Example usage for org.apache.commons.io FilenameUtils getFullPath

Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils getFullPath.

Prototype

public static String getFullPath(String filename) 

Source Link

Document

Gets the full path from a full filename, which is the prefix + path.

Usage

From source file:MSUmpire.DIA.DIAPack.java

private String GetSkylineFolder() {
    return FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_Skyline/";
}

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From source file:MSUmpire.DIA.TargetMatchScoring.java

public static TargetMatchScoring LibraryMatchReadJS(String Filename, String LibID)
        throws FileNotFoundException {

    if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID
            + "_LibMatch.serFS").exists()) {
        return null;
    }//from ww  w  .  jav a2  s .c  om
    TargetMatchScoring match = null;
    try {
        Logger.getRootLogger()
                .info("Loading Target library match results to file:" + FilenameUtils.getFullPath(Filename)
                        + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser...");
        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename)
                + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser");
        ObjectInputStream in = new ObjectInputStream(fileIn);
        match = (TargetMatchScoring) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return null;
    }
    return match;
}

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From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

private boolean JavaSerializationCluster2CurveUnfragRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
            + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.ser").exists()) {
        return false;
    }/*from  w w w. j  a  va2 s . co m*/
    try {
        Logger.getRootLogger().debug("Reading UnfragPrecursorFragCorr serialization from file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.ser...");
        FileInputStream fileIn = new FileInputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.ser");
        ObjectInputStream in = new ObjectInputStream(fileIn);
        UnFragIonClu2Cur = (HashMap<Integer, ArrayList<PrecursorFragmentPairEdge>>) in.readObject();
        in.close();
        fileIn.close();

    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}

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From source file:MSUmpire.DIA.TargetMatchScoring.java

public boolean LibraryMatchWriteJS() throws FileNotFoundException {
    try {/*w  w  w  .j a  va  2 s .  c  om*/
        Logger.getRootLogger()
                .info("Writing Target match results to file:" + FilenameUtils.getFullPath(Filename)
                        + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser...");
        FileOutputStream fout2 = new FileOutputStream(FilenameUtils.getFullPath(Filename)
                + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser", false);
        ObjectOutputStream oos = new ObjectOutputStream(fout2);
        oos.writeObject(this);
        oos.close();
        fout2.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}

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From source file:com.bekwam.resignator.ResignatorAppMainViewController.java

@FXML
public void browseSource() {
    if (logger.isDebugEnabled()) {
        logger.debug("[BROWSE SOURCE]");
    }/*from  w  w  w  .j  a v  a2s .  c  o m*/

    clearValidationErrors();

    switch (activeProfile.getArgsType()) {
    case JAR:
        FileChooser fileChooser = new FileChooser();
        fileChooser.setTitle("Select Source JAR");
        fileChooser.setInitialDirectory(new File(jarDir));
        fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("JAR", "*.jar"));

        File f = fileChooser.showOpenDialog(stage);
        if (f != null) {
            if (logger.isDebugEnabled()) {
                logger.debug("[BROWSE SOURCE] selected file={}", f.getAbsolutePath());
            }
            tfSourceFile.setText(f.getAbsolutePath());

            jarDir = FilenameUtils.getFullPath(f.getAbsolutePath());
        }
        break;
    case FOLDER:
        DirectoryChooser dirChooser = new DirectoryChooser();
        dirChooser.setTitle("Select Source Folder");
        dirChooser.setInitialDirectory(new File(jarDir));

        File d = dirChooser.showDialog(stage);
        if (d != null) {
            if (logger.isDebugEnabled()) {
                logger.debug("[BROWSE SOURCE] selected dir={}", d.getAbsolutePath());
            }
            tfSourceFile.setText(d.getAbsolutePath());

            jarDir = FilenameUtils.getFullPath(d.getAbsolutePath());
        }
        break;
    }
}

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From source file:MSUmpire.DIA.TargetMatchScoring.java

public boolean LibraryMatchWrite() throws FileNotFoundException {
    try {//from   w ww .  ja v  a2s  . c o  m
        Logger.getRootLogger()
                .info("Writing Target match results to file:" + FilenameUtils.getFullPath(Filename)
                        + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS...");
        FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(Filename)
                + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS", false);
        FSTObjectOutput out = new FSTObjectOutput(fout);
        out.writeObject(this);
        out.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}

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From source file:com.bekwam.resignator.ResignatorAppMainViewController.java

@FXML
public void browseTarget() {
    if (logger.isDebugEnabled()) {
        logger.debug("[BROWSE TARGET]");
    }//from   ww w  .j a va 2 s  . c o  m

    clearValidationErrors();

    switch (activeProfile.getArgsType()) {
    case JAR:
        FileChooser fileChooser = new FileChooser();
        fileChooser.setTitle("Select Target JAR");
        fileChooser.setInitialDirectory(new File(jarDir));
        fileChooser.getExtensionFilters().addAll(new FileChooser.ExtensionFilter("JAR", "*.jar"));

        File f = fileChooser.showOpenDialog(stage);
        if (f != null) {
            if (logger.isDebugEnabled()) {
                logger.debug("[BROWSE TARGET] selected file={}", f.getAbsolutePath());
            }
            tfTargetFile.setText(f.getAbsolutePath());

            jarDir = FilenameUtils.getFullPath(f.getAbsolutePath());
        }
        break;
    case FOLDER:
        DirectoryChooser dirChooser = new DirectoryChooser();
        dirChooser.setTitle("Select Target Folder");
        dirChooser.setInitialDirectory(new File(jarDir));

        File d = dirChooser.showDialog(stage);
        if (d != null) {
            if (logger.isDebugEnabled()) {
                logger.debug("[BROWSE TARGET] selected dir={}", d.getAbsolutePath());
            }
            tfTargetFile.setText(d.getAbsolutePath());

            jarDir = FilenameUtils.getFullPath(d.getAbsolutePath());
        }
        break;
    }
}

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From source file:MSUmpire.DIA.DIAPack.java

public void GenerateRawMGF() throws IOException, Exception {

    if (RawMGFExist()) {
        return;// w  w w . j  a v  a 2 s . c  o  m
    }
    Logger.getRootLogger().info("Extracting pseudo MS/MS spectra with raw intensity");
    HashMap<Integer, ArrayList<PseudoMSMSProcessing>> ScanList = new HashMap<>();
    HashMap<String, PseudoMSMSProcessing> UnfragScanList = new HashMap<>();
    parameter.BoostComplementaryIon = false;
    ExecutorService executorPool = Executors.newFixedThreadPool(NoCPUs);
    for (LCMSPeakDIAMS2 DIAwindow : DIAWindows) {
        DIAwindow.ReadPeakCluster();
        DIAwindow.ReadPrecursorFragmentClu2Cur();
        DIAwindow.BuildFragmentMS1ranking();
        DIAwindow.FilterByCriteria();
        DIAwindow.BuildFragmentUnfragranking();
        DIAwindow.FilterByCriteriaUnfrag();
        for (PeakCluster ms1cluster : MS1FeatureMap.PeakClusters) {
            if (DIAwindow.DIA_MZ_Range.getX() <= ms1cluster.GetMaxMz()
                    && DIAwindow.DIA_MZ_Range.getY() >= ms1cluster.TargetMz()
                    && DIAwindow.FragmentsClu2Cur.containsKey(ms1cluster.Index)) {
                DIAwindow.ExtractFragmentForPeakCluser(ms1cluster);
                if (DIAwindow.Last_MZ_Range == null || DIAwindow.Last_MZ_Range.getY() < ms1cluster.TargetMz()) {
                    PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms1cluster, parameter);
                    executorPool.execute(mSMSProcessing);
                    if (!ScanList.containsKey(ms1cluster.Index)) {
                        ScanList.put(ms1cluster.Index, new ArrayList<PseudoMSMSProcessing>());
                    }
                    ScanList.get(ms1cluster.Index).add(mSMSProcessing);
                }
            }
        }

        for (PeakCluster ms2cluster : DIAwindow.PeakClusters) {
            if (DIAwindow.DIA_MZ_Range.getX() <= ms2cluster.TargetMz()
                    && DIAwindow.DIA_MZ_Range.getY() >= ms2cluster.TargetMz()
                    && DIAwindow.UnFragIonClu2Cur.containsKey(ms2cluster.Index)) {
                DIAwindow.ExtractFragmentForUnfragPeakCluser(ms2cluster);
                PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms2cluster, parameter);
                executorPool.execute(mSMSProcessing);
                UnfragScanList.put(DIAwindow.WindowID + ";" + ms2cluster.Index, mSMSProcessing);
            }
        }
        DIAwindow.ClearAllPeaks();
        System.gc();
        Logger.getRootLogger()
                .info("(Memory usage:" + Math.round(
                        (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1048576)
                        + "MB)");
    }
    executorPool.shutdown();

    try {
        executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
    } catch (InterruptedException e) {
        Logger.getRootLogger().info("interrupted..");
    }
    ReadScanNoMapping();
    String mgffile = GetSkylineFolder() + GetForLibQ1Name() + ".mgf";
    FileWriter mgfWriter = new FileWriter(mgffile, false);

    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q1.keySet())) {
        int ClusterIndex = ScanClusterMap_Q1.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = null;
        for (PseudoMSMSProcessing MS2Processing : ScanList.get(ClusterIndex)) {
            mSMSProcessing = MS2Processing;
            for (PrecursorFragmentPairEdge fragmentClusterUnit : MS2Processing.fragments) {
                Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz,
                        fragmentClusterUnit.Intensity);
            }
        }
        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter.write(mgfString.toString());
    }
    mgfWriter.close();

    ////////////////////////////////////////////////////////////////////////////////
    String mgffile2 = GetSkylineFolder() + GetForLibQ2Name() + ".mgf";
    FileWriter mgfWriter2 = new FileWriter(mgffile2, false);

    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q2.keySet())) {
        int ClusterIndex = ScanClusterMap_Q2.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = null;
        for (PseudoMSMSProcessing MS2Processing : ScanList.get(ClusterIndex)) {
            mSMSProcessing = MS2Processing;
            for (PrecursorFragmentPairEdge fragmentClusterUnit : MS2Processing.fragments) {
                Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz,
                        fragmentClusterUnit.Intensity);
            }
        }
        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter2.write(mgfString.toString());
    }

    mgfWriter2.close();

    ////////////////////////////////
    String mgffile3 = GetSkylineFolder() + GetForLibQ3Name() + ".mgf";
    FileWriter mgfWriter3 = new FileWriter(mgffile3, false);
    mzXMLParser Q3mzxml = new mzXMLParser(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".mzXML",
            parameter, SpectralDataType.DataType.DDA, null, NoCPUs);
    Q3mzxml.GetAllScanCollectionByMSLabel(false, true, false, false);
    for (final int ScanNo : new java.util.TreeSet<>(ScanClusterMap_Q3.keySet())) {
        String key = ScanClusterMap_Q3.get(ScanNo);
        XYPointCollection Scan = new XYPointCollection();
        PseudoMSMSProcessing mSMSProcessing = UnfragScanList.get(key);

        for (PrecursorFragmentPairEdge fragmentClusterUnit : mSMSProcessing.fragments) {
            Scan.AddPointKeepMaxIfValueExisted(fragmentClusterUnit.FragmentMz, fragmentClusterUnit.Intensity);
        }

        StringBuilder mgfString = new StringBuilder();
        mgfString.append("BEGIN IONS\n");
        mgfString.append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n");
        mgfString.append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n");
        mgfString.append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n");
        mgfString.append("TITLE=ClusterIndex:" + mSMSProcessing.Precursorcluster.Index + "\n");
        for (int i = 0; i < Scan.PointCount(); i++) {
            mgfString.append(Scan.Data.get(i).getX()).append(" ").append(Scan.Data.get(i).getY()).append("\n");
        }
        mgfString.append("END IONS\n\n");
        mgfWriter3.write(mgfString.toString());
    }
    mgfWriter3.close();
}

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From source file:com.sonicle.webtop.vfs.VfsManager.java

private String doRenameStoreFile(int storeId, String path, String newName)
        throws FileSystemException, SQLException, DAOException, WTException {
    SharingLinkDAO dao = SharingLinkDAO.getInstance();
    FileObject tfo = null, ntfo = null;
    Connection con = null;// w  w  w .jav  a  2  s  .co m

    try {
        tfo = getTargetFileObject(storeId, path);
        String newPath = FilenameUtils
                .separatorsToUnix(FilenameUtils.concat(FilenameUtils.getFullPath(path), newName));
        ntfo = getTargetFileObject(storeId, newPath);

        logger.debug("Renaming store file [{}, {} -> {}]", storeId, path, newPath);
        try {
            con = WT.getConnection(SERVICE_ID, false);

            dao.deleteByStorePath(con, storeId, path);
            tfo.moveTo(ntfo);
            DbUtils.commitQuietly(con);

        } catch (FileSystemException ex1) {
            DbUtils.rollbackQuietly(con);
            throw ex1;
        } finally {
            DbUtils.closeQuietly(con);
        }
        return newPath;

    } finally {
        IOUtils.closeQuietly(tfo);
        IOUtils.closeQuietly(ntfo);
    }
}

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From source file:MSUmpire.DIA.DIAPack.java

private void FindPSMRT() {
    try {//from  w ww.  j av  a2 s.  c o m
        if (!new File(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".mzXML").exists()) {
            Logger.getRootLogger()
                    .warn(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".mzXML doesn't exsit.");
            return;
        }
        if (!new File(FilenameUtils.getFullPath(Filename) + GetQ2Name() + ".mzXML").exists()) {
            Logger.getRootLogger()
                    .warn(FilenameUtils.getFullPath(Filename) + GetQ2Name() + ".mzXML doesn't exsit.");
            return;
        }
        if (!new File(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".mzXML").exists()) {
            Logger.getRootLogger()
                    .warn(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".mzXML doesn't exsit.");
            return;
        }

        mzXMLParser mgfname1 = new mzXMLParser(FilenameUtils.getFullPath(Filename) + GetQ1Name() + ".mzXML",
                parameter, SpectralDataType.DataType.DDA, null, NoCPUs);
        mzXMLParser mgfname2 = new mzXMLParser(FilenameUtils.getFullPath(Filename) + GetQ2Name() + ".mzXML",
                parameter, SpectralDataType.DataType.DDA, null, NoCPUs);
        mzXMLParser mgfname3 = new mzXMLParser(FilenameUtils.getFullPath(Filename) + GetQ3Name() + ".mzXML",
                parameter, SpectralDataType.DataType.DDA, null, NoCPUs);
        HashMap<String, mzXMLParser> mgfs = new HashMap<>();
        mgfs.put(GetQ1Name(), mgfname1);
        mgfs.put(GetQ2Name(), mgfname2);
        mgfs.put(GetQ3Name(), mgfname3);
        for (PSM psm : IDsummary.PSMList.values()) {
            if (psm.RetentionTime == -1f) {
                psm.RetentionTime = mgfs.get(psm.GetRawNameString()).GetScanElutionTimeMap().get(psm.ScanNo);
                psm.NeighborMaxRetentionTime = psm.RetentionTime;
            }
        }
    } catch (Exception ex) {
        Logger.getRootLogger().warn("Exception trying to fill PSM RTs");
    }
}

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