List of usage examples for java.io FileWriter write
public void write(int c) throws IOException
From source file:mendeley2kindle.KindleDAO.java
public void commit() throws IOException { File path = new File(kindleLocal); File file = new File(path, KINDLE_COLLECTIONS_JSON); log.log(Level.FINER, "writing collections data: " + file); if (!file.exists() || file.canWrite()) { file.getParentFile().mkdirs();// w ww. j a va2s . com FileWriter fw = new FileWriter(file); fw.write(collections.toString()); fw.close(); log.log(Level.FINE, "Saved kindle collections: " + file); } else { log.log(Level.SEVERE, "CANNOT write Kindle collections data. Aborting..." + file); } }
From source file:MSUmpire.SearchResultWriter.PepXMLWriter.java
public void Write() throws IOException, XmlPullParserException { int minlength = Integer.MAX_VALUE; int maxlength = 0; int maxmiss = 0; for (PepIonID pepIonID : PepList) { if (pepIonID.Sequence.length() > maxlength) { maxlength = pepIonID.Sequence.length(); }//from www . j a va 2s .c o m if (pepIonID.Sequence.length() < minlength) { minlength = pepIonID.Sequence.length(); } if (pepIonID.getNMissedCleavages() > maxmiss) { maxmiss = pepIonID.getNMissedCleavages(); } } FastaParser_V2 fastaparser = FastaParser_V2.FasterSerialzationRead(Fasta); if (fastaparser == null) { fastaparser = new FastaParser_V2(Fasta); fastaparser.digestion(maxmiss, minlength, maxlength, "DECOY"); } Header(); sb.append("<msms_run_summary base_name=\"" + FilenameUtils.getBaseName(Filename) + "\" search_engine=\"Umpire\" >\n"); SearchSummary(); int index = 0; for (PepIonID pepIonID : PepList) { ArrayList<ParentProtein> parentprots = new ArrayList<>(); if (!fastaparser.PeptideList.containsKey(pepIonID.Sequence)) { Logger.getRootLogger().warn(pepIonID.Sequence + " is not found as tryptic peptides in " + Fasta + ". Searching protein sequences.."); for (String acc : fastaparser.ProteinList.keySet()) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(pepIonID.Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(pepIonID.Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(pepIonID.Sequence) + pepIonID.Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } else { for (String acc : fastaparser.PeptideList.get(pepIonID.Sequence).Proteins) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(pepIonID.Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(pepIonID.Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(pepIonID.Sequence) + pepIonID.Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } if (parentprots.isEmpty()) { Logger.getRootLogger().warn(pepIonID.Sequence + " is not found in " + Fasta); } else { sb.append("<spectrum_query spectrum=\"" + pepIonID.GetKey() + "\" precursor_neutral_mass=\"" + pepIonID.CalcNeutralPepMass() + "\" assumed_charge=\"" + pepIonID.Charge + "\" index=\"" + (index++) + "\" retention_time_sec=\"" + pepIonID.PeakRT * 60f + "\">\n" + "<search_result>\n" + "<search_hit hit_rank=\"1\" peptide=\"" + pepIonID.Sequence + "\" peptide_prev_aa=\"" + parentprots.get(0).PreAA + "\" peptide_next_aa=\"" + parentprots.get(0).NextAA + "\" protein=\"" + parentprots.get(0).Acc + "\" protein_descr=\"" + parentprots.get(0).Des + "\" num_tot_proteins=\"" + parentprots.size() + "\" num_matched_ions=\"" + pepIonID.GetFragCount() + "\" tot_num_ions=\"" + 2 * (pepIonID.Sequence.length() - 1) + "\" calc_neutral_pep_mass=\"" + pepIonID.CalcNeutralPepMass() + "\" massdiff=\"" + (pepIonID.CalcNeutralPepMass() - pepIonID.ObservedMass()) + "\" num_missed_cleavages=\"" + pepIonID.getNMissedCleavages() + "\" is_rejected=\"0\">\n"); for (int i = 1; i < parentprots.size(); i++) { sb.append("<alternative_protein protein=\"" + parentprots.get(i).Acc + "\" protein_descr=\"" + parentprots.get(i).Des + "\" num_tol_term=\"2\" peptide_prev_aa=\"" + parentprots.get(i).PreAA + "\" peptide_next_aa=\"" + parentprots.get(i).NextAA + "\"/>"); } // + "<modification_info modified_peptide=\"KITIADCGQLE\">\n" // + "<mod_aminoacid_mass position=\"7\" mass=\"160.0306\"/>\n" // + "</modification_info>\n" // + "<analysis_result analysis=\"peptideprophet\">\n" // + "<peptideprophet_result probability=\"0.8297\" all_ntt_prob=\"(0.0059,0.3657,0.8297)\">\n" // + "<search_score_summary>\n" // + "<parameter name=\"fval\" value=\"1.6872\"/>\n" // + "<parameter name=\"ntt\" value=\"2\"/>\n" // + "<parameter name=\"nmc\" value=\"0\"/>\n" // + "<parameter name=\"massd\" value=\"4.011\"/>\n" // + "<parameter name=\"isomassd\" value=\"0\"/>\n" // + "</search_score_summary>\n" // + "</peptideprophet_result>\n" // + "</analysis_result>\n" sb.append("<analysis_result analysis=\"interprophet\">\n" + "<interprophet_result probability=\"" + pepIonID.TargetedProbability() + "\">\n" // + "<search_score_summary>\n" // + "<parameter name=\"nrs\" value=\"0\"/>\n" // + "<parameter name=\"nsi\" value=\"0\"/>\n" // + "<parameter name=\"nsm\" value=\"0\"/>\n" // + "</search_score_summary>\n" + "</interprophet_result>\n" + "</analysis_result>\n" + "</search_hit>\n" + "</search_result>\n" + "</spectrum_query>\n"); } } sb.append("</msms_run_summary>\n"); sb.append("</msms_pipeline_analysis>\n"); FileWriter writer = new FileWriter(Filename); writer.write(sb.toString()); writer.close(); }
From source file:c3.ops.priam.backup.MetaData.java
@SuppressWarnings("unchecked") public void set(List<AbstractBackupPath> bps, String snapshotName) throws Exception { File metafile = createTmpMetaFile(); FileWriter fr = new FileWriter(metafile); try {/*w w w . java2 s . c o m*/ JSONArray jsonObj = new JSONArray(); for (AbstractBackupPath filePath : bps) jsonObj.add(filePath.getRemotePath()); fr.write(jsonObj.toJSONString()); } finally { IOUtils.closeQuietly(fr); } AbstractBackupPath backupfile = pathFactory.get(); backupfile.parseLocal(metafile, BackupFileType.META); backupfile.time = backupfile.parseDate(snapshotName); try { upload(backupfile); addToRemotePath(backupfile.getRemotePath()); if (metaRemotePaths.size() > 0) { notifyObservers(); } } finally { FileUtils.deleteQuietly(metafile); } }
From source file:de.uzk.hki.da.cb.CreateDCAction.java
private void writeDCBackToPIP(String audience, String updatedDcContent) throws IOException { wa.pipMetadataFile(audience, METADATA_STREAM_ID_DC).delete(); FileWriter fw = null; try {//from w w w . j a v a 2 s .co m fw = new FileWriter(wa.pipMetadataFile(audience, METADATA_STREAM_ID_DC)); fw.write(updatedDcContent); } catch (Exception e) { throw new RuntimeException(e); } finally { if (fw != null) fw.close(); } }
From source file:fr.paris.lutece.plugins.rss.service.RssGeneratorService.java
/** * Creates the pushrss file in the directory * * @param strRssFileName The file's name that must be deleted * @param strRssDocument The content of the new RSS file *///from w w w . j a v a 2 s .c o m public static void createFileRss(String strRssFileName, String strRssDocument) { FileWriter fileRssWriter; try { // fetches the pushRss directory path String strFolderPath = AppPathService.getPath(RssGeneratorService.PROPERTY_RSS_STORAGE_FOLDER_PATH, ""); // Test if the pushRss directory exist and create it if it doesn't exist if (!new File(strFolderPath).exists()) { File fileFolder = new File(strFolderPath); fileFolder.mkdir(); } // Creates a temporary RSS file String strFileRss = AppPathService.getPath(RssGeneratorService.PROPERTY_RSS_STORAGE_FOLDER_PATH, "") + strRssFileName; String strFileDirectory = AppPathService.getPath(RssGeneratorService.PROPERTY_RSS_STORAGE_FOLDER_PATH, ""); File fileRss = new File(strFileRss); File fileRssDirectory = new File(strFileDirectory); File fileRssTemp = File.createTempFile("tmp", null, fileRssDirectory); fileRssWriter = new FileWriter(fileRssTemp); fileRssWriter.write(strRssDocument); fileRssWriter.flush(); fileRssWriter.close(); // Deletes the file if the file exists and renames the temporary file into the file if (new File(strFileRss).exists()) { File file = new File(strFileRss); file.delete(); } fileRssTemp.renameTo(fileRss); } catch (IOException e) { AppLogService.error(e.getMessage(), e); } catch (NullPointerException e) { AppLogService.error(e.getMessage(), e); } }
From source file:com.tealeaf.ResourceDownloaderTask.java
private void stringToFile(File file, String content) { FileWriter fileWriter = null; try {// ww w . j a va 2 s . co m fileWriter = new FileWriter(file); fileWriter.write(content); fileWriter.close(); } catch (IOException e) { logger.log(e); } finally { try { fileWriter.close(); } catch (IOException e) { logger.log(e); } } }
From source file:com.jgui.ttscrape.htmlunit.FetchController.java
private void writeContent(int i, HtmlPage currentPage) { try {//from w ww . ja va 2 s.c o m FileWriter writer = new FileWriter("results/raw" + i + ".xml"); writer.write(currentPage.asXml()); writer.close(); } catch (Exception ex) { logger.error("Failed to write raw content", ex); } }
From source file:com.dmsl.anyplace.tasks.DownloadRadioMapTaskXY.java
@Override protected String doInBackground(Void... params) { try {/* w ww . jav a 2 s .c o m*/ if (json_req == null) return "Error creating the request!"; // check sdcard state File root; try { root = AnyplaceUtils.getRadioMapFoler(ctx, mBuildID, mFloor_number); } catch (Exception e) { return e.getMessage(); } // rename the radiomap according to the floor String filename_radiomap_download = AnyplaceUtils.getRadioMapFileName(mFloor_number); String mean_fname = filename_radiomap_download; String rbf_weights_fname = mean_fname.replace(".txt", "-rbf-weights.txt"); String parameters_fname = mean_fname.replace(".txt", "-parameters.txt"); File okfile = new File(root, "ok.txt"); if (!mForceDonwload && okfile.exists()) { success = true; return "Successfully read radio map from cache!"; } okfile.delete(); // changed in order to receive only the radio map for the // current floor String response = NetworkUtils.downloadHttpClientJsonPost(AnyplaceAPI.getRadioDownloadXY(), json_req); JSONObject json = new JSONObject(response); if (json.getString("status").equalsIgnoreCase("error")) { return "Error Message: " + json.getString("message"); } String means = json.getString("map_url_mean"); String parameters = json.getString("map_url_parameters"); String weights = json.getString("map_url_weights"); // create the credentials JSON in order to send and download the // radio map JSONObject json_credentials = new JSONObject(); json_credentials.put("username", "username"); json_credentials.put("password", "pass"); String cred_str = json_credentials.toString(); String ms = NetworkUtils.downloadHttpClientJsonPost(means, cred_str); String ps = NetworkUtils.downloadHttpClientJsonPost(parameters, cred_str); String ws = NetworkUtils.downloadHttpClientJsonPost(weights, cred_str); // check if the files downloaded correctly if (ms.contains("error") || ps.contains("error") || ws.contains("error")) { json = new JSONObject(response); return "Error Message: " + json.getString("message"); } FileWriter out; out = new FileWriter(new File(root, rbf_weights_fname)); out.write(ws); out.close(); out = new FileWriter(new File(root, parameters_fname)); out.write(ps); out.close(); out = new FileWriter(new File(root, mean_fname)); out.write(ms); out.close(); out = new FileWriter(okfile); out.write("ok;version:0;"); out.close(); success = true; return "Successfully saved radio maps!"; } catch (ConnectTimeoutException e) { return "Connecting to Anyplace service is taking too long!"; } catch (SocketTimeoutException e) { return "Communication with the server is taking too long!"; } catch (Exception e) { return "Error downloading radio maps [ " + e.getMessage() + " ]"; } }
From source file:fast.servicescreen.server.RequestServiceImpl.java
/** * This method try to form a given String * into a file, and save it as .js//from w w w.j a va 2 s .c o m * */ @SuppressWarnings("deprecation") @Override public String saveJsFileOnServer(boolean isLocal, String opName, String preHTMLCode, String transCode, String postHTMLCode) { //the HTML file content String htmlContent = preHTMLCode + transCode + postHTMLCode; String answer = ""; try { //getting class path path = "."; String classLocation = getClassLocation(); String installDir; int prefixLength; //if local save into war, if not save into webapps folder if (isLocal) { prefixLength = classLocation.indexOf("ServiceScreenDesignerWep"); prefixLength += "ServiceScreenDesignerWep".length(); path = classLocation.substring(0, prefixLength) + "/wrapper/"; } else { prefixLength = classLocation.indexOf("ServiceDesignerWep"); prefixLength += "ServiceDesignerWep".length(); installDir = classLocation.substring(0, prefixLength); path = URLDecoder.decode(installDir) + "/wrapper/"; if (new File(path).mkdir()) { answer += "Create folder 'wrapper' "; } } //configure filename (for html) String baseFileName = path + opName + "Op"; String fileName = baseFileName + ".html"; //write file FileWriter writer = new FileWriter(fileName, false); writer.write(htmlContent); writer.close(); //configure filename (for javascript) fileName = baseFileName + ".js"; writer = new FileWriter(fileName, false); //write file writer.write(transCode); writer.close(); answer += "The file now exists in: " + path; } catch (Exception e) { answer += " Error: " + e.getLocalizedMessage(); return answer; } return answer; }
From source file:com.nts.alphamaleWeb.controller.ServiceController.java
@RequestMapping("/exportJobs") @ResponseBody//ww w. j a va 2 s . co m public String exportJobs(@RequestParam(required = true) String jobJsons) { ResultBody<Boolean> result = new ResultBody<Boolean>(); try { String fileName = "export_" + System.currentTimeMillis() + ".txt"; File file = new File(fileName); FileWriter fw = new FileWriter(file, false); fw.write(jobJsons); fw.flush(); fw.close(); result.setCode(Code.OK, true); } catch (Exception e) { e.printStackTrace(); result.setCode(Code.F100); } return result.toJson(); }