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:com.opendoorlogistics.studio.appframe.AppFrame.java

@Override
public void saveDatastoreWithoutUserPrompt(File file) {
    String ext = FilenameUtils.getExtension(file.getAbsolutePath()).toLowerCase();

    // ensure we have spreadsheet extension
    if (!ext.equals("xls") && !ext.equals("xlsx")) {
        ext = "xlsx";
        String filename = FilenameUtils.removeExtension(file.getAbsolutePath()) + "." + ext;
        file = new File(filename);
    }//ww w  .j a v a  2 s.  c om

    final File finalFile = file;
    final String finalExt = ext;

    String message = "Saving " + file;
    final ProgressDialog<Boolean> pd = new ProgressDialog<>(AppFrame.this, message, false, true);
    pd.setLocationRelativeTo(this);
    pd.setText("Saving file, please wait.");
    final ExecutionReport report = new ExecutionReportImpl();
    pd.start(new Callable<Boolean>() {

        @Override
        public Boolean call() throws Exception {
            // return PoiIO.export(loaded.getDs(), finalFile,
            // finalExt.equals("xlsx"));
            try {
                return loaded.save(finalFile, finalExt.equals("xlsx"),
                        ProgressPanel.createProcessingApi(getApi(), pd), report);
            } catch (Throwable e) {
                report.setFailed(e);
                return false;
            }

        }
    }, new OnFinishedSwingThreadCB<Boolean>() {

        @Override
        public void onFinished(Boolean result, boolean userCancelled, boolean userFinishedNow) {

            if (result == false) {
                report.setFailed("Could not save file " + finalFile.getAbsolutePath());
                ExecutionReportDialog.show(AppFrame.this, "Error saving file", report);
            } else {
                loaded.onSaved(finalFile);

                if (report.size() > 0) {
                    ExecutionReportDialog.show(AppFrame.this, "Warning saving file", report);
                }

                PreferencesManager.getSingleton().addRecentFile(finalFile);
                PreferencesManager.getSingleton().setDirectory(PrefKey.LAST_IO_DIR, finalFile);
            }
            updateAppearance();
        }
    });

}

From source file:ffx.potential.bonded.SturmMethod.java

/**
 * Write out loop coordinates and determine oxygen placement.
 *
 * @param r_n//from   w w  w .  ja  va 2  s  . c om
 * @param r_a
 * @param r_c
 * @param stt_res
 * @param end_res
 * @param molAss
 * @param counter
 * @param writeFile
 *
 * @return the File.
 */
public File writePDBBackbone(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res,
        MolecularAssembly molAss, int counter, boolean writeFile) {

    Polymer[] newChain = molAss.getChains();
    ArrayList<Atom> backBoneAtoms;
    double[] xyz_n = new double[3];
    double[] xyz_a = new double[3];
    double[] xyz_c = new double[3];

    xyz_o[0][0] = 0.0;
    xyz_o[0][1] = 0.0;
    xyz_o[0][2] = 0.0;
    xyz_o[4][0] = 0.0;
    xyz_o[4][1] = 0.0;
    xyz_o[4][2] = 0.0;

    ArrayList<Atom> OAtoms = new ArrayList<>();

    for (int i = stt_res + 1; i < end_res; i++) {
        Residue newResidue = newChain[0].getResidue(i);
        backBoneAtoms = newResidue.getBackboneAtoms();
        for (Atom backBoneAtom : backBoneAtoms) {
            switch (backBoneAtom.getAtomType().name) {
            case "C":
                xyz_c[0] = r_c[i - stt_res][0];
                xyz_c[1] = r_c[i - stt_res][1];
                xyz_c[2] = r_c[i - stt_res][2];
                backBoneAtom.moveTo(xyz_c);
                break;
            case "N":
                xyz_n[0] = r_n[i - stt_res][0];
                xyz_n[1] = r_n[i - stt_res][1];
                xyz_n[2] = r_n[i - stt_res][2];
                backBoneAtom.moveTo(xyz_n);
                break;
            case "CA":
                xyz_a[0] = r_a[i - stt_res][0];
                xyz_a[1] = r_a[i - stt_res][1];
                xyz_a[2] = r_a[i - stt_res][2];
                backBoneAtom.moveTo(xyz_a);
                break;
            case "HA":
                newResidue.deleteAtom(backBoneAtom);
                break;
            case "H":
                newResidue.deleteAtom(backBoneAtom);
                break;
            case "O":
                OAtoms.add(backBoneAtom);
                break;
            default:
                newResidue.deleteAtom(backBoneAtom);
                break;
            }
        }

        ArrayList<Atom> sideChainAtoms = newResidue.getSideChainAtoms();
        for (Atom sideChainAtom : sideChainAtoms) {
            newResidue.deleteAtom(sideChainAtom);
        }
    }

    int oCount = 0;
    for (int i = stt_res + 1; i < end_res; i++) {
        Residue newResidue = newChain[0].getResidue(i);
        backBoneAtoms = newResidue.getBackboneAtoms();
        Atom CA = new Atom("CA");
        Atom N = new Atom("N");
        Atom C = new Atom("C");
        Atom O = OAtoms.get(oCount);

        for (Atom backBoneAtom : backBoneAtoms) {
            switch (backBoneAtom.getAtomType().name) {
            case "C":
                C = backBoneAtom;
                break;
            case "N":
                N = backBoneAtom;
                break;
            case "CA":
                CA = backBoneAtom;
                break;
            default:
                break;
            }
        }
        BondedUtils.intxyz(O, C, 1.2255, CA, 122.4, N, 180, 0);
        xyz_o[i - stt_res][0] = O.getX();
        xyz_o[i - stt_res][1] = O.getY();
        xyz_o[i - stt_res][2] = O.getZ();

        oCount++;
    }

    File file = molAss.getFile();

    /**
     * for (int i = stt_res; i <= end_res; i++) { double[] xyz =
     * molAss.getBackBoneAtoms().get(i).getXYZ(); }
     */
    String filename = FilenameUtils.removeExtension(file.getAbsolutePath());
    if (!filename.contains("_loop")) {
        filename = filename + "_loop";
    }

    File modifiedFile = new File(filename + ".pdb_" + counter);
    PDBFilter modFilter = new PDBFilter(modifiedFile, molAss, null, null);

    if (writeFile) {
        modFilter.writeFile(modifiedFile, true);
    }

    return (modifiedFile);
}

From source file:edu.cornell.med.icb.goby.modes.CompactAlignmentToAnnotationCountsMode.java

private void processOneBasename(final Object2ObjectMap<String, ObjectList<Annotation>> allAnnots,
        BufferedWriter writer, final String inputFile, final String inputBasename, GenomicRange range)
        throws IOException {

    WeightsInfo weights = null;/*  w w  w .  j  ava 2 s  .co m*/
    if (weightParams.useWeights) {
        weights = loadWeights(inputBasename, weightParams.useWeights, weightParams.weightId);
        if (weights != null) {
            System.err.println(
                    "Weights have been provided and loaded and will be used to reweight transcript counts.");
        }
    }
    final AlignmentReaderFactory factory = filterAmbiguousReads ? new NonAmbiguousAlignmentReaderFactory()
            : new DefaultAlignmentReaderFactory();
    final int numberOfReferences;
    final DoubleIndexedIdentifier referenceIds;
    {
        final AlignmentReader reader = factory.createReader(inputBasename);
        reader.readHeader();
        numberOfReferences = reader.getNumberOfTargets();

        referenceIds = new DoubleIndexedIdentifier(reader.getTargetIdentifiers());
        reader.close();
    }
    System.out.println(String.format("Alignment contains %d reference sequences", numberOfReferences));
    if (genomicRange != null) {
        genomicRange.resolveChromosomeIndices(referenceIds);
    }
    final AnnotationCountIterateAlignments iterateAlignment = new AnnotationCountIterateAlignments();
    iterateAlignment.setWeightInfo(weightParams, weights);
    iterateAlignment.parseIncludeReferenceArgument(includeReferenceNameCommas);

    // Iterate through the alignment and retrieve algs:
    System.out.println("Loading alignment " + inputBasename + "..");
    iterateAlignment.setAlignmentReaderFactory(factory);
    iterateAlignment.iterate(genomicRange, inputBasename);

    final long numAlignedReadsInSample = iterateAlignment.getNumAlignedReadsInSample();
    final AnnotationCountInterface[] algs = iterateAlignment.getAlgs();
    final IntSortedSet referencesToProcess = iterateAlignment.getReferencesSelected();

    final String sampleId = FilenameUtils.getBaseName(inputBasename);

    deCalculator.setNumAlignedInSample(sampleId, numAlignedReadsInSample);

    if (outputFilename == null) {
        // output filename was not provided on the command line. We make one output per input basename
        if (writeAnnotationCounts) {
            final String outputFileTmp = FilenameUtils.removeExtension(inputFile) + ".ann-counts.tsv";
            writer = new BufferedWriter(new FileWriter(outputFileTmp));
            writer.write(
                    "basename\tmain-id\tsecondary-id\ttype\tchro\tstrand\tlength\tstart\tend\tin-count\tover-count\tRPKM\tlog2(RPKM+1)\texpression\tnum-exons\n");
        }
    }

    writeAnnotationCounts(allAnnots, writer, inputBasename, referenceIds, algs, referencesToProcess);

    if (outputFilename == null) {
        // output filename was not provided on the command line. We close each basename output.
        IOUtils.closeQuietly(writer);
    }

}

From source file:ffx.algorithms.AbstractOSRW.java

public void setOptimization(boolean osrwOptimization, MolecularAssembly molAss) {
    this.osrwOptimization = osrwOptimization;
    this.molecularAssembly = molAss;
    File file = molecularAssembly.getFile();
    String fileName = FilenameUtils.removeExtension(file.getAbsolutePath());
    if (pdbFilter == null) {
        pdbFile = new File(fileName + "_opt.pdb");
        pdbFilter = new PDBFilter(new File(fileName + "_opt.pdb"), molecularAssembly, null, null);
    }/*from   ww w  .ja va  2 s  .c o m*/

}

From source file:com.turn.griffin.GriffinLibCacheUtil.java

public Optional<String> decompressFile(String compressedFile, GriffinCompression compression) {

    Preconditions.checkNotNull(compressedFile);
    Preconditions.checkNotNull(compression);

    if (!new File(compressedFile).exists()) {
        logger.error(String.format("Cannot decompress; %s does not exit", compressedFile));
        Preconditions.checkState(false);
    }//from w  ww.ja v  a2s  . c o m

    if (compression == GriffinCompression.NONE) {
        return Optional.of(compressedFile);
    }

    String plainFile = FilenameUtils.removeExtension(compressedFile);
    InputStream is = null;
    FileOutputStream os = null;
    try {
        switch (compression) {
        case GZIP:
            is = new GzipCompressorInputStream(new FileInputStream(compressedFile));
            break;
        case BZIP2:
            is = new BZip2CompressorInputStream(new FileInputStream(compressedFile));
            break;
        case SNAPPY:
            is = new SnappyInputStream(new FileInputStream(compressedFile));
            break;
        default:
            /* Unknown compression type */
            Preconditions.checkState(false);
        }
        os = new FileOutputStream(plainFile);
        ByteStreams.copy(is, os);
        os.flush();
        return Optional.of(plainFile);

    } catch (IOException e) {
        logger.error(String.format("Failed to decompress file %s", compressedFile), e);
        return Optional.fromNullable(null);

    } finally {
        IOUtils.closeQuietly(is);
        IOUtils.closeQuietly(os);
    }
}

From source file:eu.prestoprime.plugin.mserve.MServeTasks.java

@WfService(name = "mserve_transcode2webm", version = "1.1.2")
public void transcodeToWebM(Map<String, String> sParams, Map<String, String> dParamsString,
        Map<String, File> dParamsFile) throws TaskExecutionFailedException {

    // get static parameters
    String url = sParams.get("mserve.url");

    // get dynamic parameters
    String sipID = dParamsString.get("sipID");
    String fileID = dParamsString.get("mserveFileID");
    String userID = dParamsString.get("userID");

    // get serviceID
    String serviceID = ConfigurationManager.getUserInstance().getService(userID, "mserve");

    // get SIP//from w w  w .j  a  v  a  2 s.  com
    SIP sip = null;
    try {
        sip = P4DataManager.getInstance().getSIPByID(sipID);

        // run FFmbc
        MServeClient cl = new MServeClient(url, serviceID);

        Map<String, String> params = new HashMap<>();

        if (Boolean.parseBoolean(dParamsString.get("isMXF")))
            params.put("args", "-map_audio_channel 0:1:0:0:1 -vf crop=720:576:0:32 -vf scale=360:288 -f webm");
        else
            params.put("args", "-vf scale=360:288 -f webm");

        File output = cl.runMServeTask(fileID, MServeTask.ffmbc, params);

        // MD5
        MessageDigestExtractor mde = new MessageDigestExtractor();
        ToolOutput<MessageDigestExtractor.AttributeType> toolOutput = mde.extract(output.getAbsolutePath());
        String md5sum = toolOutput.getAttribute(MessageDigestExtractor.AttributeType.MD5);

        // get outputVideo
        String outputVideoName = FilenameUtils.removeExtension(
                FilenameUtils.getName(sip.getAVMaterial("application/mxf", "FILE").get(0))) + ".webm";
        String outputVideo = dParamsString.get("videosFolder") + File.separator + outputVideoName;
        File targetFile = new File(outputVideo);

        // copy webm to p4 storage
        FileUtils.copyFile(output, targetFile);

        // update SIP
        sip.addFile("video/webm", "FILE", outputVideo, md5sum, targetFile.length());

        dParamsFile.put("webm", new File(outputVideo));

    } catch (DataException e) {
        e.printStackTrace();
        throw new TaskExecutionFailedException("Unable to find SIP...");
    } catch (IPException e) {
        e.printStackTrace();
        throw new TaskExecutionFailedException("Unable to work with SIP...");
    } catch (MServeException | ToolException e) {
        e.printStackTrace();
        throw new TaskExecutionFailedException("Unable to run FFmbc extractor on MServe...");
    } catch (IOException e) {
        e.printStackTrace();
        throw new TaskExecutionFailedException("Unable to copy the output file...");
    } finally {
        // release SIP
        P4DataManager.getInstance().releaseIP(sip);
    }
}

From source file:edu.ur.ir.repository.service.DefaultRepositoryService.java

/**
 * Create a file information object with an empty file.
 * @throws edu.ur.file.IllegalFileSystemNameException 
 * //from   w  ww. ja v  a  2 s  .c  om
 * @see edu.ur.ir.repository.RepositoryService#createFileInfo(edu.ur.ir.repository.Repository, java.lang.String)
 */
public FileInfo createFileInfo(Repository repository, String fileName)
        throws edu.ur.file.IllegalFileSystemNameException {

    String extension = null;
    if (fileName != null) {
        extension = FilenameUtils.getExtension(fileName);
    }

    return fileServerService.createEmptyFile(repository.getFileDatabase(), uniqueNameGenerator.getNextName(),
            extension, FilenameUtils.removeExtension(fileName));
}

From source file:com.pdftron.pdf.utils.Utils.java

public static String getDisplayNameFromImageUri(Context context, Uri imageUri, String backupFilepath) {
    if (null == context || null == imageUri) {
        return null;
    }/*from  www.  j  av a 2  s . c o m*/
    try {
        String filename = Utils.getUriColumnInfo(context, imageUri, MediaStore.Images.Media.DISPLAY_NAME);
        if (Utils.isNullOrEmpty(filename)) {
            if (!Utils.isNullOrEmpty(backupFilepath)) {
                filename = FilenameUtils.getBaseName(backupFilepath);
            }
        }
        return FilenameUtils.removeExtension(filename);
    } catch (Exception e) {
        AnalyticsHandlerAdapter.getInstance().sendException(e);
    }
    return null;
}

From source file:net.minecraftforge.common.crafting.CraftingHelper.java

private static boolean loadRecipes(ModContainer mod) {
    JsonContext ctx = new JsonContext(mod.getModId());

    return findFiles(mod, "assets/" + mod.getModId() + "/recipes", root -> {
        Path fPath = root.resolve("_constants.json");
        if (fPath != null && Files.exists(fPath)) {
            BufferedReader reader = null;
            try {
                reader = Files.newBufferedReader(fPath);
                JsonObject[] json = JsonUtils.fromJson(GSON, reader, JsonObject[].class);
                ctx.loadConstants(json);
            } catch (IOException e) {
                FMLLog.log.error("Error loading _constants.json: ", e);
                return false;
            } finally {
                IOUtils.closeQuietly(reader);
            }//from w  w w .  j  av a 2  s .  co m
        }
        return true;
    }, (root, file) -> {
        Loader.instance().setActiveModContainer(mod);

        String relative = root.relativize(file).toString();
        if (!"json".equals(FilenameUtils.getExtension(file.toString())) || relative.startsWith("_"))
            return true;

        String name = FilenameUtils.removeExtension(relative).replaceAll("\\\\", "/");
        ResourceLocation key = new ResourceLocation(ctx.getModId(), name);

        BufferedReader reader = null;
        try {
            reader = Files.newBufferedReader(file);
            JsonObject json = JsonUtils.fromJson(GSON, reader, JsonObject.class);
            if (json.has("conditions")
                    && !CraftingHelper.processConditions(JsonUtils.getJsonArray(json, "conditions"), ctx))
                return true;
            IRecipe recipe = CraftingHelper.getRecipe(json, ctx);
            ForgeRegistries.RECIPES.register(recipe.setRegistryName(key));
        } catch (JsonParseException e) {
            FMLLog.log.error("Parsing error loading recipe {}", key, e);
            return false;
        } catch (IOException e) {
            FMLLog.log.error("Couldn't read recipe {} from {}", key, file, e);
            return false;
        } finally {
            IOUtils.closeQuietly(reader);
        }
        return true;
    });
}

From source file:com.ftb2om2.view.MultiplePane.java

private void addDifficultyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_addDifficultyActionPerformed
    PathGetter file = new PathGetter();
    String name = file.getPath(false, false, false);
    if (name != null) {
        File fileName = new File(name);
        DefaultTableModel model = (DefaultTableModel) difficultyTable.getModel();
        model.addRow(/*from   ww w. j a v a 2  s  . c  om*/
                new Object[] { fileName.getName(), name, FilenameUtils.removeExtension(fileName.getName()) });
    }
}