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

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

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  6. removeExtension

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.uwsoft.editor.proxy.ResolutionManager.java

public void createResizedAnimations(ResolutionEntryVO resolution) {
    ProjectManager projectManager = facade.retrieveProxy(ProjectManager.NAME);
    String currProjectPath = projectManager.getCurrentProjectPath();

    // Unpack spine orig
    File spineSourceDir = new File(currProjectPath + File.separator + "assets/orig/spine-animations");
    if (spineSourceDir.exists()) {
        for (File entry : spineSourceDir.listFiles()) {
            if (entry.isDirectory()) {
                String animName = FilenameUtils.removeExtension(entry.getName());
                createResizedSpineAnimation(animName, resolution);
            }/*from   w w  w  . j  ava 2  s  .c om*/
        }
    }

    //Unpack sprite orig
    File spriteSourceDir = new File(currProjectPath + File.separator + "assets/orig/sprite-animations");
    if (spriteSourceDir.exists()) {
        for (File entry : spriteSourceDir.listFiles()) {
            if (entry.isDirectory()) {
                String animName = FilenameUtils.removeExtension(entry.getName());
                createResizedSpriteAnimation(animName, resolution);
            }
        }
    }
}

From source file:ffx.algorithms.DiscountPh.java

/**
 * Construct a "Discrete-Continuous" Monte-Carlo titration engine.
 * For traditional discrete titration, use Protonate.
 * For traditional continuous titration, run mdesv for populations.
 * //from  www  .ja v a  2s  . co m
 * @param mola the molecular assembly
 * @param mcStepFrequency number of MD steps between switch attempts
 * @param pH the simulation pH
 * @param thermostat the MD thermostat
 */
// java.lang.Double, java.lang.Integer, java.lang.Integer, java.lang.Boolean, java.lang.String, java.lang.Integer, null)
DiscountPh(MolecularAssembly mola, ExtendedSystem esvSystem, MolecularDynamics molDyn, double timeStep,
        double printInterval, double saveInterval, boolean initVelocities, String fileType,
        double writeRestartInterval, File dyn) {
    this.mola = mola;
    this.esvSystem = esvSystem;
    this.molDyn = molDyn;
    this.dt = timeStep;
    this.printInterval = printInterval;
    this.saveInterval = saveInterval;
    this.initVelocities = initVelocities;
    this.fileType = fileType;
    this.writeRestartInterval = writeRestartInterval;
    this.dynLoader = dyn;

    this.ff = mola.getForceField();
    this.ffe = mola.getPotentialEnergy();
    this.originalFilename = FilenameUtils.removeExtension(mola.getFile().getAbsolutePath()) + "_dyn.pdb";
    SystemFilter.setVersioning(SystemFilter.Versioning.PREFIX_ABSOLUTE);
    library = RotamerLibrary.getDefaultLibrary();

    // Print system props.
    System.getProperties().keySet().stream().filter(k -> {
        String key = k.toString().toLowerCase();
        for (String prefix : keyPrefixes) {
            if (key.startsWith(prefix)) {
                return true;
            }
        }
        return false;
    }).forEach(key -> SB.logf(" #%s=%s", key.toString(), System.getProperty(key.toString())));
    SB.printIfPresent(" Advanced option flags:");

    if (testInterpolation) {
        testInterpolation();
        System.exit(0);
    }

    // Set the rotamer library in case we do rotamer MC moves.
    library.setLibrary(RotamerLibrary.ProteinLibrary.Richardson);
    library.setUseOrigCoordsRotamer(false);

    logf(" Running DISCOuNT-pH dynamics @ system pH %.2f\n", pH);

    ffe.reInit();
}

From source file:com.googlecode.fascinator.portal.services.impl.CachingDynamicPageServiceImpl.java

/**
 * Renders the Velocity template with the specified form data.
 * // w  w  w . j  av a2 s .  c  o  m
 * @param portalId the portal to get the template from
 * @param pageName the page template to render
 * @param out render results will be written to this output stream
 * @param formData request form data
 * @param sessionState current session
 * @return MIME type of the response
 */
@Override
public String render(String portalId, String pageName, OutputStream out, FormData formData,
        JsonSessionState sessionState) {

    // remove extension for special cases
    boolean isAjax = pageName.endsWith(AJAX_EXT);
    boolean isScript = pageName.endsWith(SCRIPT_EXT);
    if (isAjax || isScript) {
        pageName = FilenameUtils.removeExtension(pageName);
    }

    // setup script and velocity context
    String contextPath = request.getContextPath();
    int serverPort = requestGlobals.getHTTPServletRequest().getServerPort();

    Map<String, Object> bindings = new HashMap<String, Object>();
    bindings.put("systemConfig", config);
    bindings.put("Services", scriptingServices);
    bindings.put("systemProperties", System.getProperties());
    bindings.put("request", request);
    bindings.put("httpServletRequest", requestGlobals.getHTTPServletRequest());
    bindings.put("response", response);
    bindings.put("formData", formData);
    bindings.put("sessionState", sessionState);
    bindings.put("security", security);
    bindings.put("contextPath", contextPath);
    bindings.put("scriptsPath", portalPath + "/" + portalId + "/scripts");
    bindings.put("portalDir", portalPath + "/" + portalId);
    bindings.put("portalId", portalId);
    String urlBase = this.urlBase;
    if (StringUtils.isEmpty(urlBase)) {
        urlBase = getURL(requestGlobals.getHTTPServletRequest(), config);
    } else if (config.getString(null, "portal", "urlBases", portalId) != null) {
        urlBase = config.getString(null, "portal", "urlBases", portalId);
    }
    bindings.put("urlBase", urlBase);
    if (versionString == null) {
        bindings.put("portalPath", urlBase + portalId);
    } else {
        bindings.put("portalPath", urlBase + "verNum" + versionString + "/" + portalId);
    }
    bindings.put("defaultPortal", defaultPortal);
    bindings.put("pageName", pageName);
    bindings.put("serverPort", serverPort);
    bindings.put("toolkit", toolkit);
    bindings.put("log", log);
    bindings.put("notifications", houseKeeping.getUserMessages());
    bindings.put("bindings", bindings);
    StorageDataUtil dataUtil = new StorageDataUtil();
    bindings.put("jsonUtil", dataUtil);
    // run page and template scripts
    Set<String> messages = new HashSet<String>();
    bindings.put("page", evalScript(portalId, layoutName, bindings, messages));
    bindings.put("StringUtils", StringUtils.class);
    bindings.put("StringEscapeUtils", StringEscapeUtils.class);
    bindings.put("self", evalScript(portalId, pageName, bindings, messages));

    // try to return the proper MIME type
    String mimeType = "text/html";
    Object mimeTypeAttr = request.getAttribute("Content-Type");
    if (mimeTypeAttr != null) {
        mimeType = mimeTypeAttr.toString();
    }

    // stop here if the scripts have already sent a response
    boolean committed = response.isCommitted();
    if (committed) {
        // log.debug("Response has been sent or redirected");
        return mimeType;
    }

    if (velocityService.resourceExists(portalId, pageName + ".vm") != null) {
        // set up the velocity context
        VelocityContext vc = new VelocityContext();
        for (String key : bindings.keySet()) {
            vc.put(key, bindings.get(key));
        }
        vc.put("velocityContext", vc);
        if (!messages.isEmpty()) {
            vc.put("renderMessages", messages);
        }

        try {
            // render the page content
            log.debug("Rendering page {}/{}.vm...", portalId, pageName);
            StringWriter pageContentWriter = new StringWriter();
            velocityService.renderTemplate(portalId, pageName, vc, pageContentWriter);
            if (isAjax || isScript) {
                out.write(pageContentWriter.toString().getBytes("UTF-8"));
            } else {
                vc.put("pageContent", pageContentWriter.toString());
            }
        } catch (Exception e) {
            ByteArrayOutputStream eOut = new ByteArrayOutputStream();
            e.printStackTrace(new PrintStream(eOut));
            String eMsg = eOut.toString();
            log.error("Failed to render page ({})!\n=====\n{}\n=====",
                    isAjax ? "ajax" : (isScript ? "script" : "html"), eMsg);
            String errorMsg = "<pre>Page content template error: " + pageName + "\n" + eMsg + "</pre>";
            if (isAjax || isScript) {
                try {
                    out.write(errorMsg.getBytes());
                } catch (Exception e2) {
                    log.error("Failed to output error message!");
                }
            } else {
                vc.put("pageContent", errorMsg);
            }
        }

        if (!(isAjax || isScript)) {
            try {
                // render the page using the layout template
                log.debug("Rendering layout {}/{}.vm for page {}.vm...",
                        new Object[] { portalId, layoutName, pageName });
                Writer pageWriter = new OutputStreamWriter(out, "UTF-8");
                velocityService.renderTemplate(portalId, layoutName, vc, pageWriter);
                pageWriter.close();
            } catch (Exception e) {
                throw new RuntimeException(e);
            }
        }
    }

    return mimeType;
}

From source file:de.teamgrit.grit.preprocess.tokenize.GeneralTokenizer.java

/**
 * On the submission level, this function gathers all relevant files and
 * returns them.//w w w  .  j a  v  a  2s  .co  m
 * 
 * @param location
 *            Where to look for files
 * @return Files matching suffixRegex in the given folder
 */
private List<Path> extractSubmissionFiles(Path location) {
    List<Path> submissionFiles = new LinkedList<>();

    m_log.info("Extracting files.");

    // Check if our location has any submissions files (as recognized by
    // their suffix. if so, note it.
    for (File currentFile : location.toFile().listFiles()) {

        // unpack archives
        if (currentFile.toString().matches(m_archiveRegex)) {
            try {
                // the number indicates to which level of a zipfile nested
                // zipfiles will be extracted
                ArchiveHandler unzipper = new ZipfileHandler(5, Paths.get(".").toFile());

                Path unzippedDir = Paths.get(FilenameUtils.removeExtension(currentFile.toString()));

                unzipper.extractZip(currentFile, unzippedDir.toFile());

                submissionFiles.add(unzippedDir);

            } catch (FileNotFoundException | ZipException e) {
                m_log.info("Error while unzipping ilias submission" + e.getMessage());
            } catch (NoProperParameterException e) {
                m_log.info("Bad parameters for zip." + e.getMessage());
            }
        } else if (currentFile.toString().matches(m_sourceSuffixRegex)) {
            m_log.info("Found: " + currentFile.toString());
            if (!submissionFiles.contains(location)) {
                submissionFiles.add(location);
            }
        } else {
            m_log.info("found invalid file: " + currentFile.toString());
        }
    }
    return submissionFiles;
}

From source file:ch.cyberduck.ui.cocoa.odb.EditorFactory.java

/**
 * Determine the human readable application name for a given bundle identifier.
 *
 * @param bundleIdentifier//from   w  w  w  .  j  a  v  a2s  .  co  m
 * @return
 */
public static String getApplicationName(String bundleIdentifier) {
    if (!applicationNameCache.containsKey(bundleIdentifier)) {
        log.debug("getApplicationName:" + bundleIdentifier);
        final String path = NSWorkspace.sharedWorkspace()
                .absolutePathForAppBundleWithIdentifier(bundleIdentifier);
        if (StringUtils.isBlank(path)) {
            log.warn("Cannot determine installation path for " + bundleIdentifier);
            applicationNameCache.put(bundleIdentifier, null);
            return null;
        }
        NSBundle app = NSBundle.bundleWithPath(path);
        if (null == app) {
            log.error("Loading bundle failed:" + path);
            applicationNameCache.put(bundleIdentifier, null);
            return null;
        }
        NSDictionary dict = app.infoDictionary();
        if (null == dict) {
            log.error("Loading application dictionary failed:" + path);
            applicationNameCache.put(bundleIdentifier, null);
            return null;
        }
        final NSObject name = dict.objectForKey("CFBundleName");
        if (null == name) {
            log.warn("No CFBundleName for " + bundleIdentifier);
            applicationNameCache.put(bundleIdentifier,
                    FilenameUtils.removeExtension(LocalFactory.createLocal(path).getDisplayName()));
        } else {
            applicationNameCache.put(bundleIdentifier, name.toString());
        }
    }
    return applicationNameCache.get(bundleIdentifier);
}

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

public void createResizedAnimations(ResolutionEntryVO resolution) {
    ProjectManager projectManager = facade.retrieveProxy(ProjectManager.NAME);
    String currProjectPath = projectManager.getCurrentWorkingPath() + File.separator
            + projectManager.getCurrentProjectVO().projectName;

    // Unpack spine orig
    File spineSourceDir = new File(currProjectPath + File.separator + "assets/orig/spine-animations");
    if (spineSourceDir.exists()) {
        for (File entry : spineSourceDir.listFiles()) {
            if (entry.isDirectory()) {
                String animName = FilenameUtils.removeExtension(entry.getName());
                createResizedSpineAnimation(animName, resolution);
            }/*from  w  w  w .  ja va  2  s .co  m*/
        }
    }

    //Unpack sprite orig
    File spriteSourceDir = new File(currProjectPath + File.separator + "assets/orig/sprite-animations");
    if (spriteSourceDir.exists()) {
        for (File entry : spriteSourceDir.listFiles()) {
            if (entry.isDirectory()) {
                String animName = FilenameUtils.removeExtension(entry.getName());
                createResizedSpriteAnimation(animName, resolution);
            }
        }
    }
}

From source file:net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler.java

public void actionPerformed(ActionEvent e) {

    String command = e.getActionCommand();

    // Actions for raw data files

    if (command.equals("SHOW_TIC")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        TICVisualizerModule.setupNewTICVisualizer(selectedFiles);
    }//from   ww w. j a  v a2  s  .  co m

    if (command.equals("SHOW_SPECTRUM")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        SpectraVisualizerModule module = MZmineCore.getModuleInstance(SpectraVisualizerModule.class);
        ParameterSet parameters = MZmineCore.getConfiguration()
                .getModuleParameters(SpectraVisualizerModule.class);
        parameters.getParameter(SpectraVisualizerParameters.dataFiles)
                .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        ExitCode exitCode = parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
        MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
        if (exitCode == ExitCode.OK)
            module.runModule(project, parameters, new ArrayList<Task>());
    }

    if (command.equals("SHOW_IDA")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        IDAVisualizerModule.showIDAVisualizerSetupDialog(selectedFiles[0]);

    }

    if (command.equals("SHOW_2D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        TwoDVisualizerModule.show2DVisualizerSetupDialog(selectedFiles[0]);
    }

    if (command.equals("SHOW_3D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        ThreeDVisualizerModule.setupNew3DVisualizer(selectedFiles[0]);
    }

    if (command.equals("SORT_FILES")) {
        // save current selection
        TreePath savedSelection[] = tree.getSelectionPaths();
        RawDataFile selectedFiles[] = tree.getSelectedObjects(RawDataFile.class);
        OrderDataFilesModule module = MZmineCore.getModuleInstance(OrderDataFilesModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(OrderDataFilesModule.class);
        params.getParameter(OrderDataFilesParameters.dataFiles)
                .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }

    if (command.equals("REMOVE_EXTENSION")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        for (RawDataFile file : selectedFiles) {
            file.setName(FilenameUtils.removeExtension(file.toString()));
        }
        tree.updateUI();
    }

    if (command.equals("REMOVE_FILE")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        PeakList allPeakLists[] = MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
        for (RawDataFile file : selectedFiles) {
            for (PeakList peakList : allPeakLists) {
                if (peakList.hasRawDataFile(file)) {
                    String msg = "Cannot remove file " + file.getName()
                            + ", because it is present in the peak list " + peakList.getName();
                    MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), msg);
                    return;
                }
            }
            MZmineCore.getProjectManager().getCurrentProject().removeFile(file);
        }
    }

    // Actions for scans

    if (command.equals("SHOW_SCAN")) {
        Scan selectedScans[] = tree.getSelectedObjects(Scan.class);
        for (Scan scan : selectedScans) {
            SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(), scan.getScanNumber());
        }
    }

    if (command.equals("SHOW_MASSLIST")) {
        MassList selectedMassLists[] = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            SpectraVisualizerWindow window = SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(),
                    scan.getScanNumber());
            MassListDataSet dataset = new MassListDataSet(massList);
            window.addDataSet(dataset, Color.green);
        }
    }

    if (command.equals("REMOVE_MASSLIST")) {
        MassList selectedMassLists[] = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            scan.removeMassList(massList);
        }
    }

    if (command.equals("REMOVE_ALL_MASSLISTS")) {
        MassList selectedMassLists[] = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            String massListName = massList.getName();
            RawDataFile dataFiles[] = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
            for (RawDataFile dataFile : dataFiles) {
                int scanNumbers[] = dataFile.getScanNumbers();
                for (int scanNum : scanNumbers) {
                    Scan scan = dataFile.getScan(scanNum);
                    MassList ml = scan.getMassList(massListName);
                    if (ml != null)
                        scan.removeMassList(ml);
                }
            }
        }
    }

    // Actions for peak lists

    if (command.equals("SHOW_PEAKLIST_TABLES")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            PeakListTableModule.showNewPeakListVisualizerWindow(peakList);
        }
    }

    if (command.equals("SHOW_PEAKLIST_INFO")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            InfoVisualizerModule.showNewPeakListInfo(peakList);
        }
    }

    if (command.equals("SHOW_SCATTER_PLOT")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            ScatterPlotVisualizerModule.showNewScatterPlotWindow(peakList);
        }
    }

    if (command.equals("SORT_PEAKLISTS")) {
        // save current selection
        TreePath savedSelection[] = tree.getSelectionPaths();
        PeakList selectedPeakLists[] = tree.getSelectedObjects(PeakList.class);
        OrderPeakListsModule module = MZmineCore.getModuleInstance(OrderPeakListsModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(OrderPeakListsModule.class);
        params.getParameter(OrderPeakListsParameters.peakLists)
                .setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }

    if (command.equals("REMOVE_PEAKLIST")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists)
            MZmineCore.getProjectManager().getCurrentProject().removePeakList(peakList);
    }

    // Actions for peak list rows

    if (command.equals("SHOW_PEAK_SUMMARY")) {
        PeakListRow[] selectedRows = tree.getSelectedObjects(PeakListRow.class);
        for (PeakListRow row : selectedRows) {
            PeakSummaryVisualizerModule.showNewPeakSummaryWindow(row);
        }
    }

}

From source file:de.fhg.iais.asc.xslt.binaries.DownloadAndScaleBinary.java

public List<Object> createAllVariants(List<PreviewImageType> previewTypes) {
    List<Object> result = new ArrayList<Object>();

    if (this.context.isTypeAllowed("orig")) {
        makeOriginalLocallyAvailable(DOWNLOAD_PERMANENT_ONLY);
    }//from ww w .  ja v  a  2s . co m

    if ((this.mimeType == null) || (this.mimeType.equals(""))) {
        this.mimeType = detectMimetype();

        if (this.mimeType.equals("video/quicktime")) {
            this.mimeType = "video/mp4";
        }
    }

    if (this.mimeType.startsWith("audio/") || this.mimeType.startsWith("video/")
            || this.mimeType.equals("application/pdf")) { // is audio, video or pdf
        if (this.mimeType.equals("video/vimeo")) { // if external video
            result.add(this.typeSubPath);
        } else if (this.locallyAvailableOriginal == this.permanentOriginal) {
            String filepath = "full" + "/" + this.typeSubPath;
            result.add(filepath);
            File binary = new File(this.context.getBinaryRoot() + "/" + filepath);
            try {
                FileUtils.copyFile(this.locallyAvailableOriginal, binary);

            } catch (IOException e) {
                LOG.error("Can't create directory 'full': " + e);

            }
        } else if (this.downloadableURI != null) {
            result.add(this.downloadableURI);
        }
    } else if (!this.mimeType.startsWith("image/")) {
        if (this.locallyAvailableOriginal != null) {
            this.locallyAvailableOriginal.delete();
        }
    }

    if ((this.mimeType.startsWith("image/") || (this.mimeType.equals("application/pdf")))) { // is image or pdf
        if (this.context.isAnyScaleAllowed()) {
            for (PreviewImageType previewType : previewTypes) {
                if (isPreviewAllowed(previewType)) {
                    final String previewTypeName = previewType.getType();
                    String scaled = previewTypeName + "/" + FilenameUtils.removeExtension(this.typeSubPath)
                            + ".jpg";
                    if (executeScale(previewType, scaled, this.mimeType)) {
                        result.add(scaled);
                    } else { // delete file if scaling could not be executed (e.g. damaged image)
                        if (this.locallyAvailableOriginal != null) {
                            this.locallyAvailableOriginal.delete();
                        }
                    }
                }
            }
        }
    }

    return result;
}

From source file:brooklyn.entity.dns.geoscaling.GeoscalingWebClient.java

public void createPrimaryDomain(String name) {
    try {/*  w  w w. j a va  2s . c  o  m*/
        name = name.toLowerCase();
        String url = MessageFormat.format("https://{0}/{1}?module=domains", HOST, PATH);

        HttpPost request = new HttpPost(url);
        List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2);
        nameValuePairs.add(new BasicNameValuePair("MAX_FILE_SIZE", "65536"));
        nameValuePairs.add(new BasicNameValuePair("domain", FilenameUtils.removeExtension(name)));
        nameValuePairs.add(new BasicNameValuePair("tld", FilenameUtils.getExtension(name)));
        request.setEntity(new UrlEncodedFormEntity(nameValuePairs));

        sendRequest(request, true);

    } catch (Exception e) {
        throw new RuntimeException("Failed to create GeoScaling smart subdomain: " + e, e);
    }

    primaryDomains = fetchPrimaryDomains();
}

From source file:ffx.xray.Rescore.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 va 2s  .c o  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, new ParallelTeam(),
                    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;
}