { try { if (in != null) { in.close(); } } catch (IOException e) { } if (out != null) { out.flush(); out.close(); } } }
From source file:org.camera.service.FastaValidation.java
/** Output the data read from the file or URL as a string. * @exception IllegalActionException If there is no director or * if reading the file triggers an exception. */// w w w. j av a 2 s . c om public void fire() throws IllegalActionException { super.fire(); parseNumSequence.update(); boolean monitor = true; boolean parseAllSequences = true; String filePath = null; StringBuilder message = new StringBuilder(); // If the fileOrURL input port is connected and has data, then // get the file name from there. String numOfSeqBeParsedValue = getPortParamValue(); int numOfSeqBeParsed = -1; if (!ServiceUtils.checkEmptyString(numOfSeqBeParsedValue)) { try { numOfSeqBeParsed = Integer.parseInt(numOfSeqBeParsedValue); if (numOfSeqBeParsed > 0) { parseAllSequences = false; } } catch (NumberFormatException nfe) { nfe.printStackTrace(); } } if (inputPortFilePath.isOutsideConnected()) { if (inputPortFilePath.hasToken(0)) { String name = ((StringToken) inputPortFilePath.get(0)).stringValue(); // Using setExpression() rather than setToken() allows // the string to refer to variables defined in the // scope of this actor. fileParameter.setExpression(name); } } filePath = fileParameter.getExpression(); if (ServiceUtils.checkEmptyString(filePath)) { message.append("NO FILE NAME PROVIDED"); outputPortStatus.send(0, new BooleanToken(monitor)); outputPortMessage.send(0, new StringToken(String.valueOf(message.toString()))); log.debug("FILE PATH IS EMPTY"); message = null; return; } log.debug("FILE NAME: " + filePath); String type = null; if (inputPortType.isOutsideConnected()) { if (inputPortType.hasToken(0)) { type = ((StringToken) inputPortType.get(0)).stringValue(); if (type.equalsIgnoreCase(PROTEIN)) { dropDownValue.setExpression(PROTEIN); } else if (type.equalsIgnoreCase(DNA)) { dropDownValue.setExpression(DNA); } else if (type.equalsIgnoreCase(RNA)) { dropDownValue.setExpression(RNA); } } } if (ServiceUtils.checkEmptyString(dropDownValue.getExpression())) { dropDownValue.setExpression(DNA); message.append("NO SELECTION MADE FOR TYPE: DEFAULT VALUE IS SET TO DNA"); } else { message.append("SELECTION MADE BY USER FOR TYPE: ").append(dropDownValue.getExpression()); } message.append(ServiceUtils.LINESEP); type = dropDownValue.getExpression(); log.debug("SELECTED VALUE FROM DROP DOWN: " + type); BufferedReader br = null; try { br = new BufferedReader(new FileReader(filePath)); } catch (FileNotFoundException ex) { //problem reading file System.out.println("FILE NOT FOUND"); ex.printStackTrace(); System.exit(1); } Namespace nm = new SimpleNamespace("CAMERA"); //get a SequenceDB of all sequences in the file RichSequenceIterator db = null; if (type.equals(DNA)) { db = RichSequence.IOTools.readFastaDNA(br, nm); //readFasta(is, alpha); } else if (type.equals(RNA)) { db = RichSequence.IOTools.readFastaRNA(br, nm); //readFasta(is, alpha); } else if (type.equals(PROTEIN)) { db = RichSequence.IOTools.readFastaProtein(br, nm); //readFasta(is, alpha); } int number_of_sequences = 0; int icheck = 0; int problems = 0; List<String> allM = new ArrayList<String>(); RichSequence rseq = null; boolean fileStatus = true; /** * Here, I am attempting to read first sequence to check file status * before proceeding forward. I have to do this because of * clunky behavior or biojava. */ if (db.hasNext()) { try { rseq = db.nextRichSequence(); number_of_sequences++; } catch (BioException bioexcep) { fileStatus = false; System.out.println("FILE STATUS: " + fileStatus); message.append("INCORRECT FILE FORMAT OR FILE EMPTY OR FIRST SEQ HAS PROBLEM"); monitor = false; } } while (db.hasNext() && fileStatus) { number_of_sequences++; try { // Sequence seq = db.nextSequence(); rseq = db.nextRichSequence(); // log.debug("ACCESSION: " + rseq.getAccession()); //NAME, URN, & ACCESSION COULD BE VERY SIMILAR // log.debug("SEQUENCE-NAME: " + rseq.getURN()); // log.debug("SEQUENCE-ENGTH: " + rseq.length()); // log.debug("SEQUENCE: " + rseq.seqString()); /* Annotation seqAn = rseq.getAnnotation(); for (Iterator i = seqAn.keys().iterator(); i.hasNext(); ) { Object key = i.next(); Object value = seqAn.getProperty(key); log.debug(key.toString() + ": " + value.toString()); } */ //user controls how many sequences need o be parsed. if (!parseAllSequences && number_of_sequences >= numOfSeqBeParsed) { break; } } catch (ParseException parex) { monitor = false; message.append("INCORRECT FILE FORMAT OR FILE NOT PARSEABLE OR PROBLEM WITH SEQUENCES") .append(ServiceUtils.LINESEP); message.append("PROBLEM WITH SEQUENCE #: " + (number_of_sequences + 1)); // .append(ex.getMessage()); //not in fasta format or wrong alphabet parex.printStackTrace(); } catch (BioException ex) { // message.append(ex.getMessage() + "\n"); monitor = false; // message.append("HI"); //no fasta sequences in the file ex.printStackTrace(); StringWriter writer = new StringWriter(); ex.printStackTrace(new PrintWriter(writer)); String trace = writer.toString(); // The following line may give impression that the catching // IOException should obviate the need for if block. But do // not waste time trying because it does not work. The // version 1.7.1 of Biojava currently available now is quirky. if (trace.contains("IOException")) { ++icheck; if (icheck % 2 == 0) { ++problems; allM.add("Problem at sequence :: " + --number_of_sequences); } } else { ++problems; allM.add("Problem at sequence : " + number_of_sequences); } if (problems > MAXNOOFALLOWEDPROBLEMS) { message.append("Number of problems exceeded :" + MAXNOOFALLOWEDPROBLEMS); break; } } catch (Throwable throwable) { monitor = false; message.append("IN THROWABLE\n"); throwable.printStackTrace(); } finally { if (fileParameter != null) { fileParameter.close(); } } //end try block } //end while if (allM.size() > 0) { for (String m : allM) { message.append(m + "\n"); } } message.append("Number of sequences parsed from the file: ").append(String.valueOf(number_of_sequences)) .append(ServiceUtils.LINESEP); outputPortMessage.send(0, new StringToken(String.valueOf(message.toString()))); outputPortStatus.send(0, new BooleanToken(monitor)); log.debug("MESSAGE: " + message.toString()); message = null; }
From source file:de.madvertise.android.sdk.MadvertiseAd.java
/** * Constructor, blocking due to http request, should be called in a thread * pool, a request queue, a network thread * * @param context the applications context * @param json json object containing all ad information *///from w ww. j a v a 2 s.c om protected MadvertiseAd(final Context context, final JSONObject json, final MadvertiseViewCallbackListener listener) { this.mContext = context; this.mCallbackListener = listener; MadvertiseUtil.logMessage(null, Log.DEBUG, "Creating ad"); // init json arrays and print all keys / values mJsonNames = json.names(); try { mJsonValues = json.toJSONArray(mJsonNames); for (int i = 0; i < mJsonNames.length(); i++) { MadvertiseUtil.logMessage(null, Log.DEBUG, "Key => " + mJsonNames.getString(i) + " Value => " + mJsonValues.getString(i)); } markup = MadvertiseUtil.getJSONValue(json, MARKUP); if (null != markup && !markup.equals("")) { mBannerType = MadvertiseUtil.BANNER_TYPE_RICH_MEDIA; mIsMraid = true; mHasBanner = true; mBannerHeight = Integer.parseInt(MadvertiseUtil.getJSONValue(json, "height")); mBannerWidth = Integer.parseInt(MadvertiseUtil.getJSONValue(json, "width")); return; } // first get not nested values mClickUrl = MadvertiseUtil.getJSONValue(json, CLICK_URL_CODE); mText = MadvertiseUtil.getJSONValue(json, TEXT_CODE); mImpressionTrackingArray = MadvertiseUtil.getJSONArray(json, IMPRESSION_TRACKING_ARRAY_CODE); // check, if we have a banner JSONObject bannerJson = MadvertiseUtil.getJSONObject(json, "banner"); if (bannerJson == null) { return; } // logic for new ad response mBannerUrl = MadvertiseUtil.getJSONValue(bannerJson, BANNER_URL_CODE); mHasBanner = true; mBannerType = MadvertiseUtil.getJSONValue(bannerJson, "type"); // check, if rich media banner JSONObject richMediaJson = MadvertiseUtil.getJSONObject(bannerJson, "rich_media"); if (richMediaJson == null) { return; } // check, if mraid type if (!MadvertiseUtil.getJSONBoolean(richMediaJson, "mraid")) { mHasBanner = false; mBannerUrl = ""; return; } mIsMraid = true; // overwrite banner url mBannerUrl = MadvertiseUtil.getJSONValue(richMediaJson, "full_url"); // get sizes for rich media ad try { mBannerHeight = Integer.parseInt(MadvertiseUtil.getJSONValue(richMediaJson, "height")); mBannerWidth = Integer.parseInt(MadvertiseUtil.getJSONValue(richMediaJson, "width")); } catch (NumberFormatException e) { mBannerHeight = 53; mBannerWidth = 320; } } catch (JSONException e) { MadvertiseUtil.logMessage(null, Log.DEBUG, "Error in json string"); if (mCallbackListener != null) { mCallbackListener.onError(e); } e.printStackTrace(); } }
From source file:ca.mudar.parkcatcher.ui.activities.MainActivity.java
private void updateParkingTimeFromUri(Uri uri) { Log.v(TAG, "updateParkingTimeFromUri"); List<String> pathSegments = uri.getPathSegments(); // http://www.capteurdestationnement.com/map/search/2/15.5/12 // http://www.capteurdestationnement.com/map/search/2/15.5/12/h2w2e7 if ((pathSegments.size() >= 5) && (pathSegments.get(0).equals(Const.INTENT_EXTRA_URL_PATH_MAP)) && (pathSegments.get(1).equals(Const.INTENT_EXTRA_URL_PATH_SEARCH))) { try {/*from ww w . j a v a 2 s.com*/ final int day = Integer.valueOf(pathSegments.get(2)); final double time = Double.valueOf(pathSegments.get(3)); final int duration = Integer.valueOf(pathSegments.get(4)); final int hourOfDay = (int) time; final int minute = (int) ((time - hourOfDay) * 60); GregorianCalendar calendar = new GregorianCalendar(); calendar.set(Calendar.DAY_OF_WEEK, day == 7 ? Calendar.SUNDAY : day + 1); calendar.set(Calendar.HOUR_OF_DAY, hourOfDay); calendar.set(Calendar.MINUTE, minute); parkingApp.setParkingCalendar(calendar); parkingApp.setParkingDuration(duration); } catch (NumberFormatException e) { e.printStackTrace(); } } }
From source file:org.dklisiaris.downtown.helper.XMLParser.java
public ArrayList<Company> getAllCompanies(Document doc) { ArrayList<Company> companies = new ArrayList<Company>(); //Document doc = getDomElement(xml); // getting DOM element NodeList nl = doc.getElementsByTagName(KEY_PRODUCT); // looping through all item nodes <category> for (int k = 0; k < nl.getLength(); k++) { Element e = (Element) nl.item(k); int co_id = Integer.parseInt(getValue(e, KEY_ID)); int avail = getValue(e, KEY_AVAIL).equals("yes") ? 1 : 0; int level = Integer.parseInt(getValue(e, KEY_LEVEL)); int cat_id = Integer.parseInt(getAttributeFromNode(e, KEY_CATEGORY, ATTR_CATEGORY_ID)); String website = null;/*from w w w. jav a 2s. c om*/ if (avail == 1) website = getValue(e, KEY_WEBSITE); double langi = 0.0, longi = 0.0; ArrayList<String> imgs = getImgUrlsFromElem(e, KEY_IMAGE); ArrayList<String> tels = getMultiValuesFromElem(e, KEY_TEL); ArrayList<String> subcats = new ArrayList<String>(); NodeList subItems = e.getElementsByTagName(KEY_SUBCATEGORY); for (int j = 0; j < subItems.getLength(); j++) { Element subItem = (Element) subItems.item(j); subcats.add(subItem.getAttribute(ATTR_CATEGORY_ID)); } String county = getValue(e, KEY_COUNTY); String tk = getValue(e, KEY_TK); String fax = getValue(e, KEY_FAX); String strLang = getValue(e, KEY_LANG), strLong = getValue(e, KEY_LONG); //Log.d("Coords: ",strLang+" - "+strLong); if (exists(strLang) && exists(strLong)) { try { langi = Double.parseDouble(getValue(e, KEY_LANG)); longi = Double.parseDouble(getValue(e, KEY_LONG)); } catch (NumberFormatException nfe) { nfe.printStackTrace(); } } Company com = new Company(co_id, getValue(e, KEY_NAME), getValue(e, KEY_ADDRESS), getValue(e, KEY_DESC), imgs, tels, subcats, cat_id, getValue(e, KEY_AREA), county, tk, level, avail, website, fax, langi, longi); //Log.d("Namexml",pr.getName()); companies.add(com); } return companies; }
From source file:com.idega.company.business.impl.CompanyServiceImpl.java
protected ArrayList<User> getUsersByRoles(Collection<String> roles) { if (ListUtil.isEmpty(roles)) { getLogger().warning("Roles are not provided"); return null; }/*from ww w . ja v a 2 s.com*/ ArrayList<User> users = new ArrayList<User>(); GroupBusiness groupBusiness = getGroupBusiness(); if (groupBusiness == null) { return null; } UserBusiness userBusiness = getUserBusiness(); if (userBusiness == null) { return null; } AccessController accessController = CoreUtil.getIWContext().getAccessController(); for (String roleKey : roles) { Collection<Group> groupsByRole = accessController.getAllGroupsForRoleKey(roleKey, CoreUtil.getIWContext()); if (ListUtil.isEmpty(groupsByRole)) { continue; } for (Group group : groupsByRole) { if (StringUtil.isEmpty(group.getName())) { try { User user = userBusiness.getUser(Integer.valueOf(group.getId())); if (accessController.hasRole(user, roleKey) && !users.contains(user)) { users.add(user); } } catch (NumberFormatException e) { e.printStackTrace(); } catch (Exception e) { } } Collection<User> usersInGroup = null; try { usersInGroup = groupBusiness.getUsers(group); } catch (FinderException e) { } catch (Exception e) { e.printStackTrace(); } if (!ListUtil.isEmpty(usersInGroup)) { for (User user : usersInGroup) { if (!users.contains(user)) { users.add(user); } } } } } if (ListUtil.isEmpty(users)) { getLogger().warning("There are no users by role(s): " + roles); } return users; }
From source file:de.baumann.hhsmoodle.data_random.Random_Fragment.java
@Override public View onCreateView(LayoutInflater inflater, ViewGroup container, Bundle savedInstanceState) { View rootView = inflater.inflate(R.layout.fragment_screen_dice, container, false); ImageView imgHeader = (ImageView) rootView.findViewById(R.id.imageView_header); helper_main.setImageHeader(getActivity(), imgHeader); fab_dice = (FloatingActionButton) rootView.findViewById(R.id.fab_dice); lv = (ListView) rootView.findViewById(R.id.list); viewPager = (ViewPager) getActivity().findViewById(R.id.viewpager); lvItems = (ListView) rootView.findViewById(R.id.lvItems); fabLayout1 = (LinearLayout) rootView.findViewById(R.id.fabLayout1); fabLayout2 = (LinearLayout) rootView.findViewById(R.id.fabLayout2); fab = (FloatingActionButton) rootView.findViewById(R.id.fab); FloatingActionButton fab1 = (FloatingActionButton) rootView.findViewById(R.id.fab1); FloatingActionButton fab2 = (FloatingActionButton) rootView.findViewById(R.id.fab2); fab.setOnClickListener(new View.OnClickListener() { @Override//www . j a va2 s . c o m public void onClick(View view) { if (!isFABOpen) { showFABMenu(); } else { closeFABMenu(); } } }); fab1.setOnClickListener(new View.OnClickListener() { @Override public void onClick(View view) { closeFABMenu(); android.app.AlertDialog.Builder builder = new android.app.AlertDialog.Builder(getActivity()); View dialogView = View.inflate(getActivity(), R.layout.dialog_edit_entry, null); final EditText edit_title = (EditText) dialogView.findViewById(R.id.note_title_input); edit_title.setHint(R.string.title_hint); final EditText edit_cont = (EditText) dialogView.findViewById(R.id.note_text_input); edit_cont.setHint(R.string.text_hint); builder.setView(dialogView); builder.setTitle(R.string.number_edit_entry); builder.setPositiveButton(R.string.toast_yes, new DialogInterface.OnClickListener() { public void onClick(DialogInterface dialog, int whichButton) { String inputTitle = edit_title.getText().toString().trim(); String inputCont = edit_cont.getText().toString().trim(); if (db.isExist(inputTitle)) { Snackbar.make(lv, getString(R.string.toast_newTitle), Snackbar.LENGTH_LONG).show(); } else { db.insert(inputTitle, inputCont, "", "", helper_main.createDate()); dialog.dismiss(); setRandomList(); Snackbar.make(lv, R.string.bookmark_added, Snackbar.LENGTH_SHORT).show(); } } }); builder.setNegativeButton(R.string.toast_cancel, new DialogInterface.OnClickListener() { public void onClick(DialogInterface dialog, int whichButton) { dialog.cancel(); } }); final android.app.AlertDialog dialog2 = builder.create(); // Display the custom alert dialog on interface dialog2.show(); helper_main.showKeyboard(getActivity(), edit_title); } }); fab2.setOnClickListener(new View.OnClickListener() { @Override public void onClick(View view) { closeFABMenu(); Intent mainIntent = new Intent(getActivity(), Popup_courseList.class); mainIntent.setAction("courseList_random"); startActivity(mainIntent); } }); fab_dice.setOnClickListener(new View.OnClickListener() { @Override public void onClick(View view) { try { Random rand = new Random(); final int n = rand.nextInt(lvItems.getCount()); setAdapter(n); lvItems.setSelection(n - 1); } catch (NumberFormatException nfe) { nfe.printStackTrace(); } } }); //calling Notes_DbAdapter db = new Random_DbAdapter(getActivity()); db.open(); setRandomList(); setHasOptionsMenu(true); return rootView; }
From source file:org.onosproject.netconf.ctl.impl.NetconfSshdTestSubsystem.java
private boolean validateChunkedFraming(String reply) { String[] strs = reply.split(LF + HASH); int strIndex = 0; while (strIndex < strs.length) { String str = strs[strIndex]; if ((str.equals(HASH + LF))) { return true; }/*from www . j av a 2s.com*/ if (!str.equals("")) { try { if (str.equals(LF)) { return false; } int len = Integer.parseInt(str.split(LF)[0]); if (str.split(MSGLEN_PART_REGEX_PATTERN)[1].getBytes("UTF-8").length != len) { return false; } } catch (NumberFormatException e) { return false; } catch (UnsupportedEncodingException e) { e.printStackTrace(); } } strIndex++; } return true; }
From source file:com.google.android.gms.location.sample.geofencing.MainActivity.java
public void GetID() { List<NeighboringCellInfo> neighCell = null; TelephonyManager telManager = (TelephonyManager) getSystemService(Context.TELEPHONY_SERVICE); neighCell = telManager.getNeighboringCellInfo(); for (int i = 0; i < neighCell.size(); i++) { try {//from w w w.ja v a 2s. c om NeighboringCellInfo thisCell = neighCell.get(i); int thisNeighCID = thisCell.getCid(); int thisNeighRSSI = thisCell.getRssi(); Log.i("Info:", " cid:" + thisNeighCID + " - " + thisNeighRSSI); } catch (NumberFormatException e) { e.printStackTrace(); NeighboringCellInfo thisCell = neighCell.get(i); Log.i("exception", neighCell.toString()); } } String networkOperator = telManager.getNetworkOperator(); String mcc = "not avl", mnc = "not avl"; if (networkOperator != null) { mcc = networkOperator.substring(0, 3); mnc = networkOperator.substring(3); } Log.i("", "mcc:" + mcc); Log.i("", "mnc:" + mnc); }
From source file:ca.mudar.parkcatcher.ui.fragments.DetailsFragment.java
private int getIdFromUri(Uri uri) { int postId = -1; List<String> pathSegments = uri.getPathSegments(); if ((pathSegments.size() == 5) && (pathSegments.get(0).equals(Const.INTENT_EXTRA_URL_PATH_POST_ID))) { try {// ww w .j av a 2 s .c om postId = Integer.parseInt(pathSegments.get(1)); final int day = Integer.valueOf(pathSegments.get(2)); final double time = Double.valueOf(pathSegments.get(3)); final int duration = Integer.valueOf(pathSegments.get(4)); final int hourOfDay = (int) time; final int minute = (int) ((time - hourOfDay) * 60); GregorianCalendar calendar = new GregorianCalendar(); calendar.set(Calendar.DAY_OF_WEEK, day == 7 ? Calendar.SUNDAY : day + 1); calendar.set(Calendar.HOUR_OF_DAY, hourOfDay); calendar.set(Calendar.MINUTE, minute); parkingApp.setParkingCalendar(calendar); // parkingApp.setParkingTime(hourOfDay, minute); parkingApp.setParkingDuration(duration); } catch (NumberFormatException e) { e.printStackTrace(); } } return postId; }