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

List of usage examples for org.apache.commons.io FilenameUtils getBaseName

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Introduction

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

Prototype

public static String getBaseName(String filename)

Source Link

Document

Gets the base name, minus the full path and extension, from a full filename.

Usage

From source file:cu.uci.uengine.utils.RegexUtils.java

public static int getDataSetNumber(File file) throws InvalidDataSetNameException {
    String baseName = FilenameUtils.getBaseName(file.getName());

    Pattern p = Pattern.compile("\\d+$");//Digits at string end.

    Matcher m = p.matcher(baseName);
    if (!m.find()) {
        throw new InvalidDataSetNameException(String.format("DataSet %s is not a valid name.", baseName));
    }//from  w w  w . j  a va 2 s  . c o m

    int dataSetNumber = Integer.parseInt(m.group());

    return dataSetNumber;
}

From source file:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java

/**
 * @param args the command line arguments
 *///from  ww  w .j ava 2s .c  om
public static void main(String[] args) throws FileNotFoundException, IOException, Exception {
    System.out.println(
            "=================================================================================================");
    System.out.println("DIA-Umpire targeted re-extraction analysis using external library (version: "
            + UmpireInfo.GetInstance().Version + ")");
    if (args.length != 1) {
        System.out.println(
                "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params");
        return;
    }
    try {
        ConsoleLogger.SetConsoleLogger(Level.INFO);
        ConsoleLogger.SetFileLogger(Level.DEBUG,
                FilenameUtils.getFullPath(args[0]) + "diaumpire_extlibsearch.log");
    } catch (Exception e) {
    }

    Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version);
    Logger.getRootLogger().info("Parameter file:" + args[0]);

    BufferedReader reader = new BufferedReader(new FileReader(args[0]));
    String line = "";
    String WorkFolder = "";
    int NoCPUs = 2;

    String ExternalLibPath = "";
    String ExternalLibDecoyTag = "DECOY";

    float ExtProbThreshold = 0.99f;
    float RTWindow_Ext = -1f;

    TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600);
    HashMap<String, File> AssignFiles = new HashMap<>();

    //<editor-fold defaultstate="collapsed" desc="Reading parameter file">
    while ((line = reader.readLine()) != null) {
        line = line.trim();
        Logger.getRootLogger().info(line);
        if (!"".equals(line) && !line.startsWith("#")) {
            //System.out.println(line);
            if (line.equals("==File list begin")) {
                do {
                    line = reader.readLine();
                    line = line.trim();
                    if (line.equals("==File list end")) {
                        continue;
                    } else if (!"".equals(line)) {
                        File newfile = new File(line);
                        if (newfile.exists()) {
                            AssignFiles.put(newfile.getAbsolutePath(), newfile);
                        } else {
                            Logger.getRootLogger().info("File: " + newfile + " does not exist.");
                        }
                    }
                } while (!line.equals("==File list end"));
            }
            if (line.split("=").length < 2) {
                continue;
            }
            String type = line.split("=")[0].trim();
            String value = line.split("=")[1].trim();
            switch (type) {

            case "Path": {
                WorkFolder = value;
                break;
            }
            case "path": {
                WorkFolder = value;
                break;
            }
            case "Thread": {
                NoCPUs = Integer.parseInt(value);
                break;
            }
            case "Fasta": {
                tandemPara.FastaPath = value;
                break;
            }
            case "DecoyPrefix": {
                if (!"".equals(value)) {
                    tandemPara.DecoyPrefix = value;
                }
                break;
            }
            case "ExternalLibPath": {
                ExternalLibPath = value;
                break;
            }
            case "ExtProbThreshold": {
                ExtProbThreshold = Float.parseFloat(value);
                break;
            }
            case "RTWindow_Ext": {
                RTWindow_Ext = Float.parseFloat(value);
                break;
            }
            case "ExternalLibDecoyTag": {
                ExternalLibDecoyTag = value;
                if (ExternalLibDecoyTag.endsWith("_")) {
                    ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1);
                }
                break;
            }
            }
        }
    }
    //</editor-fold>

    //Initialize PTM manager using compomics library
    PTMManager.GetInstance();

    //Check if the fasta file can be found
    if (!new File(tandemPara.FastaPath).exists()) {
        Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath
                + " cannot be found, the process will be terminated, please check.");
        System.exit(1);
    }

    //Generate DIA file list
    ArrayList<DIAPack> FileList = new ArrayList<>();

    File folder = new File(WorkFolder);
    if (!folder.exists()) {
        Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found.");
        System.exit(1);
    }
    for (final File fileEntry : folder.listFiles()) {
        if (fileEntry.isFile()
                && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                        | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
            AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry);
        }
        if (fileEntry.isDirectory()) {
            for (final File fileEntry2 : fileEntry.listFiles()) {
                if (fileEntry2.isFile()
                        && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml")
                                | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml"))
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml")
                        && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) {
                    AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2);
                }
            }
        }
    }

    Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size());
    for (File fileEntry : AssignFiles.values()) {
        Logger.getRootLogger().info(fileEntry.getAbsolutePath());
    }

    for (File fileEntry : AssignFiles.values()) {
        String mzXMLFile = fileEntry.getAbsolutePath();
        if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) {
            DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs);
            Logger.getRootLogger().info(
                    "=================================================================================================");
            Logger.getRootLogger().info("Processing " + mzXMLFile);
            if (!DiaFile.LoadDIASetting()) {
                Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete");
                System.exit(1);
            }
            if (!DiaFile.LoadParams()) {
                Logger.getRootLogger().info("Loading parameters failed, job is incomplete");
                System.exit(1);
            }
            Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "....");

            //If the serialization file for ID file existed
            if (DiaFile.ReadSerializedLCMSID()) {
                DiaFile.IDsummary.ReduceMemoryUsage();
                DiaFile.IDsummary.FastaPath = tandemPara.FastaPath;
                FileList.add(DiaFile);
            }
        }
    }

    //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library">

    //External library search

    Logger.getRootLogger().info("Targeted extraction using external library");

    //Read exteranl library
    FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder,
            FilenameUtils.getBaseName(ExternalLibPath));
    if (ExlibManager == null) {
        ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath));

        //Import traML file
        ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag);
        //Check if there are decoy spectra
        ExlibManager.CheckDecoys();
        //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath);
        ExlibManager.WriteFragmentLibSerialization(WorkFolder);
    }
    Logger.getRootLogger()
            .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size());
    for (DIAPack diafile : FileList) {
        if (diafile.IDsummary == null) {
            diafile.ReadSerializedLCMSID();
        }
        //Generate RT mapping
        RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter());
        RTmap.GenerateModel();
        RTmap.GenerateMappedPepIon();

        diafile.BuildStructure();
        diafile.MS1FeatureMap.ReadPeakCluster();
        diafile.GenerateMassCalibrationRTMap();
        //Perform targeted re-extraction
        diafile.TargetedExtractionQuant(false, ExlibManager, ExtProbThreshold, RTWindow_Ext);
        diafile.MS1FeatureMap.ClearAllPeaks();
        diafile.IDsummary.ReduceMemoryUsage();
        //Remove target IDs below the defined probability threshold
        diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold);
        diafile.ExportID();
        diafile.ClearStructure();
        Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size()
                + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size());
    }

    //</editor-fold>

    Logger.getRootLogger().info("Job done");
    Logger.getRootLogger().info(
            "=================================================================================================");

}

From source file:ezbake.frack.submitter.util.JarUtil.java

public static String getRepackagedJarName(String seed) {
    String basename = FilenameUtils.getBaseName(seed);
    return basename + "-repackaged.jar";
}

From source file:ijfx.ui.utils.NamingUtils.java

public static File replaceWithExtension(File originalFile, String extension) {
    String basename = FilenameUtils.getBaseName(originalFile.getName());
    if (extension.startsWith(".") == false)
        extension = "." + extension;
    return new File(originalFile.getParentFile(), basename + extension);
}

From source file:com.github.dokandev.dokanjava.samples.memoryfs.Utils.java

public static String toShortName(String fileName) {
    String base = FilenameUtils.getBaseName(fileName);
    if (base.length() > 8)
        base = base.substring(8);/*w ww .  j  a  v a2  s. c  om*/

    String ext = FilenameUtils.getExtension(fileName);
    if (ext.length() > 3)
        ext = ext.substring(3);
    if (ext.length() > 0)
        ext = "." + ext;

    return base + ext;
}

From source file:com.opendoorlogistics.core.utils.io.TextIO.java

private static String getTableName(File file) {
    String tableName = FilenameUtils.getBaseName(file.getAbsolutePath());
    if (Strings.isEmptyWhenStandardised(tableName)) {
        tableName = "Table";
    }/* w  w  w .java2 s  . co  m*/
    return tableName;
}

From source file:com.kamike.misc.FsNameUtils.java

public static ArrayList<String> getDescriptions(String fileName) {
    ArrayList<String> ret = new ArrayList<String>();
    String baseName = FilenameUtils.getBaseName(fileName);
    String escapedName = escapeName(baseName);

    Pattern p = Pattern.compile("\\[(.*?)\\]");
    Matcher m = p.matcher(escapedName);

    while (m.find()) {
        ret.add(m.group(1));//from w  ww . j  a v  a 2  s  .  c  o m

    }
    return ret;
}

From source file:com.tomdoel.mpg2dcm.EndoscopicXmlToDicomConverter.java

public static void convert(final File xmlInputFile, final String dicomOutputPath)
        throws IOException, SAXException, ParserConfigurationException, ParseException {
    // Parse the XML file
    final EndoscopicFileProcessor converter = new EndoscopicFileProcessor(xmlInputFile);

    // Generate DICOM tags from the XML file - these will be shared across all files
    final Attributes sharedDicomAttributes = converter.getDicomAttributes();

    int seriesNumber = 0;

    // Iterate over all video files
    for (final File videoFile : converter.getVideoFileNames()) {

        seriesNumber++;/*w ww  .  ja  v a 2s. c o  m*/

        final Attributes fileDicomAttributes = new Attributes(sharedDicomAttributes);

        // Create a DICOM file in the output directory
        final File dicomOutputFile = new File(dicomOutputPath,
                FilenameUtils.getBaseName(videoFile.getName()) + ".dcm");

        // Add a series number
        fileDicomAttributes.setString(Tag.SeriesNumber, VR.IS, Integer.toString(seriesNumber));

        // We give a unique series instance UID to each video. For the first video we use the provided series UID if it exists.
        if (seriesNumber > 1 || !fileDicomAttributes.contains(Tag.SeriesNumber)) {
            fileDicomAttributes.setString(Tag.SeriesInstanceUID, VR.UI, UIDUtils.createUID());
        }

        // Add the shared DICOM tags and write to a DICOM file
        MpegFileConverter.convertWithAttributes(videoFile, dicomOutputFile, fileDicomAttributes);
    }
}

From source file:ch.unibas.fittingwizard.application.xyz.XyzFile.java

public XyzFile(File source, int atomCount, List<XyzAtom> atoms) {
    this.source = source;
    this.name = FilenameUtils.getBaseName(source.getAbsolutePath());
    this.atomCount = atomCount;
    this.atoms = atoms;
}

From source file:eu.hydrologis.jgrass.featureeditor.utils.Utilities.java

/**
 * Extracts the form file from a resource file (ex shapefile).
 * /* w  w  w .  j  a  v a2  s . c  o m*/
 * @param resourceFile the resource that has a form sidecar file.
 * @return the form file or null, if it doesn't exist.
 */
public static File getFormFile(File resourceFile) {

    String baseName = FilenameUtils.getBaseName(resourceFile.getName());
    File formFile = new File(resourceFile.getParentFile(), baseName + FORM);

    if (formFile.exists()) {
        return formFile;
    } else {
        return null;
    }
}