List of usage examples for org.apache.commons.io FilenameUtils removeExtension
public static String removeExtension(String filename)
From source file:eu.udig.style.advanced.utils.Utilities.java
/** * Generates a style based on a graphic. * //from ww w. j a v a 2 s . c om * @param graphicsPath the graphic. * @return the generated style. * @throws IOException */ public static StyleWrapper createStyleFromGraphic(File graphicsPath) throws IOException { String name = graphicsPath.getName(); ExternalGraphic exGraphic = null; if (name.toLowerCase().endsWith(".png")) { exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/png"); } else if (name.toLowerCase().endsWith(".svg")) { exGraphic = sf.createExternalGraphic(graphicsPath.toURI().toURL(), "image/svg+xml"); } else if (name.toLowerCase().endsWith(".sld")) { StyledLayerDescriptor sld = readStyle(graphicsPath); Style style = SLDs.getDefaultStyle(sld); return new StyleWrapper(style); } if (exGraphic == null) { throw new IOException("Style could not be created!"); } Graphic gr = sf.createDefaultGraphic(); gr.graphicalSymbols().clear(); gr.graphicalSymbols().add(exGraphic); Expression size = ff.literal(20); gr.setSize(size); Rule rule = sf.createRule(); PointSymbolizer pointSymbolizer = sf.createPointSymbolizer(gr, null); rule.symbolizers().add(pointSymbolizer); FeatureTypeStyle featureTypeStyle = sf.createFeatureTypeStyle(); featureTypeStyle.rules().add(rule); Style namedStyle = sf.createStyle(); namedStyle.featureTypeStyles().add(featureTypeStyle); namedStyle.setName(FilenameUtils.removeExtension(name)); return new StyleWrapper(namedStyle); }
From source file:com.mgmtp.perfload.loadprofiles.ui.AppFrame.java
/** * Exports the events file for perfLoad tests. This method is registered on the {@link EventBus} * and called when the specified event is posted. * //from w w w .j a v a2s . co m * @param e * the event that triggers calling of this method when posted on the event bus */ @Subscribe public void exportEventListForPerfLoad(final ToolsExportEventListAction.Event e) throws IOException { if (checkLoadProfileEntityDirty() && checkLoadProfilePropertiesDirty()) { File dir = loadProfileEventsFile != null ? loadProfileEventsFile : loadProfileConfigFile.getParentFile(); JFileChooser fc = SwingUtils.createFileChooser(dir, "Load Profile BaseLoadProfileEvent Files (*.perfload)", "perfload"); fc.setAccessory(new SaveAccessoryPanel()); if (loadProfileEventsFile == null) { loadProfileEventsFile = new File( FilenameUtils.removeExtension(loadProfileConfigFile.getAbsolutePath()) + ".perfload"); } File file = showSaveDialog(fc, loadProfileEventsFile, "perfload"); if (file != null) { loadProfileEventsFile = file; LoadProfileConfig lpc = createLoadProfileConfig(); LoadTestConfiguration ltc = loadProfilesController.createLoadTestConfiguration(lpc, getSelectedTargets(), getSelectedClients()); List<LoadCurveAssignment> loadCurveAssignments = ltc.getLoadCurveAssignments(); Set<Operation> operations = newHashSet(); int caCount = loadCurveAssignments.size(); double maxTime = 0; // max time for histogram creation List<LoadCurve> loadCurves = newArrayListWithCapacity(caCount); for (LoadCurveAssignment loadCurveAssignment : loadCurveAssignments) { LoadCurve loadCurve = loadCurveAssignment.getLoadCurve(); loadCurves.add(loadCurve); operations.add(loadCurveAssignment.getOperation()); double[] timeValues = loadCurve.getTimeValues(); maxTime = max(maxTime, timeValues[timeValues.length - 1]); } EventDistributor.addScaledLoadCurvesToAssignments(ltc, loadCurves); List<LoadEvent> clientEventList = EventDistributor.createClientEventList(ltc); List<BaseLoadProfileEvent> events = newArrayListWithExpectedSize(clientEventList.size()); // One time and marker events are added separately for (OneTime oneTime : getOneTimes()) { double startTimeInHours = oneTime.t0 / 60d; // We must add one event per target for (Target target : oneTime.targets) { LoadEvent event = new LoadEvent(startTimeInHours, oneTime.getOperation()); event.setProcessId(0); // 1 added later to make it zero-based event.setDaemonId(1); event.setTarget(target); clientEventList.add(event); } } events.addAll(clientEventList); for (Marker marker : getMarkers()) { double time = marker.left / 60d; MarkerEvent event = new MarkerEvent(marker.name, time, MarkerEvent.Type.left); events.add(event); time = marker.right / 60d; event = new MarkerEvent(marker.name, time, MarkerEvent.Type.right); events.add(event); } Collections.sort(events, new LoadEventComparator()); StrBuilder sb = new StrBuilder(); sb.appendln("# Created: " + new Date()); sb.appendln("# Load Profile Config File: " + loadProfileConfigFile.getName()); sb.append("# Load Profile Name: " + txtName.getText()); EventDistributor.writeEventListForPerfLoadClientsToFile(file, sb.toString(), events); // Create additional histogram file if selected dir = file.getParentFile(); final String baseName = FilenameUtils.getBaseName(file.getName()); int numClients = ltc.getClients().size(); SaveAccessoryPanel sap = (SaveAccessoryPanel) fc.getAccessory(); Collection<LoadEvent> loadEvents = transform(filter(clientEventList, new IsLoadEventPredicate()), new EventToLoadEventFunction()); if (sap.isEventDistriChecked()) { for (int i = 0; i < numClients; ++i) { for (LoadCurve loadCurve : loadCurves) { File f = new File(dir, baseName + "-event-distri-client-" + i + "-" + loadCurve.getName() + ".csv"); PlotFileCreator.createPlot(f, loadEvents, loadCurve, i, LoadCurveCalculator.timeUnit_minute); } } } if (sap.isOperationHistogramChecked()) { for (Operation operation : operations) { String opName = operation.getName(); File f = new File(dir, baseName + "-histogram-operation-" + opName + ".csv"); PlotFileCreator.createOperationHistogram(f, loadEvents, opName, (int) maxTime * 2, 0., maxTime, LoadCurveCalculator.timeUnit_minute); } } if (sap.isClientLoadHistrogramChecked()) { for (int i = 0; i < numClients; i++) { File f = new File(dir, baseName + "-histogram-client-load-" + i + ".csv"); PlotFileCreator.createClientHistogram(f, loadEvents, i, (int) maxTime * 2, 0., maxTime, LoadCurveCalculator.timeUnit_minute); } } } } }
From source file:ffx.algorithms.mc.RosenbluthChiAllMove.java
/** * For validation. Performs Monte Carlo chi moves WITHOUT biasing. * Give ALL CHIs a random theta simultaneously. * Accept on the vanilla Metropolis criterion. *///from w w w . j a va 2 s . c om private boolean engage_controlAll() { report.append(String.format(" Rosenbluth Control Move: %4d %s\n", moveNumber, target)); double origEnergy = totalEnergy(); double origChi[] = RotamerLibrary.measureRotamer(target, false); double newChi[] = new double[origChi.length]; System.arraycopy(origChi, 0, newChi, 0, origChi.length); for (int i = 0; i < origChi.length; i++) { if (doChi[i]) { double theta = rand.nextDouble(360.0) - 180; newChi[i] = theta; } } proposedChis = newChi; Rotamer newState = createRotamer(target, newChi); RotamerLibrary.applyRotamer(target, newState); finalEnergy = totalEnergy(); if (this.finalEnergy < CATASTROPHE_THRESHOLD) { report.append("\nWARNING: Multipole catastrophe in CBMC.\n"); report.append(" Discarding move.\n"); target.revertState(origState); updateAll(); Wn = -1.0; Wo = 1000; logger.info(report.toString()); return false; } double dU = finalEnergy - origEnergy; double criterion = FastMath.exp(-beta * dU); double rng = rand.nextDouble(); report.append(String.format(" move (thetas): ")); for (int i = 0; i < newChi.length; i++) { report.append(String.format("%7.2f ", newChi[i])); } report.append(String.format("\n")); report.append(String.format(" orig, final, dU: %.2g %.2g %.2g\n", origEnergy, finalEnergy, dU)); report.append(String.format(" crit, rng: %.2g %.2g\n", criterion, rng)); if (rng < criterion) { accepted = true; numAccepted++; report.append(String.format(" Accepted! %5d NewEnergy: %.4f Chi:", numAccepted, finalEnergy)); for (int k = 0; k < proposedChis.length; k++) { report.append(String.format(" %7.2f", proposedChis[k])); } report.append(String.format("\n")); updateAll(); if (!noSnaps) { PDBFilter writer = new PDBFilter(mola.getFile(), mola, null, null); String filename = FilenameUtils.removeExtension(mola.getFile().toString()); filename = mola.getFile().getAbsolutePath(); if (!filename.contains("_mc")) { filename = FilenameUtils.removeExtension(filename) + "_mc.pdb"; } File file = new File(filename); writer.writeFile(file, false); } } else { accepted = false; report.append(String.format(" Denied. %5d NewEnergy: %.4f Chi:", numAccepted, origEnergy)); for (int k = 0; k < origChi.length; k++) { report.append(String.format(" %7.2f", origChi[k])); } report.append(String.format("\n")); target.revertState(origState); } updateAll(); endTime = System.nanoTime(); double took = (endTime - startTime) * NS_TO_MS; if (logTimings) { report.append(String.format(" Timing (ms): %.2f", took)); } logger.info(report.toString()); return accepted; }
From source file:net.minecraftforge.common.ForgeHooks.java
private static boolean loadAdvancements(Map<ResourceLocation, Advancement.Builder> map, ModContainer mod) { return CraftingHelper.findFiles(mod, "assets/" + mod.getModId() + "/advancements", null, (root, file) -> { 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(mod.getModId(), name); if (!map.containsKey(key)) { BufferedReader reader = null; try { reader = Files.newBufferedReader(file); Advancement.Builder builder = JsonUtils.fromJson(AdvancementManager.GSON, reader, Advancement.Builder.class); map.put(key, builder);/* w ww . j ava 2 s . c o m*/ } catch (JsonParseException jsonparseexception) { FMLLog.log.error("Parsing error loading built-in advancement " + key, (Throwable) jsonparseexception); return false; } catch (IOException ioexception) { FMLLog.log.error("Couldn't read advancement " + key + " from " + file, (Throwable) ioexception); return false; } finally { IOUtils.closeQuietly(reader); } } return true; }); }
From source file:it.drwolf.ridire.session.async.Mapper.java
private File uncompressGzippedArcFile(File f) throws IOException { FileInputStream fin = new FileInputStream(f.getAbsolutePath()); BufferedInputStream in = new BufferedInputStream(fin); File uncompressedFile = new File(FilenameUtils.removeExtension(f.getAbsolutePath())); FileOutputStream out = new FileOutputStream(uncompressedFile); GzipCompressorInputStream gzIn = new GzipCompressorInputStream(in, true); final byte[] buffer = new byte[1024]; int n = 0;// www .j av a 2 s. c o m while (-1 != (n = gzIn.read(buffer))) { out.write(buffer, 0, n); } out.close(); gzIn.close(); return uncompressedFile; }
From source file:ffx.algorithms.DiscountPh.java
private void writeSnapshot(String extension) { String filename = FilenameUtils.removeExtension(originalFilename); if (snapshotType == Snapshots.INTERLEAVED) { if (filename.contains("_dyn")) { filename = filename.replace("_dyn", format("_dyn_%d.pdb", ++snapshotIndex)); } else {//from w w w. j a v a 2s . co m filename = FilenameUtils.removeExtension(filename) + format("_dyn_%d.pdb", ++snapshotIndex); } } else { if (!extension.startsWith(".")) { extension = "." + extension; } filename = filename + format("_%d", ++snapshotIndex) + extension; } File file = new File(filename); PDBFilter writer = new PDBFilter(file, mola, null, null); writer.writeFile(file, false); }
From source file:ffx.potential.ForceFieldEnergy.java
/** * <p>/*from w w w . jav a2 s . co m*/ * energy</p> * * @param gradient a boolean. * @param print a boolean. * @return a double. */ public double energy(boolean gradient, boolean print) { try { bondTime = 0; angleTime = 0; stretchBendTime = 0; ureyBradleyTime = 0; outOfPlaneBendTime = 0; torsionTime = 0; piOrbitalTorsionTime = 0; torsionTorsionTime = 0; improperTorsionTime = 0; vanDerWaalsTime = 0; electrostaticTime = 0; restraintBondTime = 0; ncsTime = 0; coordRestraintTime = 0; totalTime = System.nanoTime(); // Zero out the potential energy of each bonded term. bondEnergy = 0.0; angleEnergy = 0.0; stretchBendEnergy = 0.0; ureyBradleyEnergy = 0.0; outOfPlaneBendEnergy = 0.0; torsionEnergy = 0.0; piOrbitalTorsionEnergy = 0.0; torsionTorsionEnergy = 0.0; improperTorsionEnergy = 0.0; totalBondedEnergy = 0.0; // Zero out potential energy of restraint terms restraintBondEnergy = 0.0; ncsEnergy = 0.0; restrainEnergy = 0.0; // Zero out bond and angle RMSDs. bondRMSD = 0.0; angleRMSD = 0.0; // Zero out the potential energy of each non-bonded term. vanDerWaalsEnergy = 0.0; permanentMultipoleEnergy = 0.0; polarizationEnergy = 0.0; totalElectrostaticEnergy = 0.0; totalNonBondedEnergy = 0.0; // Zero out the solvation energy. solvationEnergy = 0.0; // Zero out the relative solvation energy (sequence optimization) relativeSolvationEnergy = 0.0; nRelativeSolvations = 0; esvBias = 0.0; // Zero out the total potential energy. totalEnergy = 0.0; // Zero out the Cartesian coordinate gradient for each atom. if (gradient) { for (int i = 0; i < nAtoms; i++) { atoms[i].setXYZGradient(0.0, 0.0, 0.0); atoms[i].setLambdaXYZGradient(0.0, 0.0, 0.0); } } /** * Computed the bonded energy terms in parallel. */ try { bondedRegion.setGradient(gradient); parallelTeam.execute(bondedRegion); } catch (Exception e) { e.printStackTrace(); logger.severe(e.toString()); } if (!lambdaBondedTerms) { /** * Compute restraint terms. */ if (ncsTerm) { ncsTime = -System.nanoTime(); ncsEnergy = ncsRestraint.residual(gradient, print); ncsTime += System.nanoTime(); } if (restrainTerm && !coordRestraints.isEmpty()) { coordRestraintTime = -System.nanoTime(); for (CoordRestraint restraint : coordRestraints) { restrainEnergy += restraint.residual(gradient, print); } coordRestraintTime += System.nanoTime(); } if (comTerm) { comRestraintTime = -System.nanoTime(); comRestraintEnergy = comRestraint.residual(gradient, print); comRestraintTime += System.nanoTime(); } /** * Compute non-bonded terms. */ if (vanderWaalsTerm) { vanDerWaalsTime = -System.nanoTime(); vanDerWaalsEnergy = vanderWaals.energy(gradient, print); nVanDerWaalInteractions = this.vanderWaals.getInteractions(); vanDerWaalsTime += System.nanoTime(); } if (multipoleTerm) { electrostaticTime = -System.nanoTime(); totalElectrostaticEnergy = particleMeshEwald.energy(gradient, print); permanentMultipoleEnergy = particleMeshEwald.getPermanentEnergy(); polarizationEnergy = particleMeshEwald.getPolarizationEnergy(); nPermanentInteractions = particleMeshEwald.getInteractions(); solvationEnergy = particleMeshEwald.getGKEnergy(); nGKInteractions = particleMeshEwald.getGKInteractions(); electrostaticTime += System.nanoTime(); } } if (relativeSolvationTerm) { List<Residue> residuesList = molecularAssembly.getResidueList(); for (Residue residue : residuesList) { if (residue instanceof MultiResidue) { Atom refAtom = residue.getSideChainAtoms().get(0); if (refAtom != null && refAtom.getUse()) { /** * Reasonably confident that it should be -=, as we * are trying to penalize residues with strong * solvation energy. */ double thisSolvation = relativeSolvation.getSolvationEnergy(residue, false); relativeSolvationEnergy -= thisSolvation; if (thisSolvation != 0) { nRelativeSolvations++; } } } } } totalTime = System.nanoTime() - totalTime; totalBondedEnergy = bondEnergy + restraintBondEnergy + angleEnergy + stretchBendEnergy + ureyBradleyEnergy + outOfPlaneBendEnergy + torsionEnergy + piOrbitalTorsionEnergy + improperTorsionEnergy + torsionTorsionEnergy + ncsEnergy + restrainEnergy; totalNonBondedEnergy = vanDerWaalsEnergy + totalElectrostaticEnergy + relativeSolvationEnergy; totalEnergy = totalBondedEnergy + totalNonBondedEnergy + solvationEnergy; if (esvTerm) { esvBias = esvSystem.getBiasEnergy(null); totalEnergy += esvBias; } } catch (EnergyException ex) { if (printOnFailure) { String timeString = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy_MM_dd-HH_mm_ss")); String filename = String.format("%s-ERROR-%s.pdb", FilenameUtils.removeExtension(molecularAssembly.getFile().getName()), timeString); PotentialsFunctions ef = new PotentialsUtils(); filename = ef.versionFile(filename); logger.info(String.format(" Writing on-error snapshot to file %s", filename)); ef.saveAsPDB(molecularAssembly, new File(filename)); } if (ex.doCauseSevere()) { logger.log(Level.SEVERE, " Error in calculating energies or gradients", ex); return 0.0; } else { throw ex; // Rethrow exception } } if (print || printOverride) { if (printCompact) { logger.info(this.toString()); } else { StringBuilder sb = new StringBuilder(); if (gradient) { sb.append("\n Computed Potential Energy and Atomic Coordinate Gradients\n"); } else { sb.append("\n Computed Potential Energy\n"); } sb.append(this); logger.info(sb.toString()); } } return totalEnergy; }
From source file:WpRDFFunctionLibrary.java
public static void mergeGpmltoSingleFile(String gpmlLocation) throws IOException, XMLStreamException, ParserConfigurationException, SAXException, TransformerException { // Based on: http://stackoverflow.com/questions/10759775/how-to-merge-1000-xml-files-into-one-in-java //for (int i = 1; i < 8 ; i++) { Writer outputWriter = new FileWriter("/tmp/WpGPML.xml"); XMLOutputFactory xmlOutFactory = XMLOutputFactory.newFactory(); XMLEventWriter xmlEventWriter = xmlOutFactory.createXMLEventWriter(outputWriter); XMLEventFactory xmlEventFactory = XMLEventFactory.newFactory(); xmlEventWriter.add(xmlEventFactory.createStartDocument("ISO-8859-1", "1.0")); xmlEventWriter.add(xmlEventFactory.createStartElement("", null, "PathwaySet")); xmlEventWriter.add(xmlEventFactory.createAttribute("creationData", basicCalls.now())); XMLInputFactory xmlInFactory = XMLInputFactory.newFactory(); File dir = new File(gpmlLocation); File[] rootFiles = dir.listFiles(); //the section below is only in case of analysis sets for (File rootFile : rootFiles) { String fileName = FilenameUtils.removeExtension(rootFile.getName()); System.out.println(fileName); String[] identifiers = fileName.split("_"); System.out.println(fileName); String wpIdentifier = identifiers[identifiers.length - 2]; String wpRevision = identifiers[identifiers.length - 1]; //Pattern pattern = Pattern.compile("_(WP[0-9]+)_([0-9]+).gpml"); //Matcher matcher = pattern.matcher(fileName); //System.out.println(matcher.find()); //String wpIdentifier = matcher.group(1); File tempFile = new File(constants.localAllGPMLCacheDir() + wpIdentifier + "_" + wpRevision + ".gpml"); //System.out.println(matcher.group(1)); //String wpRevision = matcher.group(2); //System.out.println(matcher.group(2)); if (!(tempFile.exists())) { System.out.println(tempFile.getName()); Document currentGPML = basicCalls.openXmlFile(rootFile.getPath()); basicCalls.saveDOMasXML(WpRDFFunctionLibrary.addWpProvenance(currentGPML, wpIdentifier, wpRevision), constants.localCurrentGPMLCache() + tempFile.getName()); }/*from w w w.j a v a 2 s. c om*/ } dir = new File("/tmp/GPML"); rootFiles = dir.listFiles(); for (File rootFile : rootFiles) { System.out.println(rootFile); XMLEventReader xmlEventReader = xmlInFactory.createXMLEventReader(new StreamSource(rootFile)); XMLEvent event = xmlEventReader.nextEvent(); // Skip ahead in the input to the opening document element try { while (event.getEventType() != XMLEvent.START_ELEMENT) { event = xmlEventReader.nextEvent(); } do { xmlEventWriter.add(event); event = xmlEventReader.nextEvent(); } while (event.getEventType() != XMLEvent.END_DOCUMENT); xmlEventReader.close(); } catch (Exception e) { System.out.println("Malformed gpml file"); } } xmlEventWriter.add(xmlEventFactory.createEndElement("", null, "PathwaySet")); xmlEventWriter.add(xmlEventFactory.createEndDocument()); xmlEventWriter.close(); outputWriter.close(); }
From source file:com.iyonger.apm.web.service.PerfTestService.java
private String buildReportName(String key, File file) { String reportName = FilenameUtils.removeExtension(file.getName()); if (key.equals(reportName)) { return reportName; }/*from w w w . j a v a 2s . com*/ String[] baseName = StringUtils.split(reportName, "-", 2); if (SingleConsole.INTERESTING_PER_TEST_STATISTICS.contains(baseName[0]) && baseName.length >= 2) { reportName = baseName[1]; } return reportName; }
From source file:ffx.potential.ForceFieldEnergy.java
/** * {@inheritDoc}/* ww w . j a v a 2 s. c o m*/ */ @Override public double energyAndGradient(double x[], double g[], boolean verbose) { /** * Un-scale the coordinates. */ if (optimizationScaling != null) { int len = x.length; for (int i = 0; i < len; i++) { x[i] /= optimizationScaling[i]; } } setCoordinates(x); double e = energy(true, verbose); // Try block already exists inside energy(boolean, boolean), so only // need to try-catch getGradients. try { getGradients(g); /** * Scale the coordinates and gradients. */ if (optimizationScaling != null) { int len = x.length; for (int i = 0; i < len; i++) { x[i] *= optimizationScaling[i]; g[i] /= optimizationScaling[i]; } } return e; } catch (EnergyException ex) { ex.printStackTrace(); if (printOnFailure) { String timeString = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy_MM_dd-HH_mm_ss")); String filename = String.format("%s-ERROR-%s.pdb", FilenameUtils.removeExtension(molecularAssembly.getFile().getName()), timeString); PotentialsFunctions ef = new PotentialsUtils(); filename = ef.versionFile(filename); logger.info(String.format(" Writing on-error snapshot to file %s", filename)); ef.saveAsPDB(molecularAssembly, new File(filename)); } if (ex.doCauseSevere()) { ex.printStackTrace(); logger.log(Level.SEVERE, " Error in calculating energies or gradients", ex); } else { ex.printStackTrace(); throw ex; // Rethrow exception } return 0; // Should ordinarily be unreachable. } }