List of usage examples for java.util LinkedList remove
public E remove(int index)
From source file:com.github.lindenb.jvarkit.tools.misc.BamTile.java
@Override public Collection<Throwable> call(final String inputName) throws Exception { SAMRecordIterator iter = null;/*from w w w .j av a2 s. c o m*/ SamReader sfr = null; SAMFileWriter sfw = null; try { sfr = openSamReader(inputName); SAMFileHeader header1 = sfr.getFileHeader(); if (header1 == null) { return wrapException("File header missing"); } if (header1.getSortOrder() != SAMFileHeader.SortOrder.coordinate) { return wrapException("File header not sorted on coordinate"); } SAMFileHeader header2 = header1.clone(); header2.addComment(getName() + ":" + getVersion() + ":" + getProgramCommandLine()); sfw = openSAMFileWriter(header2, true); SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1); iter = sfr.iterator(); LinkedList<SAMRecord> buffer = new LinkedList<>(); for (;;) { SAMRecord rec = null; if (iter.hasNext()) { rec = progress.watch(iter.next()); if (rec.getReadUnmappedFlag()) continue; if (!buffer.isEmpty()) { SAMRecord last = buffer.getLast(); if (last.getReferenceIndex() == rec.getReferenceIndex() && last.getAlignmentStart() <= rec.getAlignmentStart() && last.getAlignmentEnd() >= rec.getAlignmentEnd()) { continue; } } } if (rec == null || (!buffer.isEmpty() && buffer.getLast().getReferenceIndex() != rec.getReferenceIndex())) { while (!buffer.isEmpty()) { sfw.addAlignment(buffer.removeFirst()); } if (rec == null) break; } buffer.add(rec); if (buffer.size() > 2) { int index = buffer.size(); SAMRecord prev = buffer.get(index - 3); SAMRecord curr = buffer.get(index - 2); SAMRecord next = buffer.get(index - 1); if (prev.getAlignmentEnd() >= next.getAlignmentStart() || curr.getAlignmentEnd() <= prev.getAlignmentEnd()) { buffer.remove(index - 2); } else if (curr.getAlignmentStart() == prev.getAlignmentStart() && curr.getAlignmentEnd() > prev.getAlignmentEnd()) { buffer.remove(index - 3); } } while (buffer.size() > 3) { sfw.addAlignment(buffer.removeFirst()); } } progress.finish(); LOG.info("done"); return Collections.emptyList(); } catch (Exception err) { return wrapException(err); } finally { CloserUtil.close(iter); CloserUtil.close(sfr); CloserUtil.close(sfw); } }
From source file:org.ocsoft.rosetto.models.base.elements.values.ListValue.java
/** * ????????./*from ww w. j a v a 2 s .c o m*/ * ????????????????. * ???????????. * ????ActionCall??. * @param func ?? * @return ???? */ public Map<String, RosettoValue> bind(RosettoFunction func, Scope currentScope) { if (func == null) throw new IllegalArgumentException("???null??"); //?? Map<String, RosettoValue> result = new HashMap<String, RosettoValue>(); //???? LinkedList<String> funcArgs = new LinkedList<String>(); //??????????? int requiredArgsCount = 0; //???????? for (String s : func.getArguments()) { int eqIndex = s.indexOf("="); if (eqIndex == -1) { //????????? funcArgs.add(s); //???????? requiredArgsCount++; } else { //???? String key = s.substring(0, eqIndex); RosettoValue value = Values.create(s.substring(eqIndex + 1, s.length())); //? funcArgs.add(key); //??????? result.put(key, value); } } //?????? //?? for (Entry<String, RosettoValue> e : getMap().entrySet()) { //?Entry??funcArgs?????funcArg boolean removed = funcArgs.remove(e.getKey()); //???? if (removed) requiredArgsCount--; //?? result.put(e.getKey(), e.getValue()); } //?? String mutableArg = searchMutableArg(funcArgs); if (mutableArg != null) { //???????? //???????? //??????????-1 if (requiredArgsCount - 1 > getList().size()) { throw new IllegalArgumentException("???????: " + getList().toString() + "|" + func.getArguments()); } //???????????????? //?? List<RosettoValue> margs = new LinkedList<RosettoValue>(); for (int i = 0; i < getList().size(); i++) { RosettoValue v = getList().get(i); if (!funcArgs.isEmpty()) { //???????????pop????????? String farg = funcArgs.pollFirst(); //?????????? if (farg.equals(mutableArg)) { //?????????????? if (!funcArgs.isEmpty()) { throw new IllegalArgumentException("mutable args must be last element"); } //?? margs.add(v); } //???????? result.put(farg, v); } else { //?? margs.add(v); } } //????? if (margs.size() > 0) { //????? String margName = mutableArg.substring(1); //listvalue??? result.put(margName, new ListValue(margs)); } } else { //??????? if (requiredArgsCount > getList().size()) { throw new IllegalArgumentException("???????: " + getList().toString() + "|" + func.getArguments()); } else if (funcArgs.size() < getList().size()) { throw new IllegalArgumentException( "?????: " + getList().toString() + "|" + func.getArguments()); } for (RosettoValue value : getList()) { //????????? if (value.getType() == ValueType.ACTION_CALL) { //ActionCall?????? result.put(funcArgs.pollFirst(), ((ActionCall) value).evaluate(currentScope)); } else { result.put(funcArgs.pollFirst(), value); } } } return result; }
From source file:edu.cornell.med.icb.clustering.QTClusterer.java
/** * Eliminate any instances that will never cluster with anything else. * @param calculator The distance calculator to use. * @param qualityThreshold The threshold that determines whether or not an instance will cluster * @param instanceList The list of instance to check * @param clusterProgressLogger Where to log progress * @return A non-null but possibly empty list of clusters that each contain a single instance *///from w ww .j a v a 2s . c o m private IntList identifySingletonClusters(final SimilarityDistanceCalculator calculator, final double qualityThreshold, final LinkedList<Integer> instanceList, final ProgressLogger clusterProgressLogger) { LOGGER.info("Searching for instances that will form singleton clusters"); final IntArrayList singletonClusters = new IntArrayList(); for (int i = 0; i < instanceCount; i++) { boolean singleton = true; for (final int j : instanceList) { if (i != j) { final double distance = calculator.distance(i, j); if (distance <= qualityThreshold) { // the instance i is likely to be clustered with some j singleton = false; break; } } } // instance i is too far from anything else to ever cluster so it's a singleton cluster if (singleton) { if (LOGGER.isTraceEnabled()) { LOGGER.trace("adding singleton instance " + i + " to cluster " + clusterCount); } // i is a singleton cluster singletonClusters.add(i); // and we can remove it from further consideration later // note: we have to remove the "element i" and not the "element at i" instanceList.remove(Integer.valueOf(i)); if (logClusterProgress) { clusterProgressLogger.update(); } } } LOGGER.info(singletonClusters.size() + " singleton instances found"); // save the singletons for last since we ideally want to return clusters in size order singletonClusters.trim(); return singletonClusters; }
From source file:org.openconcerto.sql.element.SQLElement.java
public synchronized final void removeFromMDPath(final String mdVariant) { final LinkedList<String> newL = new LinkedList<String>(this.mdPath); if (newL.remove(mdVariant)) this.mdPath = Collections.unmodifiableList(newL); }
From source file:org.guzz.GuzzContextImpl.java
protected void initUnOrderedService(Map services, LinkedList queuedServices, ServiceInfo serviceInfo) { if (serviceInfo.hasDependedServices()) { queuedServices.addLast(serviceInfo); String[] dependsOn = serviceInfo.getDependedServices(); for (int k = 0; k < dependsOn.length; k++) { for (int i = 0; i < queuedServices.size(); i++) { String queueServiceName = ((ServiceInfo) queuedServices.get(i)).getServiceName(); if (queueServiceName.equals(dependsOn[k])) { throw new InvalidConfigurationException("cycle dependencies found in guzz services. From [" + queueServiceName + "] to [" + dependsOn[k] + "]."); }//from w ww . j a va 2 s .co m } //add depended-services from un-inited-services to the queuedServices ServiceInfo si = (ServiceInfo) services.remove(dependsOn[k]); if (si != null) { //process the depended service first. initUnOrderedService(services, queuedServices, si); } else { //the service may have already been registered to the ServiceManager } } //Depended services have been inited. Start the current one. Service s = ServiceManagerImpl.createNewService(this, configServer, serviceInfo); serviceManager.registerService(s); queuedServices.remove(serviceInfo); } else { Service s = ServiceManagerImpl.createNewService(this, configServer, serviceInfo); serviceManager.registerService(s); } }
From source file:Interfaces.EstadisticaConocioGui.java
/** * Creates new form EstadisticaConocioGui *//*from w w w .j a v a 2 s . co m*/ public EstadisticaConocioGui(java.awt.Frame parent, boolean modal) { super(parent, modal); initComponents(); abrirBase(); LazyList<Socio> socios = Socio.findAll(); Iterator<Socio> it = socios.iterator(); Socio s; String nosConocio; Boolean activo; Integer[] nosConocioSuma = { 0, 0, 0, 0, 0, 0 }; LinkedList<Pair<Integer, Integer>> actividadesRealizan = new LinkedList<>(); LazyList<Arancel> aranceles = Arancel.findAll(); Iterator<Arancel> itArancel = aranceles.iterator(); while (itArancel.hasNext()) { Pair<Integer, Integer> par = new Pair<>(itArancel.next().getInteger("id"), 0); actividadesRealizan.add(par); } while (it.hasNext()) { s = it.next(); nosConocio = s.getString("NOSCONOCIOPOR"); activo = s.getBoolean("ACTIVO"); switch (nosConocio) { case "NO ESPECIFICA": nosConocioSuma[0]++; break; case "VIO EL GIMNASIO": nosConocioSuma[1]++; break; case "POR RADIO": nosConocioSuma[2]++; break; case "POR TV": nosConocioSuma[3]++; break; case "REDES SOCIALES": nosConocioSuma[4]++; break; case "UN AMIGO/A": nosConocioSuma[5]++; break; } if (activo) { LazyList<Socioarancel> arancelesSocio = Socioarancel.where("id_socio = ?", s.getId()); Iterator<Socioarancel> itAr = arancelesSocio.iterator(); while (itAr.hasNext()) { Socioarancel ar = itAr.next(); boolean sume = false; int i = 0; while (i < actividadesRealizan.size() && !sume) { if (actividadesRealizan.get(i).first() == ar.getInteger("id_arancel")) { Pair<Integer, Integer> aux = new Pair<>(actividadesRealizan.get(i).first(), actividadesRealizan.get(i).second() + 1); actividadesRealizan.remove(i); actividadesRealizan.add(i, aux); sume = true; } i++; } } } } DefaultCategoryDataset datasetConocio = new DefaultCategoryDataset(); datasetConocio.setValue(nosConocioSuma[0], "nos conocieron", "NO ESPECIFICA"); datasetConocio.setValue(nosConocioSuma[1], "nos conocieron", "VIO EL GIMNASIO"); datasetConocio.setValue(nosConocioSuma[2], "nos conocieron", "POR RADIO"); datasetConocio.setValue(nosConocioSuma[3], "nos conocieron", "POR TV"); datasetConocio.setValue(nosConocioSuma[4], "nos conocieron", "REDES SOCIALES"); datasetConocio.setValue(nosConocioSuma[5], "nos conocieron", "UN AMIGO/A"); JFreeChart chart = ChartFactory.createBarChart3D("Estadisticas por donde nos conocieron", "donde", "cantidad de personas", datasetConocio, PlotOrientation.VERTICAL, true, true, false); // Creacin del panel con el grfico ChartPanel panelGrafico = new ChartPanel(chart); pnlConocio.add(panelGrafico); DefaultCategoryDataset datasetAct = new DefaultCategoryDataset(); for (int i = 0; i < actividadesRealizan.size(); i++) { String nombreAct = Arancel.findById(actividadesRealizan.get(i).first()).getString("nombre"); datasetAct.setValue(actividadesRealizan.get(i).second(), "actividad", nombreAct); } JFreeChart chartAct = ChartFactory.createBarChart3D("Estadisticas que actividad realizan", "actividad", "cantidad de personas", datasetAct, PlotOrientation.VERTICAL, true, true, false); // Creacin del panel con el grfico ChartPanel panelGraficoAc = new ChartPanel(chartAct); pnlAct.add(panelGraficoAc); }
From source file:uk.ac.diamond.scisoft.analysis.rcp.inspector.InspectionTab.java
final public int[] getOrder(int rank) { if (rank == 1) return new int[] { 0 }; LinkedList<Integer> orders = new LinkedList<Integer>(); for (int i = 0; i < rank; i++) orders.add(i);//from w ww .j av a2 s . c o m int[] cOrder = new int[rank]; int i = 0; for (PlotAxisProperty p : paxes) { if (!p.isInSet()) continue; int d = p.getDimension(); cOrder[i++] = d; orders.remove((Integer) d); } for (; i < rank; i++) { int d = orders.removeFirst(); cOrder[i] = d; } return cOrder; }
From source file:net.lightbody.bmp.proxy.jetty.http.HttpContext.java
/** Get the file classpath of the context. * This method makes a best effort to return a complete file * classpath for the context.//w ww. ja va2 s. c o m * It is obtained by walking the classloader hierarchy and looking for * URLClassLoaders. The system property java.class.path is also checked for * file elements not already found in the loader hierarchy. * @return Path of files and directories for loading classes. * @exception IllegalStateException HttpContext.initClassLoader * has not been called. */ public String getFileClassPath() throws IllegalStateException { ClassLoader loader = getClassLoader(); if (loader == null) throw new IllegalStateException("Context classloader not initialized"); LinkedList paths = new LinkedList(); LinkedList loaders = new LinkedList(); // Walk the loader hierarchy while (loader != null) { loaders.add(0, loader); loader = loader.getParent(); } // Try to handle java2compliant modes loader = getClassLoader(); if (loader instanceof ContextLoader && !((ContextLoader) loader).isJava2Compliant()) { loaders.remove(loader); loaders.add(0, loader); } for (int i = 0; i < loaders.size(); i++) { loader = (ClassLoader) loaders.get(i); if (log.isDebugEnabled()) log.debug("extract paths from " + loader); if (loader instanceof URLClassLoader) { URL[] urls = ((URLClassLoader) loader).getURLs(); for (int j = 0; urls != null && j < urls.length; j++) { try { Resource path = Resource.newResource(urls[j]); if (log.isTraceEnabled()) log.trace("path " + path); File file = path.getFile(); if (file != null) paths.add(file.getAbsolutePath()); } catch (Exception e) { LogSupport.ignore(log, e); } } } } // Add the system classpath elements from property. String jcp = System.getProperty("java.class.path"); if (jcp != null) { StringTokenizer tok = new StringTokenizer(jcp, File.pathSeparator); while (tok.hasMoreTokens()) { String path = tok.nextToken(); if (!paths.contains(path)) { if (log.isTraceEnabled()) log.trace("PATH=" + path); paths.add(path); } else if (log.isTraceEnabled()) log.trace("done=" + path); } } StringBuffer buf = new StringBuffer(); Iterator iter = paths.iterator(); while (iter.hasNext()) { if (buf.length() > 0) buf.append(File.pathSeparator); buf.append(iter.next().toString()); } if (log.isDebugEnabled()) log.debug("fileClassPath=" + buf); return buf.toString(); }
From source file:uk.ac.diamond.scisoft.analysis.rcp.inspector.InspectionTab.java
@Override protected void repopulateCombos(String oldName, String newName) { if (combos == null) return;/*from ww w . ja v a2 s. c om*/ if (daxes != null && daxes.size() != 1) { super.repopulateCombos(oldName, newName); return; } // cascade through plot axes strings and indices // reduce choice each time int cSize = combos.size() - comboOffset; LinkedList<String> sAxes = getAllAxisNames(); int jmax = daxes.size(); if (jmax == 0) return; boolean fromAxisSelection = oldName != null && newName != null; String a = null; for (int i = 0; i < cSize; i++) { Combo c = combos.get(i + comboOffset); a = (fromAxisSelection && i < jmax) ? daxes.get(i).getSelectedName() : c.getItem(c.getSelectionIndex()); c.removeAll(); if (!sAxes.contains(a)) { a = sAxes.get(0); } if (!fromAxisSelection) { if (i < jmax) daxes.get(i).selectAxis(a, false); } for (String p : sAxes) c.add(p); c.setText(a); sAxes.remove(a); if (paxes != null) { PlotAxisProperty p = paxes.get(i + comboOffset); if (p.isInSet()) { p.setName(a, false); } } } if (a != null && paxes != null) { if (paxes.get(cSize - 1 + comboOffset).isInSet()) { paxes.get(cSize - 1 + comboOffset).setName(a); } } }
From source file:uk.ac.diamond.scisoft.analysis.rcp.inspector.InspectionTab.java
@Override protected void populateCombos() { Combo c = combos.get(0);//from w w w . j a v a2s. co m c.removeAll(); c.add(CONSTANT); String name = dataset == null ? null : dataset.getName(); if (name == null || name.length() == 0) c.add(DATA); else c.add(name); c.setText(CONSTANT); if (paxes != null) { PlotAxisProperty p = paxes.get(0); p.setName(CONSTANT, false); } if (daxes != null && daxes.size() != 1) { super.populateCombos(); return; } int cSize = combos.size() - comboOffset; LinkedList<String> sAxes = getAllAxisNames(); int jmax = daxes.size(); for (int i = 0; i < cSize; i++) { c = combos.get(i + comboOffset); c.removeAll(); PlotAxisProperty p = paxes.get(i + comboOffset); String a; if (i < jmax) { a = daxes.get(i).getSelectedName(); if (!sAxes.contains(a)) { a = sAxes.getLast(); } } else { a = sAxes.getLast(); } p.clear(); int pmax = sAxes.size(); for (int j = 0; j < pmax; j++) { String n = sAxes.get(j); p.put(j, n); c.add(n); } c.setText(a); sAxes.remove(a); p.setName(a, false); p.setInSet(true); } }