List of usage examples for org.apache.commons.collections CollectionUtils addAll
public static void addAll(Collection collection, Object[] elements)
From source file:edu.isi.misd.scanner.network.registry.web.controller.StudyController.java
@RequestMapping(value = BASE_PATH, method = { RequestMethod.GET,
RequestMethod.HEAD }, produces = HEADER_JSON_MEDIA_TYPE)
public @ResponseBody List<Study> getStudies(@RequestParam Map<String, String> paramMap) {
Map<String, String> params = validateParameterMap(paramMap, REQUEST_PARAM_STUDY_NAME,
REQUEST_PARAM_USER_NAME);//from w w w. jav a 2 s. c o m
String studyName = params.get(REQUEST_PARAM_STUDY_NAME);
String userName = params.get(REQUEST_PARAM_USER_NAME);
List<Study> studies = new ArrayList<Study>();
if (studyName != null) {
Study study = studyRepository.findByStudyName(studyName);
if (study == null) {
throw new ResourceNotFoundException(studyName);
}
studies.add(study);
} else if (userName != null) {
return studyRepository.findStudiesForUserName(userName);
} else {
Iterator iter = studyRepository.findAll().iterator();
CollectionUtils.addAll(studies, iter);
}
return studies;
}
From source file:com.google.gdt.eclipse.designer.launch.AbstractGwtLaunchConfigurationDelegate.java
public String[] getClasspathAll(ILaunchConfiguration configuration) throws CoreException { List<String> entries = new ArrayList<String>(); // add source folders IProject project;// ww w.ja va 2s . co m { String projectName = configuration.getAttribute(IJavaLaunchConfigurationConstants.ATTR_PROJECT_NAME, ""); project = Utils.getProject(projectName); addSourceFolders(new HashSet<IProject>(), entries, project); } // add usual project classpath entries // we add them after source folders because GWT Shell compiles sources itself { String[] originalEntries = super.getClasspath(configuration); CollectionUtils.addAll(entries, originalEntries); } // add GWT DEV jar entries.add(Utils.getDevLibPath(project).toPortableString()); // return entries.toArray(new String[entries.size()]); }
From source file:com.esofthead.mycollab.spring.MyBatisConfiguration.java
private Resource[] buildBatchMapperResources(String... resourcesPath) throws IOException { ArrayList<Resource> resources = new ArrayList<>(); for (String resourcePath : resourcesPath) { CollectionUtils.addAll(resources, buildMapperResources(resourcePath)); }/*from w w w .ja va 2s .c om*/ return resources.toArray(new Resource[0]); }
From source file:edu.scripps.fl.curves.CurveFit.java
public static void fit(Curve curve) { log.debug("Fitting Curve: " + curve); double y[] = (double[]) ConvertUtils.convert(curve.getResponses(), double[].class); double x[] = (double[]) ConvertUtils.convert(curve.getConcentrations(), double[].class); for (int ii = 0; ii < x.length; ii++) x[ii] = Math.log10(x[ii]); // max, min and range double minY = Double.MAX_VALUE; double maxY = -Double.MAX_VALUE; double maxResp = y[y.length - 1]; for (int i = 0; i < y.length; i++) { minY = Math.min(minY, y[i]); maxY = Math.max(maxY, y[i]); }//from w ww .j av a 2 s . co m curve.setResponseMin(minY); curve.setResponseMax(maxY); curve.setResponseRange(maxY - minY); curve.setMaxResponse(maxResp); // fit boolean flags[] = null; Map maps[] = null; double fitValues[] = null; Object fitResults[] = HillFit.doHill(x, y, null, HillConstants.FIT_ITER_NO, HillConstants.P4_FIT); if (fitResults != null) { flags = (boolean[]) fitResults[0]; fitValues = (double[]) fitResults[1]; maps = (Map[]) fitResults[2]; } if (fitValues != null) { curve.setYZero(fitValues[6]); curve.setLogEC50(fitValues[0]); curve.setYInflection(fitValues[1]); curve.setHillSlope(fitValues[2]); curve.setR2(fitValues[3]); double ec50 = 1000000D * Math.exp(Math.log(10D) * curve.getLogEC50()); double testEC50 = Math.pow(10, curve.getLogEC50()); Double ic50 = null; double logIC50 = BatchHill.iccalc(curve.getYZero(), curve.getYInflection(), curve.getLogEC50(), curve.getHillSlope(), 50D); if (logIC50 < 0.0D) ic50 = 1000000D * Math.exp(Math.log(10D) * logIC50); int dn = Math.max(1, x.length - 4); double df = dn; double p = HillStat.calcPValue(curve.getYZero(), curve.getYInflection(), curve.getLogEC50(), curve.getHillSlope(), x, y, flags); int mask = 0; for (int i = 0; i < x.length; i++) if (!flags[i]) mask++; double ss = HillStat.calcHillDeviation(curve.getLogEC50(), curve.getYZero(), curve.getYInflection(), curve.getHillSlope(), flags, null, x, y); curve.setEC50(ec50); curve.setIC50(ic50); curve.setPHill(p); curve.setSYX(ss / df); for (int ii = 0; ii < flags.length; ii++) { if (flags[ii] == true) { curve.setMasked(true); break; } } } else { curve.setLogEC50(null); curve.setHillSlope(null); curve.setR2(null); curve.setYInflection(null); curve.setYZero(null); curve.setEC50(null); curve.setIC50(null); curve.setPHill(null); curve.setSYX(null); curve.setMasked(false); flags = new boolean[x.length]; } // masks List<Boolean> masks = new ArrayList<Boolean>(flags.length); CollectionUtils.addAll(masks, (Boolean[]) ConvertUtils.convert(flags, Boolean[].class)); curve.setMask(masks); // classify curveClassification(curve, y, x, flags); // rank double rank = -BatchHill.calcRank(curve.getCurveClass(), curve.getMaxResponse(), curve.getResponseRange()); curve.setRank(rank); }
From source file:edu.isi.misd.scanner.network.registry.web.controller.StudyRequestedSiteController.java
@RequestMapping(value = BASE_PATH, method = { RequestMethod.GET,
RequestMethod.HEAD }, produces = HEADER_JSON_MEDIA_TYPE)
public @ResponseBody List<StudyRequestedSite> getStudyRequestedSites(
@RequestParam Map<String, String> paramMap) {
Map<String, String> params = validateParameterMap(paramMap, REQUEST_PARAM_SITE_ID, REQUEST_PARAM_STUDY_ID);
String siteId = params.get(REQUEST_PARAM_SITE_ID);
String studyId = params.get(REQUEST_PARAM_STUDY_ID);
List<StudyRequestedSite> studyRequestedSites = new ArrayList<StudyRequestedSite>();
if (siteId != null) {
return studyRequestedSiteRepository
.findBySiteSiteId(validateIntegerParameter(REQUEST_PARAM_SITE_ID, siteId));
} else if (studyId != null) {
return studyRequestedSiteRepository
.findByStudyStudyId(validateIntegerParameter(REQUEST_PARAM_STUDY_ID, studyId));
} else {// w ww.jav a 2 s . c om
Iterator iter = studyRequestedSiteRepository.findAll().iterator();
CollectionUtils.addAll(studyRequestedSites, iter);
}
return studyRequestedSites;
}
From source file:edu.isi.misd.scanner.network.registry.web.controller.AnalysisInstanceController.java
@RequestMapping(value = BASE_PATH, method = { RequestMethod.GET,
RequestMethod.HEAD }, produces = HEADER_JSON_MEDIA_TYPE)
public @ResponseBody List<AnalysisInstance> getAnalysisInstances(@RequestParam Map<String, String> paramMap) {
Map<String, String> params = validateParameterMap(paramMap, REQUEST_PARAM_STUDY_ID,
REQUEST_PARAM_USER_NAME);// www. j a va 2s .co m
if (!params.isEmpty()) {
String studyId = params.get(REQUEST_PARAM_STUDY_ID);
String userName = params.get(REQUEST_PARAM_USER_NAME);
if ((studyId != null) && (userName != null)) {
return analysisInstanceRepository.findByStudyIdAndUserNameFilteredByStudyRole(
validateIntegerParameter(REQUEST_PARAM_STUDY_ID, studyId), userName);
}
if (studyId != null) {
return analysisInstanceRepository
.findByStudyStudyId(validateIntegerParameter(REQUEST_PARAM_STUDY_ID, studyId));
}
if (studyId == null) {
throw new BadRequestException("Required parameter missing: " + REQUEST_PARAM_STUDY_ID);
}
}
List<AnalysisInstance> analysisInstances = new ArrayList<AnalysisInstance>();
Iterator iter = analysisInstanceRepository.findAll().iterator();
CollectionUtils.addAll(analysisInstances, iter);
return analysisInstances;
}
From source file:edu.isi.misd.scanner.network.registry.web.controller.DataSetDefinitionController.java
@RequestMapping(value = BASE_PATH, method = { RequestMethod.GET,
RequestMethod.HEAD }, produces = HEADER_JSON_MEDIA_TYPE)
public @ResponseBody List<DataSetDefinition> getDataSetDefinitions(@RequestParam Map<String, String> paramMap) {
Map<String, String> params = validateParameterMap(paramMap, REQUEST_PARAM_STUDY_ID,
REQUEST_PARAM_USER_NAME);/*from w w w . ja va2 s . co m*/
if (!params.isEmpty()) {
String studyId = params.get(REQUEST_PARAM_STUDY_ID);
String userName = params.get(REQUEST_PARAM_USER_NAME);
if ((studyId != null) && (userName != null)) {
return dataSetDefinitionRepository.findDataSetsForStudyIdAndUserNameFilteredByStudyPolicy(
validateIntegerParameter(REQUEST_PARAM_STUDY_ID, studyId), userName);
}
if (studyId != null) {
return dataSetDefinitionRepository.findDataSetsForStudyIdFilteredByStudyPolicy(
validateIntegerParameter(REQUEST_PARAM_STUDY_ID, studyId));
}
if (studyId == null) {
throw new BadRequestException("Required parameter missing: " + REQUEST_PARAM_STUDY_ID);
}
}
List<DataSetDefinition> dataSetDefinitions = new ArrayList<DataSetDefinition>();
Iterator iter = dataSetDefinitionRepository.findAll().iterator();
CollectionUtils.addAll(dataSetDefinitions, iter);
return dataSetDefinitions;
}
From source file:de.xirp.ui.widgets.dialogs.ProfileLookupDialog.java
/** * Opens the dialog.//from ww w . java 2s. co m * * @return The chosen profile. * * @see de.xirp.profile.Profile */ public Profile open() { dialogShell = new XShell(parent, SWT.DIALOG_TRIM | SWT.APPLICATION_MODAL); dialogShell.addShellListener(new ShellAdapter() { /* (non-Javadoc) * @see org.eclipse.swt.events.ShellAdapter#shellClosed(org.eclipse.swt.events.ShellEvent) */ @Override public void shellClosed(ShellEvent e) { SWTUtil.secureDispose(dialogShell); } }); dialogShell.setSize(WIDTH, HEIGHT); dialogShell.setTextForLocaleKey("ProfileLookupDialog.gui.title"); //$NON-NLS-1$ image = ImageManager.getSystemImage(SystemImage.QUESTION); dialogShell.setImage(image); SWTUtil.setGridLayout(dialogShell, 2, true); list = new XList(dialogShell, SWT.BORDER | SWT.SINGLE | SWT.H_SCROLL | SWT.V_SCROLL); SWTUtil.setGridData(list, true, true, SWT.FILL, SWT.FILL, 2, 1); profiles = new ArrayList<Profile>(ProfileManager.getProfiles()); profiles.addAll(ProfileManager.getIncompleteProfiles()); for (Profile p : profiles) { Vector<String> itm = new Vector<String>(); CollectionUtils.addAll(itm, list.getItems()); if (!itm.contains(p)) { if (p.isComplete()) { list.add(p.getName() + I18n.getString("ProfileLookupDialog.list.postfix.complete")); //$NON-NLS-1$ } else { list.add(p.getName() + I18n.getString("ProfileLookupDialog.list.postfix.incomplete")); //$NON-NLS-1$ } } } list.addSelectionListener(new SelectionAdapter() { /* (non-Javadoc) * @see org.eclipse.swt.events.ShellAdapter#shellClosed(org.eclipse.swt.events.ShellEvent) */ @Override public void widgetSelected(SelectionEvent e) { if (list.getSelectionCount() > 0) { ok.setEnabled(true); } else { ok.setEnabled(false); } } }); ok = new XButton(dialogShell, XButtonType.OK); ok.setEnabled(false); SWTUtil.setGridData(ok, true, false, SWT.FILL, SWT.CENTER, 1, 1); ok.addSelectionListener(new SelectionAdapter() { /* (non-Javadoc) * @see org.eclipse.swt.events.ShellAdapter#shellClosed(org.eclipse.swt.events.ShellEvent) */ @Override public void widgetSelected(SelectionEvent e) { int idx = list.getSelectionIndex(); profile = profiles.get(idx); dialogShell.close(); } }); cancel = new XButton(dialogShell, XButtonType.CANCEL); SWTUtil.setGridData(cancel, true, false, SWT.FILL, SWT.CENTER, 1, 1); cancel.addSelectionListener(new SelectionAdapter() { /* (non-Javadoc) * @see org.eclipse.swt.events.ShellAdapter#shellClosed(org.eclipse.swt.events.ShellEvent) */ @Override public void widgetSelected(SelectionEvent e) { dialogShell.close(); } }); dialogShell.setDefaultButton(ok); list.setSelectionWithEvent(0); dialogShell.layout(); SWTUtil.centerDialog(dialogShell); dialogShell.open(); SWTUtil.blockDialogFromReturning(dialogShell); return profile; }
From source file:edu.cornell.med.icb.R.RUtils.java
/** * Can be used to start a rserve instance. * @param threadPool The ExecutorService used to start the Rserve process * @param rServeCommand Full path to command used to start Rserve process * @param host Host where the command should be sent * @param port Port number where the command should be sent * @param username Username to send to the server if authentication is required * @param password Password to send to the server if authentication is required * @return The return value from the Rserve instance *//* w w w . j a va 2 s . co m*/ static Future<Integer> startup(final ExecutorService threadPool, final String rServeCommand, final String host, final int port, final String username, final String password) { if (LOG.isInfoEnabled()) { LOG.info("Attempting to start Rserve on " + host + ":" + port); } return threadPool.submit(new Callable<Integer>() { public Integer call() throws IOException { final List<String> commands = new ArrayList<String>(); // if the host is not local, use ssh to exec the command if (!"localhost".equals(host) && !"127.0.0.1".equals(host) && !InetAddress.getLocalHost().equals(InetAddress.getByName(host))) { commands.add("ssh"); commands.add(host); } // TODO - this will fail when spaces are in the the path to the executable CollectionUtils.addAll(commands, rServeCommand.split(" ")); commands.add("--RS-port"); commands.add(Integer.toString(port)); final String[] command = commands.toArray(new String[commands.size()]); LOG.debug(ArrayUtils.toString(commands)); final ProcessBuilder builder = new ProcessBuilder(command); builder.redirectErrorStream(true); final Process process = builder.start(); BufferedReader br = null; try { final InputStream is = process.getInputStream(); final InputStreamReader isr = new InputStreamReader(is); br = new BufferedReader(isr); String line; while ((line = br.readLine()) != null) { if (LOG.isDebugEnabled()) { LOG.debug(host + ":" + port + "> " + line); } } process.waitFor(); if (LOG.isInfoEnabled()) { LOG.info("Rserve on " + host + ":" + port + " terminated"); } } catch (InterruptedException e) { LOG.error("Interrupted!", e); process.destroy(); Thread.currentThread().interrupt(); } finally { IOUtils.closeQuietly(br); } final int exitValue = process.exitValue(); if (LOG.isInfoEnabled()) { LOG.info("Rserve on " + host + ":" + port + " returned " + exitValue); } return exitValue; } }); }
From source file:com.cyclopsgroup.waterview.navigator.impl.DefaultNavigatorNode.java
/** * Overwrite or implement method getParentNodes() * * @see com.cyclopsgroup.waterview.navigator.NavigatorNode#getParentNodes() *//*from w ww . j a v a 2 s. c om*/ public synchronized NavigatorNode[] getParentNodes() { if (parentNodes == null) { List parents = new ArrayList(); NavigatorNode parent = (NavigatorNode) getParentNode(); if (parent != null) { CollectionUtils.addAll(parents, parent.getParentNodes()); parents.add(parent); } parentNodes = (NavigatorNode[]) parents.toArray(NavigatorNode.EMPTY_ARRAY); } return parentNodes; }