List of usage examples for java.util Vector get
public synchronized E get(int index)
From source file:edu.ku.brc.specify.dbsupport.AccessionAutoNumberAlphaNum.java
@Override protected String getHighestObject(final UIFieldFormatterIFace formatter, final Session session, final String value, final Pair<Integer, Integer> yearPos, final Pair<Integer, Integer> pos) throws Exception { Division currDivision = AppContextMgr.getInstance().getClassObject(Division.class); String ansSQL = "SELECT ans.AutonumberingSchemeID, ans.FormatName, ans.IsNumericOnly, ans.SchemeName, dv.Name, dv.DivisionID " + "FROM autonumberingscheme ans " + "Inner Join autonumsch_div ad ON ans.AutoNumberingSchemeID = ad.AutoNumberingSchemeID " + "Inner Join division dv ON ad.DivisionID = dv.UserGroupScopeId WHERE dv.UserGroupScopeId = %d AND FormatName = '%s'"; String sql = String.format(ansSQL, currDivision.getId(), formatter.getName()); log.debug(sql);// w w w . ja va 2 s . c om Vector<Object[]> rows = BasicSQLUtils.query(sql); Integer ansID = null; if (rows.size() == 1) { ansID = (Integer) rows.get(0)[0]; } else if (rows.size() == 0) { errorMsg = "There are NO formatters named [" + formatter.getName() + "]"; } else { errorMsg = "Too many Formatters named [" + formatter.getName() + "]"; } if (ansID == null) { log.debug(errorMsg); return null; } //String sql = "SELECT autonumberingscheme.FormatName, autonumberingscheme.SchemeName, autonumberingscheme.IsNumericOnly, collection.CollectionName, discipline.Name, division.Name, accession.AccessionNumber FROM autonumberingscheme Inner Join autonumsch_coll ON autonumberingscheme.AutoNumberingSchemeID = autonumsch_coll.AutoNumberingSchemeID Inner Join collection ON autonumsch_coll.CollectionID = collection.UserGroupScopeId Inner Join discipline ON collection.DisciplineID = discipline.UserGroupScopeId Inner Join division ON discipline.DivisionID = division.UserGroupScopeId Inner Join accession ON division.UserGroupScopeId = accession.DivisionID "; //String ansToDivLong = "SELECT ans.FormatName, ans.SchemeName, ans.IsNumericOnly, c.CollectionName, ds.Name, dv.Name FROM autonumberingscheme ans Inner Join autonumsch_coll ac ON ans.AutoNumberingSchemeID = ac.AutoNumberingSchemeID Inner Join collection c ON ac.CollectionID = c.UserGroupScopeId Inner Join discipline ds ON c.DisciplineID = ds.UserGroupScopeId Inner Join division dv ON ds.DivisionID = dv.UserGroupScopeId "; String ansToDivSQL = "SELECT dv.UserGroupScopeId DivID FROM autonumberingscheme ans " + "Inner Join autonumsch_div ad ON ans.AutoNumberingSchemeID = ad.AutoNumberingSchemeID " + "Inner Join division dv ON ad.DivisionID = dv.UserGroupScopeId " + "WHERE ans.AutoNumberingSchemeID = %d"; ansToDivSQL = String.format(ansToDivSQL, ansID); log.debug(ansToDivSQL); Vector<Integer> divIds = new Vector<Integer>(); for (Object[] row : BasicSQLUtils.query(ansToDivSQL)) { divIds.add((Integer) row[0]); } Integer yearVal = null; if (yearPos != null && StringUtils.isNotEmpty(value) && value.length() >= yearPos.second) { yearVal = extractIntegerValue(yearPos, value).intValue(); } StringBuilder sb = new StringBuilder( "SELECT a.accessionNumber FROM Accession a Join a.division dv Join dv.numberingSchemes ans WHERE ans.id = "); AutoNumberingScheme accessionAutoNumScheme = currDivision .getNumberingSchemesByType(Accession.getClassTableId()); if (accessionAutoNumScheme != null && accessionAutoNumScheme.getAutoNumberingSchemeId() != null) { sb.append(accessionAutoNumScheme.getAutoNumberingSchemeId()); sb.append(" AND dv.id in ("); for (Integer dvId : divIds) { sb.append(dvId); sb.append(','); } sb.setLength(sb.length() - 1); sb.append(')'); } else { UIRegistry.showError("There is no AutonumberingScheme for the Accession formatter!"); return ""; } if (yearVal != null) { sb.append(" AND "); sb.append(yearVal); sb.append(" = substring(" + fieldName + "," + (yearPos.first + 1) + "," + (yearPos.second - yearPos.first) + ")"); } sb.append(" ORDER BY"); try { if (yearPos != null) { sb.append(" substring(" + fieldName + "," + (yearPos.first + 1) + "," + (yearPos.second - yearPos.first) + ") desc"); } if (pos != null) { if (yearPos != null) { sb.append(", "); } sb.append(" substring(" + fieldName + "," + (pos.first + 1) + "," + (pos.second - pos.first) + ") desc"); } System.out.println("AccessionAutoNumberAlphaNum - " + sb.toString()); List<?> list = session.createQuery(sb.toString()).setMaxResults(1).list(); if (list.size() == 1) { return list.get(0).toString(); } } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(AccessionAutoNumberAlphaNum.class, ex); ex.printStackTrace(); } return null; }
From source file:de.ipbhalle.metfrag.main.CommandLineTool.java
/** * TODO adding inchi and inchi key generation * /*from w ww . j a v a2 s . co m*/ * save the results of the metfrag run * * @param results * @throws CDKException */ public static void saveResults(List<MetFragResult> results) { if (results == null || results.size() == 0) { System.out.println("Error: No results."); return; } MoleculeSet setOfMolecules = new MoleculeSet(); SmilesGenerator sg = new SmilesGenerator(); //uncomment if inchi generation is avaiable on your system - jni-inchi /*org.openscience.cdk.inchi.InChIGeneratorFactory factory = null; try { factory = org.openscience.cdk.inchi.InChIGeneratorFactory.getInstance(); } catch (CDKException e3) { e3.printStackTrace(); }*/ for (MetFragResult result : results) { IAtomContainer tmp = result.getStructure(); tmp = AtomContainerManipulator.removeHydrogens(tmp); String smiles = sg.createSMILES(tmp); tmp.setProperty("DatabaseID", result.getCandidateID()); tmp.setProperty("NoPeaksExplained", result.getPeaksExplained()); tmp.setProperty("SMILES", smiles); //uncomment if inchi generation is avaiable on your system - jni-inchi /* IAtomContainer tmp_clone = null; try { tmp_clone = (IAtomContainer)tmp.clone(); } catch (CloneNotSupportedException e2) { e2.printStackTrace(); } if(factory != null && tmp_clone != null) { try { AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(tmp_clone); } catch (CDKException e1) { } org.openscience.cdk.tools.CDKHydrogenAdder hAdder = org.openscience.cdk.tools.CDKHydrogenAdder.getInstance(tmp_clone.getBuilder()); for(int i = 0; i < tmp_clone.getAtomCount(); i++) { try { hAdder.addImplicitHydrogens(tmp_clone, tmp_clone.getAtom(i)); } catch(Exception e) { continue; } } AtomContainerManipulator.convertImplicitToExplicitHydrogens(tmp_clone); try { org.openscience.cdk.inchi.InChIGenerator gen = factory.getInChIGenerator(tmp_clone); if(gen != null) { String inchi = gen.getInchi(); tmp.setProperty("InChI", inchi); } } catch (CDKException e) { } }*/ tmp.setProperty("PeakScore", result.getRawPeakMatchScore()); tmp.setProperty("BondEnergyScore", result.getRawBondEnergyScore()); tmp.setProperty("Score", result.getScore()); for (IBond bond : tmp.bonds()) { if (bond.getStereo() == null) bond.setStereo(Stereo.UP_OR_DOWN); } String matchedPeaksString = ""; Vector<PeakMolPair> pairs = result.getFragments(); for (int k = 0; k < pairs.size(); k++) { PeakMolPair fragment = pairs.get(k); if (k == result.getFragments().size()) matchedPeaksString += fragment.getPeak().getMass() + " " + fragment.getPeak().getRelIntensity(); else matchedPeaksString += fragment.getPeak().getMass() + " " + fragment.getPeak().getRelIntensity() + " "; } if (!matchedPeaksString.equals("")) tmp.setProperty("PeaksExplained", matchedPeaksString); setOfMolecules.addAtomContainer(tmp); } try { SDFWriter writer = new SDFWriter(new FileWriter(new File( resultspath + System.getProperty("file.separator") + "results_" + sampleName + ".sdf"))); try { writer.write(setOfMolecules); } catch (CDKException e) { System.out.println("Error: Could not write results file."); } writer.close(); } catch (IOException e) { System.out.println("Error: Could not write results file."); } if (verbose) System.out.println("wrote " + setOfMolecules.getAtomContainerCount() + " molecules to " + resultspath); }
From source file:edu.uga.cs.fluxbuster.clustering.hierarchicalclustering.DistanceMatrix.java
/** * Retrieves the distance between the clusters at the supplied indexes * /* w ww.ja v a 2 s .c om*/ * @param p * the indexes of the clusters * @return the distance between the clusters, if the indexes are not within * the bounds of the distance matrix Float.MAX_VALUE is returned */ private float distanceHelper(IndexPair p) { int i = p.getI(); int j = p.getJ(); if (i >= 0 && i < distMatrix.size() && j >= 0 && j < distMatrix.size()) { try { Vector<Float> row = distMatrix.get(i); return row.get(j); } catch (Exception e) { if (log.isErrorEnabled()) { log.error("Error retrieving distance.", e); } } } return Float.MAX_VALUE; }
From source file:edu.ku.brc.af.ui.db.TextFieldFromPickListTable.java
public void setValue(final Object value, final String defaultValue) { dataObj = value;// w w w. j a va 2 s . c o m if (value != null) { if (adapter == null) { setText(value.toString()); return; } if (adapter.isTabledBased()) { String data = null; boolean isFormObjIFace = value instanceof FormDataObjIFace; Vector<PickListItemIFace> items = adapter.getList(); for (int i = 0; i < items.size(); i++) { PickListItemIFace pli = items.get(i); Object valObj = pli.getValueObject(); if (valObj != null) { if (isFormObjIFace && valObj instanceof FormDataObjIFace) { //System.out.println(((FormDataObjIFace)value).getId().longValue()+" "+(((FormDataObjIFace)valObj).getId().longValue())); if (((FormDataObjIFace) value).getId() .intValue() == (((FormDataObjIFace) valObj).getId().intValue())) { data = pli.getTitle(); break; } } else if (pli.getValue().equals(value.toString())) { data = pli.getTitle(); break; } } } if (data == null) { data = StringUtils.isNotEmpty(defaultValue) ? defaultValue : ""; //$NON-NLS-1$ } setText(data); } else { boolean fnd = false; setText(""); for (PickListItemIFace item : adapter.getList()) { if (item.getValue() == null && value == null) { break; } else if (item.getValue() != null && value != null && item.getValue().equals(value.toString())) { setText(item.getTitle()); fnd = true; break; } } if (!fnd && !adapter.isReadOnly()) { setText(value != null ? value.toString() : defaultValue); } } repaint(); } else { if (nullIndex == null) { if (adapter != null) { int inx = 0; for (PickListItemIFace item : adapter.getList()) { if (item != null && item.getValue() != null && item.getValue().equals("|null|")) { nullIndex = inx; setText(item.getTitle()); break; } inx++; } if (nullIndex == null) { nullIndex = -1; } } } else if (nullIndex > -1) { PickListItemIFace item = adapter.getList().get(nullIndex); if (item != null) { setText(item.getTitle()); } return; } else if (nullIndex == -1) { setText(""); } } }
From source file:peakmlviewer.view.IntensityView.java
public void update(int event) { graph.clear();/*from w w w. ja v a2 s .c o m*/ if (event != Document.UPDATE_INIT) { Document document = getMainWnd().getDocument(); IPeak peak = document.getCurrentPeak(); if (peak == null) return; Vector<IPeak> peaks = IPeak.unpack(peak); Header header = document.getHeader(); for (SetInfo setinfo : header.getSetInfos()) { // retrieve all the peaks for this set Vector<IPeak> set = IPeak.peaksOfMeasurements(peaks, setinfo.getAllMeasurementIDs()); // grab the intensities and add to the data double intensities[] = new double[set.size()]; for (int i = 0; i < set.size(); ++i) intensities[i] = set.get(i).getIntensity(); graph.addData(setinfo.getID(), intensities); } } }
From source file:com.feilong.commons.core.tools.json.JsonUtilTest.java
/** * Test vector.// w ww .ja v a 2s. com */ @Test public void testVector() { Vector<Integer> vector = new Vector<Integer>(); vector.add(1); vector.add(2222); vector.add(3333); vector.add(55555); log.info("vector:{}", JsonUtil.format(vector)); log.info("" + vector.get(0)); }
From source file:com.nidhinova.tools.ssh.SFTPClient.java
public void deleteRemoteFolder(String root, String relativepath) throws SftpException { this.sftp.cd(this.sftp.getHome()); this.sftp.cd(root + "/" + relativepath); _logger.debug(">cd " + root + "/" + relativepath); String pwd = this.sftp.pwd(); _logger.debug("pwd=" + pwd); //delete all files Vector<ChannelSftp.LsEntry> files; files = this.sftp.ls("*.*"); _logger.debug("# files = " + (files == null ? "0" : files.size())); if (files != null) { for (int i = 0; i < files.size(); i++) { ChannelSftp.LsEntry file = files.get(i); this.sftp.rm(file.getFilename()); _logger.debug("Deleted file " + file.getFilename()); }/*from www .j a v a 2s. c om*/ } //delete the folder String foldername = relativepath.substring(relativepath.lastIndexOf('/') + 1); this.sftp.cd(".."); pwd = this.sftp.pwd(); this.sftp.rmdir(foldername); }
From source file:edu.stanford.cfuller.imageanalysistools.clustering.ObjectClustering.java
/** * Calculates a metric of clustering goodness, which is based upon the ratio of the average distance between objects withing a cluster to the maximal distance between objects in two different clusters. * * This is used to determine whether it is actually better to subdivide a cluster into multiple clusters or not; in general having more clusters will * produce a higher likelihood score from the Gaussian mixture model clustering, so some independent metric is needed to guess at what * the best number of clusters is. Using this metric, clusters are only subdivided if the division can substantially reduce the ratio of * the distances between objects withing a cluster relative to distances of object between clusters. * * @param clusterObjects A Vector containing the ClusterObjects currently being clustered. * @param clusters A Vector containing the current cluster assignments on which the metric is to be calculated. * @param k The number of clusters. * @param n The number of cluster objects. * @return The result of applying the metric. A lower score means the clustering is better. *///from w ww. ja v a2 s. c o m public static double getInterClusterDistances(Vector<ClusterObject> clusterObjects, Vector<Cluster> clusters, int k, int n) { double[] intraClusterDists = new double[k]; int[] intraCounts = new int[k]; double[] maxIntra = new double[k]; java.util.Arrays.fill(intraClusterDists, 0.0); java.util.Arrays.fill(intraCounts, 0); java.util.Arrays.fill(maxIntra, 0.0); for (int i = 0; i < n; i++) { int i_ID = clusterObjects.get(i).getCurrentCluster().getID(); for (int j = i + 1; j < n; j++) { int j_ID = clusterObjects.get(j).getCurrentCluster().getID(); if (i_ID == j_ID) { double dist = clusterObjects.get(i).distanceTo(clusterObjects.get(j)); intraClusterDists[i_ID - 1] += dist; intraCounts[i_ID - 1]++; if (dist > maxIntra[i_ID - 1]) { maxIntra[i_ID - 1] = dist; } } } } double ratios = 0; int ratio_counts = 0; for (int i = 0; i < k; i++) { if (clusters.get(i).getObjectSet().size() == 0) { continue; } for (int j = i + 1; j < k; j++) { if (clusters.get(j).getObjectSet().size() == 0) { continue; } double maxDist = 0; for (ClusterObject i_obj : clusters.get(i).getObjectSet()) { for (ClusterObject j_obj : clusters.get(j).getObjectSet()) { double dist = i_obj.distanceTo(j_obj); if (dist > maxDist) { maxDist = dist; } } } final double zeroCountScalingFactor = 4; if (intraCounts[i] == 0) { intraCounts[i] = 1; intraClusterDists[i] = maxDist / zeroCountScalingFactor; } if (intraCounts[j] == 0) { intraCounts[j] = 1; intraClusterDists[j] = maxDist / zeroCountScalingFactor; } ratios += 2 * (intraClusterDists[i] / intraCounts[i] + intraClusterDists[j] / intraCounts[j]) / maxDist; ratio_counts++; } } if (ratio_counts == 0) { double maxElement = 0; for (double d : maxIntra) { if (d > maxElement) maxElement = d; } ratios = 4 * intraClusterDists[0] / (maxElement + 1e-9); ratio_counts = 1; } return ratios / ratio_counts; }
From source file:com.globalsight.everest.webapp.pagehandler.administration.config.fileextension.FileExtensionMainHandler.java
private String checkDependencies(FileExtensionImpl fileExtension, HttpSession session) { ResourceBundle bundle = PageHandler.getBundle(session); FileExtensionDependencyChecker depChecker = new FileExtensionDependencyChecker(); Hashtable catDeps = depChecker.categorizeDependencies(fileExtension); StringBuffer deps = new StringBuffer(); if (catDeps.size() == 0) { return null; }/*from w w w.j a va 2 s. co m*/ deps.append("<span class=\"errorMsg\">"); Object[] args = { bundle.getString("lb_file_extension") }; deps.append(MessageFormat.format(bundle.getString("msg_dependency"), args)); for (Enumeration e = catDeps.keys(); e.hasMoreElements();) { String key = (String) e.nextElement(); deps.append("<p>*** " + bundle.getString(key) + " ***<br>"); Vector values = (Vector) catDeps.get(key); for (int i = 0; i < values.size(); i++) { deps.append((String) values.get(i)); deps.append("<br>"); } } deps.append("</span>"); return deps.toString(); }
From source file:eionet.gdem.dcm.business.WorkqueueManager.java
/** * Adds new jobs into the workqueue by the given XML Schema * * @param user/*www .j ava 2 s. co m*/ * Loggedin user name. * @param sourceUrl * Source URL of XML file. * @param schemaUrl * XML Schema URL. * @return List of job IDs. * @throws DCMException */ public List<String> addSchemaScriptsToWorkqueue(String user, String sourceUrl, String schemaUrl) throws DCMException { List<String> result = new ArrayList<String>(); try { if (!SecurityUtil.hasPerm(user, "/" + Names.ACL_WQ_PATH, "i")) { LOGGER.debug("You don't have permissions jobs into workqueue!"); throw new DCMException(BusinessConstants.EXCEPTION_AUTORIZATION_QASCRIPT_UPDATE); } } catch (DCMException e) { throw e; } catch (Exception e) { LOGGER.error("Error adding job to workqueue", e); throw new DCMException(BusinessConstants.EXCEPTION_GENERAL); } XQueryService xqE = new XQueryService(); xqE.setTrustedMode(false); try { Hashtable h = new Hashtable(); Vector files = new Vector(); files.add(sourceUrl); h.put(schemaUrl, files); Vector v_result = xqE.analyzeXMLFiles(h); if (v_result != null) { for (int i = 0; i < v_result.size(); i++) { Vector v = (Vector) v_result.get(i); result.add((String) v.get(0)); } } } catch (Exception e) { e.printStackTrace(); LOGGER.error("Error adding job to workqueue", e); throw new DCMException(BusinessConstants.EXCEPTION_GENERAL); } return result; }