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.LCMSPeakStructure.LCMSPeakDIAMS2.java

private void PrepareMGF_UnfragmentIon() throws IOException {
    String mgffile4 = FilenameUtils.getFullPath(ParentmzXMLName) + GetQ3Name() + ".mgf.temp";
    //        FileWriter mgfWriter4 = new FileWriter(mgffile4, true);
    final BufferedWriter mgfWriter4 = DIAPack.get_file(DIAPack.OutputFile.Mgf_Q3, mgffile4);

    //        FileWriter mapwriter3 = new FileWriter(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + ".ScanClusterMapping_Q3", true);
    final BufferedWriter mapwriter3 = DIAPack.get_file(DIAPack.OutputFile.ScanClusterMapping_Q3,
            FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                    + ".ScanClusterMapping_Q3");

    ArrayList<PseudoMSMSProcessing> ScanList = new ArrayList<>();
    ExecutorService executorPool = Executors.newFixedThreadPool(NoCPUs);
    for (PeakCluster ms2cluster : PeakClusters) {
        ArrayList<PrecursorFragmentPairEdge> frags = UnFragIonClu2Cur.get(ms2cluster.Index);
        if (frags != null && DIA_MZ_Range.getX() <= ms2cluster.TargetMz()
                && DIA_MZ_Range.getY() >= ms2cluster.TargetMz()) {
            //            if (DIA_MZ_Range.getX() <= ms2cluster.TargetMz() && DIA_MZ_Range.getY() >= ms2cluster.TargetMz() && UnFragIonClu2Cur.containsKey(ms2cluster.Index)) {
            //                ArrayList<PrecursorFragmentPairEdge> frags = UnFragIonClu2Cur.get(ms2cluster.Index);
            ms2cluster.GroupedFragmentPeaks.addAll(frags);
            PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms2cluster, parameter);
            executorPool.execute(mSMSProcessing);
            ScanList.add(mSMSProcessing);
        }/*  ww w.j  av  a2  s .  c o  m*/
    }
    executorPool.shutdown();
    try {
        executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
    } catch (InterruptedException e) {
        Logger.getRootLogger().info("interrupted..");
    }

    for (PseudoMSMSProcessing mSMSProcessing : ScanList) {
        if (MatchedFragmentMap.size() > 0) {
            mSMSProcessing.RemoveMatchedFrag(MatchedFragmentMap);
        }
        XYPointCollection Scan = mSMSProcessing.GetScan();

        if (Scan != null && Scan.PointCount() > parameter.MinFrag) {
            parentDIA.Q3Scan++;
            //                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=").append(GetQ3Name()).append(".").append(parentDIA.Q3Scan).append(".").append(parentDIA.Q3Scan).append(".").append(mSMSProcessing.Precursorcluster.Charge).append("\n");
            //                //mgfString.append("TITLE=" + WindowID + ";ClusterIndex:" + mSMSProcessing.ms2cluster.Index + "\n");
            //                //mgfString.append("TITLE=" GetQ3Name() + WindowID + ";ClusterIndex:" + mSMSProcessing.ms2cluster.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");
            //                mgfWriter4.write(mgfString.toString());

            mgfWriter4.append("BEGIN IONS\n")
                    .append("PEPMASS=" + mSMSProcessing.Precursorcluster.TargetMz() + "\n")
                    .append("CHARGE=" + mSMSProcessing.Precursorcluster.Charge + "+\n")
                    .append("RTINSECONDS=" + mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f + "\n")
                    .append("TITLE=").append(GetQ3Name()).append(".").append(Integer.toString(parentDIA.Q3Scan))
                    .append(".").append(Integer.toString(parentDIA.Q3Scan)).append(".")
                    .append(Integer.toString(mSMSProcessing.Precursorcluster.Charge)).append("\n");
            //mgfWriter4.append("TITLE=" + WindowID + ";ClusterIndex:" + mSMSProcessing.ms2cluster.Index + "\n");
            //mgfWriter4.append("TITLE=" GetQ3Name() + WindowID + ";ClusterIndex:" + mSMSProcessing.ms2cluster.Index + "\n");

            for (int i = 0; i < Scan.PointCount(); i++) {
                mgfWriter4.append(Float.toString(Scan.Data.get(i).getX())).append(" ")
                        .append(Float.toString(Scan.Data.get(i).getY())).append("\n");
            }
            mgfWriter4.append("END IONS\n\n");

            mapwriter3.write(
                    parentDIA.Q3Scan + ";" + WindowID + ";" + mSMSProcessing.Precursorcluster.Index + "\n");
        }
        mSMSProcessing.Precursorcluster.GroupedFragmentPeaks.clear();
    }
    //        mgfWriter4.close();
    //        mapwriter3.close();
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakBase.java

private void JavaSerializationPeakClusterWrite() {
    try {//  w  w  w  .  j ava  2s . co m
        Logger.getRootLogger().info("Writing PeakCluster serialization to file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.ser...");
        FileOutputStream fout = new FileOutputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.ser",
                false);
        ObjectOutputStream oos = new ObjectOutputStream(fout);
        oos.writeObject(PeakClusters);
        oos.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
    }
}

---

From source file:com.google.gdt.eclipse.designer.hosted.tdt.HostedModeSupport.java

/**
 * @return the {@link ClassLoader} for accessing gwt-dev classes mixed with design-time support
 *         lib.// w  ww .ja  v a 2s  . co m
 */
private ClassLoader getDevClassLoader0() throws Exception {
    // prepare gwt-dev.jar location
    String devLibLocation = Utils.getDevLibLocation(moduleDescription);
    if (devLibLocation == null) {
        throw new HostedModeException(HostedModeException.NO_DEV_LIB);
    }
    String gwtLocation = FilenameUtils.getFullPath(devLibLocation);
    // add 'dev' & 'dev-designtime'
    ClassLoader devClassLoader = devClassLoaders.get(gwtLocation);
    if (devClassLoader == null) {
        URL resolvedDevLibUrl = new File(devLibLocation).toURI().toURL();
        Bundle bundle = Activator.getDefault().getBundle();
        URL devDesignUrl = FileLocator.resolve(bundle.getEntry("/gwt-dev-designtime.jar"));
        if (devDesignUrl != null) {
            // workaround for Issue 258 (https://code.google.com/p/google-plugin-for-eclipse/issues/detail?id=258)
            devDesignUrl = new URL(StringUtils.replace(devDesignUrl.toString(), " ", "%20"));
        }
        devClassLoader = new URLClassLoader(new URL[] { devDesignUrl, resolvedDevLibUrl }, null);
        devClassLoaders.put(gwtLocation, devClassLoader);
    }
    return devClassLoader;
}

---

From source file:MSUmpire.DIA.DIAPack.java

public String GetiProphExtPepxml(String tag) {
    return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename)
            + FilenameUtils.getBaseName(Filename) + "_" + tag + ".iproph.pep.xml");
}

---

From source file:MSUmpire.PSMDataStructure.LCMSID.java

private void ExportPepPSMCSV(String folder) throws IOException {
    if (folder == null | "".equals(folder)) {
        folder = FilenameUtils.getFullPath(mzXMLFileName);
    }//from w  w  w  .  j  a  v  a 2  s  .  c o m
    Logger.getRootLogger().info(
            "Writing PSM result to file:" + folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PSMs.csv...");
    FileWriter writer = new FileWriter(folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PSMs.csv");
    writer.write(
            "SpecID,Sequence,ModSeq,TPPModSeq,Modification,Charge,mz,NeutralPepMass,ObservedMass,RT,AdjustedRT,Rank,ScanNo,PreAA,NextAA,MissedCleavage,ExpectValue,MassError,Prob,Rawname,ParentPepIndex,MS1Quant\n");
    for (PepIonID pepion : PepIonList.values()) {
        for (PSM psm : pepion.GetPSMList()) {
            writer.write(psm.SpecNumber + "," + psm.Sequence + "," + psm.ModSeq + "," + psm.TPPModSeq + ","
                    + psm.GetModificationString() + "," + psm.Charge + "," + psm.ObserPrecursorMz() + ","
                    + psm.NeutralPepMass + "," + psm.ObserPrecursorMass + "," + psm.RetentionTime + ","
                    + psm.NeighborMaxRetentionTime + "," + psm.Rank + "," + psm.ScanNo + "," + psm.PreAA + ","
                    + psm.NextAA + "," + psm.MissedCleavage + "," + psm.expect + "," + psm.MassError + ","
                    + psm.Probability + "," + psm.RawDataName + "," + pepion.Index + "," + pepion.GetMS1()
                    + "\n");
        }
    }
    writer.close();
}

---

From source file:it.geosolutions.geobatch.task.TaskExecutor.java

private String setScriptArguments(final String defaultScriptPath, final String inputFilePath, String outputName,
        final File outXmlFile) throws IOException {
    String destFilePath = null;/*from  ww w.  j a v  a2s. c o m*/
    boolean overwriteOutput = false;
    if (outputName != null && outputName.trim().length() > 0) {
        overwriteOutput = true;
        if (outputName.startsWith("*.")) {
            final String outputExt = outputName.substring(2, outputName.length());
            destFilePath = new StringBuilder(FilenameUtils.getFullPath(inputFilePath)).append(File.separator)
                    .append(FilenameUtils.getBaseName(inputFilePath)).append(".").append(outputExt).toString();
        } else {
            destFilePath = new StringBuilder(FilenameUtils.getFullPath(inputFilePath)).append(File.separator)
                    .append(FilenameUtils.getBaseName(inputFilePath)).append(".").append(outputName).toString();
        }
    }

    // Create FileReader Object
    FileReader inputFileReader = new FileReader(defaultScriptPath);
    FileWriter outputFileWriter = new FileWriter(outXmlFile);

    try {

        // Create Buffered/PrintWriter Objects
        BufferedReader inputStream = new BufferedReader(inputFileReader);
        PrintWriter outputStream = new PrintWriter(outputFileWriter);

        String inLine = null;
        boolean sourcePresent = false;
        boolean destinationPresent = false;

        while ((inLine = inputStream.readLine()) != null) {
            // Handle KeyWords

            if (inLine.trim().startsWith(SOURCE_TAG_OPEN)) {
                if (inLine.trim().endsWith(SOURCE_TAG_CLOSE)) {
                    // source file specified on the same line
                    inLine = new StringBuilder(SOURCE_TAG_OPEN).append(inputFilePath).append(SOURCE_TAG_CLOSE)
                            .toString();
                } else {
                    while ((inLine = inputStream.readLine()) != null) {
                        if (inLine.trim().endsWith(SOURCE_TAG_CLOSE)) {
                            // source file specified on different lines
                            inLine = new StringBuilder(SOURCE_TAG_OPEN).append(inputFilePath)
                                    .append(SOURCE_TAG_CLOSE).toString();
                        }
                    }
                }
                sourcePresent = true;
            }

            if (inLine.trim().startsWith(DESTINATION_TAG_OPEN)) {
                if (inLine.trim().endsWith(DESTINATION_TAG_CLOSE)) {
                    // source file specified on the same line
                    if (overwriteOutput) {
                        inLine = new StringBuilder(DESTINATION_TAG_OPEN).append(destFilePath)
                                .append(DESTINATION_TAG_CLOSE).toString();
                    } else {
                        final int start = inLine.indexOf(DESTINATION_TAG_OPEN);
                        final int end = inLine.indexOf(DESTINATION_TAG_CLOSE, start + 1);
                        destFilePath = inLine.substring(start + DESTINATION_TAG_OPEN.length(), end);
                    }

                } else {
                    while ((inLine = inputStream.readLine()) != null) {
                        if (overwriteOutput) {
                            if (inLine.trim().endsWith(DESTINATION_TAG_CLOSE)) {
                                // source file specified on different lines
                                inLine = new StringBuilder(DESTINATION_TAG_OPEN).append(destFilePath)
                                        .append(DESTINATION_TAG_CLOSE).toString();
                            }
                        } else {
                            String newLine = inLine.trim();
                            if (newLine.trim().endsWith(DESTINATION_TAG_CLOSE)) {
                                // source file specified on different lines
                                if (!newLine.trim().startsWith(DESTINATION_TAG_CLOSE)) {
                                    destFilePath = newLine.substring(0, newLine.indexOf(DESTINATION_TAG_CLOSE));
                                }
                            } else {
                                if (newLine.length() > 0) {
                                    destFilePath = newLine;
                                }
                            }
                        }
                    }
                }
                destinationPresent = true;
            }

            outputStream.println(inLine);
        }

        if (sourcePresent && !destinationPresent) {
            destFilePath = inputFilePath;
        }

    } catch (IOException e) {
    } finally {
        try {
            inputFileReader.close();
        } catch (IOException e) {

        }
        try {
            outputFileWriter.close();
        } catch (IOException e) {

        }
    }

    return destFilePath;
}

---

From source file:MSUmpire.DIA.DIAPack.java

public String GetQ1Pepxml() {
    return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-"
            + FilenameUtils.getBaseName(GetQ1Name()) + ".pep.xml");
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakMS1.java

public void GenerateMassCalibrationRTMap() throws IOException {
    String pngfile = FilenameUtils.getFullPath(ScanCollectionName) + "/"
            + FilenameUtils.getBaseName(ScanCollectionName) + "_masscaliRT.png";
    XYSeries series = new XYSeries("PSM");
    XYSeriesCollection xySeriesCollection = new XYSeriesCollection();
    LoessInterpolator loessInterpolator = new LoessInterpolator(0.75, //bandwidth,
            2//robustnessIters
    );//from ww  w.j  a v  a  2s  .  c  om

    for (PSM psm : this.IDsummary.PSMList.values()) {
        float ppm = InstrumentParameter.CalcSignedPPM(psm.ObserPrecursorMass, psm.NeutralPepMass);
        series.add(new XYDataItem(psm.RetentionTime, ppm));
    }
    double x[] = new double[IDsummary.PSMList.size()];
    double y[] = new double[x.length];
    double currentmin = 0f;
    for (int i = 0; i < series.getItemCount(); i++) {
        x[i] = (double) series.getX(i);
        if (x[i] <= currentmin) {
            x[i] = currentmin + 0.0001f;
        }
        currentmin = x[i];
        y[i] = (double) series.getY(i);
    }

    Masscalibrationfunction = loessInterpolator.interpolate(x, y);
    XYSeries smoothline = new XYSeries("Loess Regression");

    double xvalue = x[0];

    while (xvalue < x[x.length - 1]) {
        smoothline.add(xvalue, Masscalibrationfunction.value(xvalue));
        xvalue += 0.05d;
    }
    xySeriesCollection.addSeries(smoothline);
    xySeriesCollection.addSeries(series);

    JFreeChart chart = ChartFactory.createScatterPlot("Mass calibration", "RT", "Mass error (ppm)",
            xySeriesCollection, PlotOrientation.VERTICAL, true, true, false);
    XYPlot xyPlot = (XYPlot) chart.getPlot();
    xyPlot.setDomainCrosshairVisible(true);
    xyPlot.setRangeCrosshairVisible(true);

    XYItemRenderer renderer = xyPlot.getRenderer();
    renderer.setSeriesPaint(1, Color.blue);
    renderer.setSeriesPaint(0, Color.BLACK);
    renderer.setSeriesShape(1, new Ellipse2D.Double(0, 0, 3, 3));
    renderer.setSeriesStroke(1, new BasicStroke(1.0f));
    xyPlot.setBackgroundPaint(Color.white);
    ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600);
}

---

From source file:MSUmpire.DIA.DIAPack.java

public String GetQ2Pepxml() {
    return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-"
            + FilenameUtils.getBaseName(GetQ2Name()) + ".pep.xml");
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakBase.java

private boolean JavaSerializationPeakClusterRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
            + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.ser").exists()) {
        return false;
    }//from  www  .  jav  a  2 s.  co m
    try {
        Logger.getRootLogger().info("Reading PeakCluster serialization from file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.ser...");

        FileInputStream fileIn = new FileInputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.ser");
        ObjectInputStream in = new ObjectInputStream(fileIn);
        PeakClusters = (ArrayList<PeakCluster>) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}

---

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