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

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

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Introduction

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

Prototype

public static String removeExtension(String filename)

Source Link

Document

Removes the extension from a filename.

Usage

From source file:ffx.xray.RescoreAndCluster.java

private File rescoreSingle(File modelFile, RescoreStrategy rscType, DoubleIndexPair[] energies, int i) {
    Path filepath = generatePath(modelFile);
    if (filepath == null) {
        logger.warning(String.format(" Could not generate path to file %s", modelFile.toPath()));
        return null;
    }/*from w ww . j  a v a  2 s .co  m*/
    String filename = pwdPath.relativize(filepath).toString();
    File retFile = modelFile;
    try {
        MolecularAssembly[] openedAssemblies = utils.open(filename);
        MolecularAssembly assembly = openedAssemblies[0];
        switch (rscType) {
        case NO_RESCORE:
            logger.warning(" Rescore is being called with rscType = NO_RESCORE");
            break;
        case ENERGY_EVAL:
            break;
        case MINIMIZE:
            logger.info(String.format("\n Running minimize on %s", filename));
            logger.info(String.format(" RMS gradient convergence criteria: %f", eps));
            utils.energy(assembly);
            utils.minimize(assembly, eps);

            String ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);

            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix).concat(ext);
            retFile = new File(filename);
            if (ext.toUpperCase().contains("XYZ")) {
                utils.saveAsXYZ(assembly, retFile);
            } else {
                utils.saveAsPDB(assembly, retFile);
            }
            break;
        case XRAY_MIN:
            logger.info(String.format("\n Running x-ray minimize on %s", filename));

            DiffractionFile diffractionFile = null;
            if (diffractionFiles.isEmpty()) {
                diffractionFile = new DiffractionFile(assembly, 1.0, false);
                diffractionFiles.add(diffractionFile);
            }
            CompositeConfiguration properties = Keyword.loadProperties(modelFile);
            DiffractionData diffractionData = new DiffractionData(assembly, properties, SolventModel.POLYNOMIAL,
                    diffractionFiles.toArray(new DiffractionFile[diffractionFiles.size()]));

            diffractionData.scaleBulkFit();
            diffractionData.printStats();
            utils.energy(assembly);

            RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData, refinementMode);
            if (eps < 0.0) {
                eps = refinementMinimize.getEps();
            }
            logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d",
                    eps, maxiter));
            refinementMinimize.minimize(eps, maxiter);
            diffractionData.scaleBulkFit();
            diffractionData.printStats();

            ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);

            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix);
            diffractionData.writeData(filename + ".mtz");
            filename = filename.concat(ext);
            diffractionData.writeModel(filename);

            retFile = new File(filename);
            if (diffractionFile != null) {
                try {
                    diffractionFiles.remove(diffractionFile);
                } catch (UnsupportedOperationException ex) {
                    // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                    diffractionFiles = new ArrayList<>();
                }
            }
            break;
        case RS_MIN:
            logger.info(String.format("\n Running real-space minimize on %s", filename));

            RealSpaceFile realspaceFile = null;
            if (mapFiles.isEmpty()) {
                realspaceFile = new RealSpaceFile(assembly);
                mapFiles.add(realspaceFile);
            }
            properties = Keyword.loadProperties(modelFile);
            RealSpaceData realspaceData = new RealSpaceData(assembly, properties,
                    mapFiles.toArray(new RealSpaceFile[mapFiles.size()]));
            utils.energy(assembly);

            refinementMinimize = new RefinementMinimize(realspaceData, refinementMode);
            if (eps < 0.0) {
                eps = 1.0;
            }
            logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d",
                    eps, maxiter));
            refinementMinimize.minimize(eps, maxiter);

            ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);
            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix).concat(ext);
            retFile = new File(filename);
            if (ext.toUpperCase().contains("XYZ")) {
                utils.saveAsXYZ(assembly, retFile);
            } else {
                utils.saveAsPDB(assembly, retFile);
            }

            if (realspaceFile != null) {
                try {
                    mapFiles.remove(realspaceFile);
                } catch (UnsupportedOperationException ex) {
                    // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                    mapFiles = new ArrayList<>();
                }
            }
            break;
        default:
            logger.severe(" No valid rescore type: FFX will not continue.");
        }
        double e = utils.returnEnergy(assembly);
        energies[i] = new DoubleIndexPair(i, e);
        utils.closeAll(openedAssemblies);
    } catch (Exception ex) {
        logger.warning(String.format(" Exception rescoring on file %s", filename));
        logger.info(ex.toString());
    }
    return retFile;
}

From source file:com.uwsoft.editor.controlles.ResolutionManager.java

public void resizeSpineAnimationForAllResolutions(File atlasFile, ProjectInfoVO currentProjectInfoVO) {

    String fileNameWithOutExt = FilenameUtils.removeExtension(atlasFile.getName());
    String tmpDir = dataManager.getCurrentWorkingPath() + File.separator
            + dataManager.getCurrentProjectVO().projectName + "/assets/orig/spine-animations" + File.separator
            + fileNameWithOutExt + File.separator + "tmp";
    File sourceFolder = new File(tmpDir);

    unpackAtlasIntoTmpFolder(atlasFile, tmpDir);
    try {/* w  ww . j  a  va2  s .  co m*/
        for (ResolutionEntryVO resolutionEntryVO : currentProjectInfoVO.resolutions) {
            FileUtils.forceMkdir(new File(dataManager.getCurrentWorkingPath() + "/"
                    + dataManager.getCurrentProjectVO().projectName + File.separator + "assets" + File.separator
                    + resolutionEntryVO.name + File.separator + "spine-animations"));
            String targetPath = dataManager.getCurrentWorkingPath() + "/"
                    + dataManager.getCurrentProjectVO().projectName + File.separator + "assets" + File.separator
                    + resolutionEntryVO.name + File.separator + "spine-animations" + File.separator
                    + fileNameWithOutExt;
            FileUtils.forceMkdir(new File(targetPath));
            File targetFolder = new File(targetPath);
            resizeImagesTmpDirToResolution(atlasFile.getName(), sourceFolder, resolutionEntryVO, targetFolder);
        }
        FileUtils.deleteDirectory(sourceFolder);
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:com.liferay.sync.engine.SyncSystemTest.java

protected Path getDependencyFilePath(Path testFilePath, String dependency) throws Exception {

    String filePathName = null;/*from  w w  w.  j  ava 2s  .  c o m*/

    if (dependency.contains("common")) {
        filePathName = FileUtil.getFilePathName("tests", "dependencies", dependency);
    } else {
        Path testFileNameFilePath = testFilePath.getFileName();

        String testFileName = testFileNameFilePath.toString();

        filePathName = FileUtil.getFilePathName("tests", "dependencies",
                FilenameUtils.removeExtension(testFileName), dependency);
    }

    return getResourceFilePath(filePathName);
}

From source file:MyFormApp.java

private void jList2AncestorAdded(javax.swing.event.AncestorEvent evt) {//GEN-FIRST:event_jList2AncestorAdded
    // TODO add your handling code here:
    // ? LIST /*w  w  w . j  a va2 s  . c  o  m*/
    for (File file : fileList) { //

        data[i] = (file.getName());
        System.out.println(data[i]);
        String imagename = FilenameUtils.removeExtension(data[i]);
        int a = i + 1;
        model.addElement(new Book(data[i], "" + a, imagename, PATH)); //    
        i = i + 1;

    }
    jList2.setModel(model);
    jList2.setCellRenderer(new BookRenderer());
}

From source file:com.uwsoft.editor.proxy.ResolutionManager.java

public void resizeSpineAnimationForAllResolutions(File atlasFile, ProjectInfoVO currentProjectInfoVO) {

    String fileNameWithOutExt = FilenameUtils.removeExtension(atlasFile.getName());
    ProjectManager projectManager = facade.retrieveProxy(ProjectManager.NAME);
    String tmpDir = projectManager.getCurrentProjectPath() + "/assets/orig/spine-animations" + File.separator
            + fileNameWithOutExt + File.separator + "tmp";
    File sourceFolder = new File(tmpDir);

    unpackAtlasIntoTmpFolder(atlasFile, tmpDir);
    try {/*from   w w  w .j  av a  2  s . co  m*/
        for (ResolutionEntryVO resolutionEntryVO : currentProjectInfoVO.resolutions) {
            FileUtils.forceMkdir(new File(projectManager.getCurrentProjectPath() + File.separator + "assets"
                    + File.separator + resolutionEntryVO.name + File.separator + "spine-animations"));
            String targetPath = projectManager.getCurrentProjectPath() + File.separator + "assets"
                    + File.separator + resolutionEntryVO.name + File.separator + "spine-animations"
                    + File.separator + fileNameWithOutExt;
            FileUtils.forceMkdir(new File(targetPath));
            File targetFolder = new File(targetPath);
            resizeImagesTmpDirToResolution(atlasFile.getName(), sourceFolder, resolutionEntryVO, targetFolder);
        }
        FileUtils.deleteDirectory(sourceFolder);
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:ca.on.oicr.pde.workflows.GATK3WorkflowTest.java

private void validateWorkflow(AbstractWorkflowDataModel w) {

    //check for null string
    for (AbstractJob j : w.getWorkflow().getJobs()) {

        String c = Joiner.on(" ").useForNull("null").join(j.getCommand().getArguments());

        //check for null string
        Assert.assertFalse(c.contains("null"), "Warning: command contains \"null\":\n" + c + "\n");

        // check for missing spaces
        Assert.assertFalse(c.matches("(.*)[^ ]--(.*)"));
    }//from ww  w  .j  a  v  a2 s  .c  o  m

    //verify bai is located in the correct provision directory
    Map<String, String> bamFileDirectories = new HashMap<>();
    for (SqwFile f : w.getFiles().values()) {
        if (FilenameUtils.isExtension(f.getProvisionedPath(), "bam")) {
            bamFileDirectories.put(FilenameUtils.removeExtension(f.getSourcePath()),
                    FilenameUtils.getPath(f.getProvisionedPath()));
        }
    }
    for (SqwFile f : w.getFiles().values()) {
        //FIXME: bai.getProvisionedPath != bai.getOutputPath ...
        // at least with seqware 1.1.0, setting output path changes where the output file will be stored,
        // but the commonly used get provisioned path will return the incorrect path to the file
        if (FilenameUtils.isExtension(f.getProvisionedPath(), "bai")) {
            //check bai is in the same provision directory its corresponding bam is in
            Assert.assertEquals(FilenameUtils.getPath(f.getOutputPath()),
                    bamFileDirectories.get(FilenameUtils.removeExtension(f.getSourcePath())));
        }
    }

    //check number of parent nodes
    Set<VariantCaller> vc = new HashSet<>();
    for (String s : StringUtils.split(w.getConfigs().get("variant_caller"), ",")) {
        vc.add(VariantCaller.valueOf(StringUtils.upperCase(s)));
    }
    int parallelism = Math.max(1, StringUtils.split(w.getConfigs().get("chr_sizes"), ",").length);
    int expectedParentNodeCount = parallelism * (vc.contains(HAPLOTYPE_CALLER) ? 1 : 0)
            + parallelism * (vc.contains(UNIFIED_GENOTYPER) ? 2 : 0); //ug indels and ug snvs
    int actualParentNodeCount = 0;
    for (AbstractJob j : w.getWorkflow().getJobs()) {
        if (j.getParents().isEmpty()) {
            actualParentNodeCount++;
        }
    }
    Assert.assertEquals(actualParentNodeCount, expectedParentNodeCount);

    //view output files
    for (AbstractJob j : w.getWorkflow().getJobs()) {
        for (SqwFile f : j.getFiles()) {
            if (f.isOutput()) {
                System.out.println(f.getProvisionedPath());
            }
        }
    }
}

From source file:com.photon.phresco.framework.impl.ApplicationManagerImpl.java

private void deleteBuildArchive(String rootModulePath, List<BuildInfo> selectedInfos, String subModuleName)
        throws PhrescoException {
    S_LOGGER.debug(/*from w  w w . ja  v a2 s  .c  o m*/
            "Entering Method AppliacationmanagerImpl.deleteBuildArchive(ProjectInfo project, List<BuildInfo> selectedInfos)");
    File file = null;
    try {
        String delFilename = null;
        for (BuildInfo selectedInfo : selectedInfos) {
            //Delete zip file
            delFilename = selectedInfo.getBuildName();
            file = new File(getBuildInfoHome(rootModulePath, subModuleName) + delFilename);
            FilenameUtils.removeExtension(file.getName());
            File temp = new File(getBuildInfoHome(rootModulePath, subModuleName)
                    + file.getName().substring(0, file.getName().length() - 4));
            file.delete();
            if (temp.exists()) {
                FileUtil.delete(temp);
            }
        }

    } catch (Exception e) {
        throw new PhrescoException(e);
    }
}

From source file:Import.pnl_import_vcf.java

private void btn_importActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btn_importActionPerformed
    // TODO add your handling code here:
    String[] singleColumns = singleColumns();
    String[] selectedFamilies = selectedFamilies();
    CheckBoxList checkList = new CheckBoxList();
    DefaultListModel model = new DefaultListModel();
    for (String a : singleColumns) {
        model.addElement(a);/*from   w  ww  .ja v  a 2s. c o m*/
    }
    checkList.setModel(model);
    String filePath = filePathField.getText();
    if (rbt_existing_tbl.isSelected()) {
        try {
            String[] selectedTableFamilies = tableFamilies();
            JTable tableMap = new JTable();
            DefaultTableModel tableMapModel = (DefaultTableModel) tableMap.getModel();
            setMapTable(tableMap, tableMapModel, selectedFamilies, selectedTableFamilies);
            int map = JOptionPane.showConfirmDialog(null, tableMap, "Please map to column",
                    JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null);
            if (map == 2) {
                return;
            }
            Object[] o = getMapPair(tableMapModel);
            String selectTableName = tbl_hbase_tables.getValueAt(tbl_hbase_tables.getSelectedRow(), 0)
                    .toString();
            String[] mappedFamilies = (String[]) o[1];
            String[] mappedTableFamilies = (String[]) o[0];
            String[] keys = getKey(selectTableName);
            importToTable.importDataJob importData = new importDataJob();
            importData.importData(filePath, selectTableName, mappedTableFamilies, mappedFamilies, keys);
        } catch (Exception ex) {
            Logger.getLogger(pnl_import_vcf.class.getName()).log(Level.SEVERE, null, ex);
        }
    } else {
        try {
            int key = JOptionPane.showConfirmDialog(null, checkList, "Please choose Key",
                    JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null);
            if (key == 2) {
                return;
            }
            Object[] selectedKey = checkList.getCheckBoxListSelectedValues();
            File f = new File(filePath);
            String fname = f.getName();
            String tableName = FilenameUtils.removeExtension(fname);
            writeKey(selectedKey, tableName);
            writeType(tableName);
            createColumnsTxt(tableName);
            ArrayList<String> list = new ArrayList<>();
            for (Object o : selectedKey) {
                list.add(o.toString());
            }
            String[] keys = list.toArray(new String[list.size()]);
            importToNewTable.createDataJob importData = new createDataJob();
            importData.importData(filePath, selectedFamilies, keys);
        } catch (Exception ex) {
            Logger.getLogger(pnl_import_vcf.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
    filePathField.setText(null);
    DefaultDualListModel dualModel = new DefaultDualListModel();
    list_dual_hbase_column_family.setModel(dualModel);
    pnl_import_vcf.showHBaseTables runabletask = new pnl_import_vcf.showHBaseTables();
    new Thread(runabletask).start();
}

From source file:com.o2d.pkayjava.editor.proxy.ResolutionManager.java

public void resizeSpineAnimationForAllResolutions(File atlasFile, ProjectInfoVO currentProjectInfoVO) {

    String fileNameWithOutExt = FilenameUtils.removeExtension(atlasFile.getName());
    ProjectManager projectManager = facade.retrieveProxy(ProjectManager.NAME);
    String tmpDir = projectManager.getCurrentWorkingPath() + File.separator
            + projectManager.getCurrentProjectVO().projectName + "/assets/orig/spine-animations"
            + File.separator + fileNameWithOutExt + File.separator + "tmp";
    File sourceFolder = new File(tmpDir);

    unpackAtlasIntoTmpFolder(atlasFile, tmpDir);
    try {//ww w.j  a v  a2s.  c o m
        for (ResolutionEntryVO resolutionEntryVO : currentProjectInfoVO.resolutions) {
            FileUtils.forceMkdir(new File(projectManager.getCurrentWorkingPath() + "/"
                    + projectManager.getCurrentProjectVO().projectName + File.separator + "assets"
                    + File.separator + resolutionEntryVO.name + File.separator + "spine-animations"));
            String targetPath = projectManager.getCurrentWorkingPath() + "/"
                    + projectManager.getCurrentProjectVO().projectName + File.separator + "assets"
                    + File.separator + resolutionEntryVO.name + File.separator + "spine-animations"
                    + File.separator + fileNameWithOutExt;
            FileUtils.forceMkdir(new File(targetPath));
            File targetFolder = new File(targetPath);
            resizeImagesTmpDirToResolution(atlasFile.getName(), sourceFolder, resolutionEntryVO, targetFolder);
        }
        FileUtils.deleteDirectory(sourceFolder);
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:edu.cornell.med.icb.goby.methylation.MethylSimilarityScan.java

private MethylationData load(String inputFilename) throws IOException {
    System.out.println("Loading..");
    final String cacheFilename = FilenameUtils.removeExtension(inputFilename) + ".cache";
    File cacheFile = new File(cacheFilename);
    if (cacheFile.canRead()) {
        try {/*from  w  ww  .ja  va  2  s  .c om*/
            System.out.println("Trying to load cache " + cacheFilename);
            System.out.flush();
            return (MethylationData) BinIO.loadObject(cacheFilename);
        } catch (ClassNotFoundException e) {
            System.err.println("Cannot load cache. Loading text file instead.");
            // continue loading as usual.
        }
    }
    MethylationData data = new MethylationData();
    TSVReader reader = new TSVReader(new FileReader(inputFilename), '\t');
    reader.setCommentPrefix("chromosome");
    int count = 0;

    while (reader.hasNext()) {
        if (reader.isCommentLine()) {
            reader.skip();
        } else {
            reader.next();
            String chr = reader.getString();
            int position = reader.getInt();
            char strand = reader.getString().charAt(0);
            // ignore type of site.
            reader.getString();
            int methylatedReadCount = reader.getInt();
            int totalReadCount = reader.getInt();

            // add element at index 'position'
            data.append(chr, strand, position, methylatedReadCount, totalReadCount);
            count++;
            if (count % 100000 == 1) {
                System.out.print(".");
            }
        }
    }
    System.out.println("done");

    System.out.println("Sorting..");
    // sort the sites by position:
    Collections.sort(data.sites, new Comparator<MethylationSite>() {
        public int compare(MethylationSite site1, MethylationSite site2) {
            if (site1.chromosome != site2.chromosome)
                return site1.chromosome - site2.chromosome;
            else
                return site1.position - site2.position;
        }
    });
    System.out.println("Saving cache..");
    System.out.flush();

    BinIO.storeObject(data, cacheFilename);
    return data;

}