List of usage examples for org.apache.commons.io FilenameUtils getBaseName
public static String getBaseName(String filename)
From source file:com.bt.download.android.gui.transfers.YouTubeDownload.java
private static File buildFile(File savePath, String name) { String baseName = FilenameUtils.getBaseName(name); String ext = FilenameUtils.getExtension(name); File f = new File(savePath, name); int i = 1;//from w w w.j a v a 2 s.c om while (f.exists() && i < Integer.MAX_VALUE) { f = new File(savePath, baseName + " (" + i + ")." + ext); i++; } return f; }
From source file:edu.cornell.med.icb.goby.algorithmic.algorithm.ExportSplicingEvents.java
public void process(final String filename) throws IOException { final AlignmentReader reader = new AlignmentReaderImpl(filename); reader.readHeader();/*w w w . j ava 2s . c om*/ final IndexedIdentifier targetIds = reader.getTargetIdentifiers(); reverseIds = new DoubleIndexedIdentifier(targetIds); sampleFilename = FilenameUtils.getBaseName(filename); lastTargetIndex = -1; for (final Alignments.AlignmentEntry entry : reader) { processEntry(eventMap, entry); } flushPreviousRef(null, eventMap); output.flush(); }
From source file:MSUmpire.DIA.RTAlignedPepIonMapping.java
public void GenerateModel() throws IOException { XYPointCollection points = new XYPointCollection(); XYSeries series = new XYSeries("Peptide ions"); XYSeriesCollection xySeriesCollection = new XYSeriesCollection(); for (PepIonID pepA : LCMSA.GetPepIonList().values()) { if (LCMSB.GetPepIonList().containsKey(pepA.GetKey())) { PepIonID pepB = LCMSB.GetPepIonList().get(pepA.GetKey()); points.AddPoint(pepA.GetRT(), pepB.GetRT()); series.add(new XYDataItem(pepA.GetRT(), pepB.GetRT())); }//from ww w . jav a 2s . c om } regression = new PiecewiseRegression(parameter.MaxCurveRTRange, parameter.MaxCurveRTRange); regression.SetData(points); float R2 = regression.GetR2(); Logger.getRootLogger() .info("Retention time prediction model:(" + FilenameUtils.getBaseName(LCMSA.mzXMLFileName) + "-" + FilenameUtils.getBaseName(LCMSB.mzXMLFileName) + ")..R2=" + R2 + "(No. of commonly identified peptide ions=" + points.PointCount() + ")"); GenerateRTMapPNG(xySeriesCollection, series, R2); }
From source file:androidGLUESigner.pdf.PDFSigner.java
/** * signs a PDF file/*from ww w . j av a 2 s . co m*/ * @param signInformation holds the reason, location, inputfilepath, ... * @param withTSA flag to decide if online TimeStamp should be received * @return the signed PDF File * @throws Exception */ public File signPDF(SignatureInfo signInformation, boolean withTSA) throws Exception { // input, temp and output PDF-files final String ORIGINAL = signInformation.getInputFilePath(); final String TMP = signInformation.getInputFilePath() + ".tmp"; final String RESULT; if (sigPath.equals("")) { RESULT = signInformation.getInputFilePath().split("\\.")[0] + SIGNED_SUFFIX; } else { RESULT = (sigPath + "/" + FilenameUtils.getBaseName(signInformation.getInputFilePath())) + SIGNED_SUFFIX; } // get the certificate-chain from the selected connection chain = connection.getCertificateChain(); // initiate the Signer with the certificates and signature info PDFSignerEngine signer = new PDFSignerEngine(); signer.setCertificateChain(chain); signer.setSiginfo(signInformation); if (withTSA) { // prepare the signature and get the digest byte[] digest = signer.prepareSign(new FileInputStream(ORIGINAL), new FileOutputStream(TMP)); byte[] state = signer.getState(); // sign the digest via connection byte[] signedHash = connection.sign(digest); // finalize the siganture by adding the signedHash into the signature PDFSignerEngine signer2 = new PDFSignerEngine(); signer2.setTsaUrl(this.tsaUrl); signer2.setState(state); signer2.finalizeSign(signedHash, new FileInputStream(TMP), new FileOutputStream(RESULT)); } else { signer.simpleSign(ORIGINAL, RESULT, connection); } //return null; return new File(RESULT); }
From source file:com.textocat.textokit.commons.io.axml.AXML2XMI.java
private File getOutputFile(File inputFile) { String baseName = FilenameUtils.getBaseName(inputFile.getPath()); return new File(outputDir, baseName + ".xmi"); }
From source file:ch.cyberduck.core.DownloadTransfer.java
@Override protected void normalize() { log.debug("normalize"); final List<Path> normalized = new Collection<Path>(); for (Path download : this.getRoots()) { if (!this.check()) { return; }/* ww w . j ava 2 s . co m*/ this.getSession().message( MessageFormat.format(Locale.localizedString("Prepare {0}", "Status"), download.getName())); boolean duplicate = false; for (Iterator<Path> iter = normalized.iterator(); iter.hasNext();) { Path n = iter.next(); if (download.isChild(n)) { // The selected file is a child of a directory already included duplicate = true; break; } if (n.isChild(download)) { iter.remove(); } if (download.getLocal().equals(n.getLocal())) { // The selected file has the same name; if downloaded as a root element // it would overwrite the earlier final String parent = download.getLocal().getParent().getAbsolute(); final String filename = download.getName(); String proposal; int no = 0; do { no++; proposal = FilenameUtils.getBaseName(filename) + "-" + no; if (StringUtils.isNotBlank(FilenameUtils.getExtension(filename))) { proposal += "." + FilenameUtils.getExtension(filename); } download.setLocal(LocalFactory.createLocal(parent, proposal)); } while (download.getLocal().exists()); if (log.isInfoEnabled()) { log.info("Changed local name to:" + download.getName()); } } } // Prunes the list of selected files. Files which are a child of an already included directory // are removed from the returned list. if (!duplicate) { normalized.add(download); } } this.setRoots(normalized); }
From source file:com.frostwire.search.tbp.TPBSearchResult.java
public TPBSearchResult(String domainName, SearchMatcher matcher) { /*/*from w w w .jav a2s. c om*/ * Matcher groups cheatsheet * 1 -> Category (useless) * 2 -> Torrent Details Page * 3 -> Title/Name * 4 -> .torrent URL * 5 -> infoHash * 6 -> MM-DD YYYY or Today HH:MM or Y-day HH:MM * 7 -> SIZE (B|KiB|MiBGiB) * 8 -> seeds */ this.detailsUrl = matcher.group(2); this.domainName = domainName; String temp = HtmlManipulator.replaceHtmlEntities(matcher.group(3)); temp = HtmlManipulator.replaceHtmlEntities(temp); // because of input this.filename = buildFilename(temp); this.displayName = FilenameUtils.getBaseName(filename); this.torrentUrl = matcher.group(4); //let's assign the magnet to this for now. this.infoHash = torrentUrl.substring(20, 60); this.creationTime = parseCreationTime(matcher.group(5)); this.size = parseSize(matcher.group(6)); this.seeds = parseSeeds(matcher.group(7)); }
From source file:MSUmpire.DIA.TargetHitPepXMLWriter.java
public void write() throws IOException, XmlPullParserException { Logger.getRootLogger().info("Writing " + Filename); int minlength = Integer.MAX_VALUE; int maxlength = 0; int maxmiss = 0; for (UmpireSpecLibMatch match : Tscoring.libTargetMatches) { PepIonID pepIonID = match.pepIonID; if (pepIonID.Sequence.length() > maxlength) { maxlength = pepIonID.Sequence.length(); }//from w w w . j av a 2 s . c o m if (pepIonID.Sequence.length() < minlength) { minlength = pepIonID.Sequence.length(); } if (pepIonID.getNMissedCleavages() > maxmiss) { maxmiss = pepIonID.getNMissedCleavages(); } } FastaParser fastaparser = new FastaParser(Fasta); fastaparser.RemoveDecoy(Decoytag); //FastaParser_V2 fastaparser = FastaParser.FasterSerialzationRead(Fasta); fastaparser.digestion(maxmiss, minlength, maxlength, Decoytag); Header(); sb.append("<msms_run_summary base_name=\"" + FilenameUtils.getBaseName(Filename) + "\" search_engine=\"interprophet\" >\n"); SearchSummary(); int index = 0; for (UmpireSpecLibMatch match : Tscoring.libTargetMatches) { //<editor-fold defaultstate="collapsed" desc="Forward hit"> PeakGroupScore bestscore = match.BestHit; String Sequence = match.pepIonID.Sequence; if (bestscore != null) { ArrayList<ParentProtein> parentprots = new ArrayList<>(); if (!fastaparser.PeptideList.containsKey(Sequence)) { //Logger.getRootLogger().warn(Sequence + " is not found as tryptic peptides in " + Fasta + ". Searching in protein sequences.."); for (String acc : fastaparser.ProteinList.keySet()) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(Sequence) + Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } else { for (String acc : fastaparser.PeptideList.get(Sequence).Proteins) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(Sequence) + Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } if (parentprots.isEmpty()) { Logger.getRootLogger().warn(Sequence + " is not found in " + Fasta); } else { sb.append("<spectrum_query spectrum=\"" + FilenameUtils.getBaseName(Filename) + "." + index + "." + index + "." + match.pepIonID.Charge + "\" start_scan=\"" + index + "\" end_scan=\"" + index + "\" precursor_neutral_mass=\"" + bestscore.PrecursorNeutralMass + "\" assumed_charge=\"" + match.pepIonID.Charge + "\" index=\"" + (index++) + "\" retention_time_sec=\"" + bestscore.PrecursorRT * 60f + "\">\n" + "<search_result>\n" + "<search_hit hit_rank=\"1\" peptide=\"" + 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=\"" + (bestscore.NoMatchB + bestscore.NoMatchY) + "\" tot_num_ions=\"" + 2 * (Sequence.length() - 1) + "\" calc_neutral_pep_mass=\"" + match.pepIonID.CalcNeutralPepMass() + "\" massdiff=\"" + (match.pepIonID.CalcNeutralPepMass() - bestscore.PrecursorNeutralMass) + "\" num_tol_term=\"2\" num_missed_cleavages=\"" + match.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=\"" + bestscore.MixtureModelLocalProb + "\" all_ntt_prob=\"(" + bestscore.MixtureModelLocalProb + "," + bestscore.MixtureModelLocalProb + "," + bestscore.MixtureModelLocalProb + ")\">\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"); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Decoy hit"> bestscore = match.BestDecoyHit; if (!fastaparser.PeptideList.containsKey(Sequence)) { continue; } String DecoySeq = fastaparser.PeptideList.get(Sequence).Decoy; if (bestscore != null) { ArrayList<ParentProtein> parentprots = new ArrayList<>(); if (!fastaparser.PeptideList.containsKey(Sequence)) { //Logger.getRootLogger().warn(Sequence + " is not found as tryptic peptides in " + Fasta + ". Searching in protein sequences.."); for (String acc : fastaparser.ProteinList.keySet()) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(Sequence) + Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } else { for (String acc : fastaparser.PeptideList.get(Sequence).Proteins) { String ProtSeq = fastaparser.ProteinList.get(acc).Seq; if (ProtSeq.contains(Sequence)) { ParentProtein prot = new ParentProtein(); prot.Acc = acc; prot.Des = fastaparser.ProteinList.get(acc).Des; int aaindex = ProtSeq.indexOf(Sequence) - 1; if (aaindex >= 0) { prot.PreAA = ProtSeq.charAt(aaindex); } aaindex = ProtSeq.indexOf(Sequence) + Sequence.length(); if (aaindex < ProtSeq.length()) { prot.NextAA = ProtSeq.charAt(aaindex); } parentprots.add(prot); } } } if (parentprots.isEmpty()) { Logger.getRootLogger().warn(Sequence + " is not found in " + Fasta); } else { sb.append("<spectrum_query spectrum=\"" + Decoytag + "_" + Sequence + "\" precursor_neutral_mass=\"" + bestscore.PrecursorNeutralMass + "\" assumed_charge=\"" + match.pepIonID.Charge + "\" index=\"" + (index++) + "\" retention_time_sec=\"" + bestscore.PrecursorRT * 60f + "\">\n" + "<search_result>\n" + "<search_hit hit_rank=\"1\" peptide=\"" + DecoySeq + "\" peptide_prev_aa=\"" + parentprots.get(0).PreAA + "\" peptide_next_aa=\"" + parentprots.get(0).NextAA + "\" protein=\"" + Decoytag + "_" + parentprots.get(0).Acc + "\" protein_descr=\"" + Decoytag + "_" + parentprots.get(0).Des + "\" num_tot_proteins=\"" + parentprots.size() + "\" num_matched_ions=\"" + (bestscore.NoMatchB + bestscore.NoMatchY) + "\" tot_num_ions=\"" + 2 * (Sequence.length() - 1) + "\" calc_neutral_pep_mass=\"" + match.pepIonID.CalcNeutralPepMass() + "\" massdiff=\"" + (match.pepIonID.CalcNeutralPepMass() - bestscore.PrecursorNeutralMass) + "\" num_missed_cleavages=\"" + match.pepIonID.getNMissedCleavages() + "\" is_rejected=\"0\">\n"); for (int i = 1; i < parentprots.size(); i++) { sb.append("<alternative_protein protein=\"" + Decoytag + "_" + parentprots.get(i).Acc + "\" protein_descr=\"" + Decoytag + "_" + 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=\"" + bestscore.MixtureModelLocalProb + "\" all_ntt_prob=\"(" + bestscore.MixtureModelLocalProb + "," + bestscore.MixtureModelLocalProb + "," + bestscore.MixtureModelLocalProb + ")\">\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"); } } //</editor-fold> } 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:ch.mlutz.plugins.t4e.tapestry.element.TapestryHtmlElement.java
public String getPath() { StringBuilder sb = new StringBuilder(); IContainer webAppFolder = parent.getWebappFolder(); IContainer currentContainer = htmlFile.getParent(); while (!currentContainer.equals(webAppFolder)) { if (sb.length() > 0) { sb.insert(0, "/"); }//from w w w .j a v a 2 s. c o m sb.insert(0, currentContainer.getName()); currentContainer = currentContainer.getParent(); } if (sb.length() > 0) { sb.append("/"); } sb.append(FilenameUtils.getBaseName(htmlFile.getName())); return sb.toString(); }
From source file:it.geosolutions.geobatch.destination.action.datamigration.RasterMigrationAction.java
@Override public Queue<EventObject> execute(Queue<EventObject> events) throws ActionException { listenerForwarder.setTask("Check configuration"); checkConfiguration();// www. ja v a 2 s. c o m // Creation of a List containing the event objects final LinkedList<EventObject> ret = new LinkedList<EventObject>(); try { // Start of the operations listenerForwarder.started(); // Until the events are present, the input files are elaborated while (!events.isEmpty()) { // Each event is polled from the list EventObject event = events.poll(); if (event instanceof FileSystemEvent) { FileSystemEvent fse = (FileSystemEvent) event; File file = fse.getSource(); // Copy doProcess(FilenameUtils.getBaseName(file.getName())); } // pass the feature config to the next action ret.add(new FileSystemEvent(((FileSystemEvent) event).getSource(), FileSystemEventType.FILE_ADDED)); } listenerForwarder.completed(); return ret; } catch (Exception t) { listenerForwarder.failed(t); throw new ActionException(this, t.getMessage(), t); } }