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 FSCluster2CurveWrite() {
    try {/*from  w ww.  j  a v  a 2s . co m*/
        Logger.getRootLogger().debug("Writing PrecursorFragmentCorr serialization to file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS...");
        FileOutputStream fout = new FileOutputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS",
                false);
        FSTObjectOutput oos = new FSTObjectOutput(fout);
        oos.writeObject(FragmentsClu2Cur);
        oos.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
    }
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

private boolean FSCluster2CurveRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
            + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS").exists()) {
        return false;
    }//from  ww  w  . j a v  a  2  s.c  o m
    try {
        Logger.getRootLogger().debug("Reading PrecursorFragmentCorr serialization from file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS...");
        FileInputStream fileIn = new FileInputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        FragmentsClu2Cur = (HashMap<Integer, ArrayList<PrecursorFragmentPairEdge>>) in.readObject();
        in.close();
        fileIn.close();

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

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

private boolean JavaSerializationCluster2CurveRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
            + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.ser").exists()) {
        return false;
    }//  w w w.  j ava2  s. c  om
    try {
        Logger.getRootLogger().debug("Reading PrecursorFragmentCorr serialization from file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.ser...");
        FileInputStream fileIn = new FileInputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.ser");
        ObjectInputStream in = new ObjectInputStream(fileIn);
        FragmentsClu2Cur = (HashMap<Integer, ArrayList<PrecursorFragmentPairEdge>>) in.readObject();
        in.close();
        fileIn.close();

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

---

From source file:ddf.metrics.reporting.internal.rest.MetricsEndpoint.java

/**
 * Returns a list of all of the metrics' names based on the list of RRD files found in the
 * metrics directory.// w ww  . ja va2s . com
 *
 * @return
 */
private List<String> getMetricsNames() {
    String[] rrdFiles = getRrdFiles();
    List<String> metricNames = new ArrayList<String>();
    if (rrdFiles != null) {
        for (String rrdFile : rrdFiles) {
            String metricsName = FilenameUtils.getFullPath(rrdFile) + FilenameUtils.getBaseName(rrdFile);
            metricNames.add(metricsName);
        }
    }

    Collections.sort(metricNames);

    LOGGER.trace("Returning " + metricNames.size() + " metrics");

    return metricNames;
}

---

From source file:MSUmpire.DIA.DIAPack.java

public void SetPepXMLPath() {
    iProphPepXMLs = new ArrayList<String>();
    String PepXMLPath1 = FilenameUtils
            .separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ1Name() + ".pep.xml");
    String PepXMLPath2 = FilenameUtils
            .separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ2Name() + ".pep.xml");
    String PepXMLPath3 = FilenameUtils
            .separatorsToUnix(FilenameUtils.getFullPath(Filename) + "interact-" + GetQ3Name() + ".pep.xml");
    iProphPepXMLs.add(PepXMLPath1);//from  w  w  w .j av a2 s.  co  m
    iProphPepXMLs.add(PepXMLPath2);
    iProphPepXMLs.add(PepXMLPath3);
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

private void FSCluster2CurveUnfragWrite() {
    try {/*from w w w . ja v  a  2s.  co m*/
        Logger.getRootLogger().debug("Writing UnfragPrecursorFragCorr serialization to file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS...");
        FileOutputStream fout = new FileOutputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS",
                false);
        FSTObjectOutput oos = new FSTObjectOutput(fout);
        oos.writeObject(UnFragIonClu2Cur);
        oos.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
    }
}

---

From source file:MSUmpire.DIA.DIAPack.java

public void ParsePepXML(DBSearchParam searchPara, LCMSID refID) throws ParserConfigurationException,
        SAXException, IOException, XmlPullParserException, ClassNotFoundException, InterruptedException {

    SetPepXMLPath();/*w w  w  . ja  v a2s  . c om*/
    IDsummary = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),
            searchPara.DecoyPrefix, searchPara.FastaPath);
    for (String pepxml : iProphPepXMLs) {
        LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename),
                searchPara.DecoyPrefix, searchPara.FastaPath);
        PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f);
        if (refID == null) {
            pepxmlid.FilterByPepDecoyFDR(searchPara.DecoyPrefix, searchPara.PepFDR);
        }
        Logger.getRootLogger().info("No. of peptide ions:" + pepxmlid.GetPepIonList().size()
                + "; Peptide level threshold: " + pepxmlid.PepProbThreshold);
        for (PepIonID pepID : pepxmlid.GetPepIonList().values()) {
            if (refID != null) {
                if (refID.GetPepIonList().containsKey(pepID.GetKey())) {
                    IDsummary.AddPeptideID(pepID);
                }
            } else {
                IDsummary.AddPeptideID(pepID);
            }
        }
    }
    IDsummary.ReMapProPep();
    Logger.getRootLogger().info("Total number of peptide ions:" + IDsummary.GetPepIonList().size());
    CheckPSMRT();
    if (MS1FeatureMap != null) {
        this.MS1FeatureMap.IDsummary = IDsummary;
    }
}

---

From source file:MSUmpire.DIA.TargetMatchScoring.java

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

    if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID
            + "_LibMatch.serFS").exists()) {
        return null;
    }//from w ww.  ja  va2 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.serFS...");
        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename)
                + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        match = (TargetMatchScoring) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return null;
    }
    return match;
}

---

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

private boolean FSCluster2CurveUnfragRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
            + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS").exists()) {
        return false;
    }/*from  w  w  w  . java 2 s.  c o  m*/
    try {
        Logger.getRootLogger().debug("Reading UnfragPrecursorFragCorr serialization from file:"
                + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS...");
        FileInputStream fileIn = new FileInputStream(
                FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName)
                        + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS");
        FSTObjectInput in = new FSTObjectInput(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;
}

---

From source file:edu.cornell.med.icb.learning.CrossValidation.java

/**
 * Report the area under the Receiver Operating Characteristic (ROC) curve. Estimates are
 * done with a leave one out evaluation.
 *
 * @param decisionValues   Decision values output by classifier. Larger values indicate more
 *                         confidence in prediction of a positive label.
 * @param labels           Correct label for item, can be 0 (negative class) or +1 (positive class).
 * @param rocCurvefilename Name of the file to plot the pdf image to
 *///  www.j av  a 2 s .  c o m
public static void plotRocCurveLOO(final double[] decisionValues, final double[] labels,
        final String rocCurvefilename) {
    assert decisionValues.length == labels.length : "number of predictions must match number of labels.";
    for (int i = 0; i < labels.length; i++) { // for each training example, leave it out:
        if (decisionValues[i] < 0) {
            decisionValues[i] = 0;
        }
        if (labels[i] < 0) {
            labels[i] = 0;
        }
    }

    // R server only understands unix style path. Convert windows to unix if needed:
    final String plotFilename = FilenameUtils.separatorsToUnix(rocCurvefilename);
    final File plotFile = new File(plotFilename);

    final RConnectionPool connectionPool = RConnectionPool.getInstance();
    RConnection connection = null;

    // CALL R ROC
    try {
        if (plotFile.exists()) {
            plotFile.delete();
        }

        connection = connectionPool.borrowConnection();
        connection.assign("predictions", decisionValues);
        connection.assign("labels", labels);
        final String cmd = " library(ROCR) \n" + "pred.svm <- prediction(predictions, labels)\n" + "pdf(\""
                + plotFilename + "\", height=5, width=5)\n"
                + "perf <- performance(pred.svm, measure = \"tpr\", x.measure = \"fpr\")\n" + "plot(perf)\n"
                + "dev.off()";

        final REXP expression = connection.eval(cmd); // attr(perf.rocOutAUC,"y.values")[[1]]
        final double valueROC_AUC = expression.asDouble();
        // System.out.println("result from R: " + valueROC_AUC);
    } catch (Exception e) {
        // connection error or otherwise
        LOG.warn("Cannot plot ROC curve to " + plotFilename + ".  Make sure Rserve (R server) "
                + "is configured and running and the owner of the Rserve process has permission "
                + "to write to the directory \"" + FilenameUtils.getFullPath(plotFile.getAbsolutePath()) + "\"",
                e);
    } finally {
        if (connection != null) {
            connectionPool.returnConnection(connection);
        }
    }
}

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