List of usage examples for java.util Vector elementAt
public synchronized E elementAt(int index)
From source file:edu.mayo.informatics.lexgrid.convert.directConversions.obo1_2.OBO2LGDynamicMapHolders.java
private void addOBODbxrefAsSource(Property prop, Vector<OBODbxref> srcVector, OBOAbbreviations abbreviations) { if ((srcVector != null) && (srcVector.size() > 0)) { for (int i = 0; i < srcVector.size(); i++) { OBODbxref dbxref = srcVector.elementAt(i); String src = dbxref.getSource(); OBOAbbreviation abb = null;/*w ww. jav a 2 s . c o m*/ if (!OBO2LGUtils.isNull(src)) { String srcVal = src; if (abbreviations != null) { abb = getAbbreviationByCodeOrURL(abbreviations, src); if ((abb != null) && (!OBO2LGUtils.isNull(abb.getAbbreviation()))) srcVal = abb.getAbbreviation(); } Source s = new Source(); if (srcVal.length() > 250) { messages_.warn("Property name: " + (prop.getPropertyName() == null ? "MISSING" : prop.getPropertyName()) + " value: " + (prop.getValue().getContent() == null ? "MISSING" : prop.getValue().getContent()) + " source too long for storage: " + srcVal + " Truncating to 250 characters"); srcVal = srcVal.substring(0, 237) + "(TRUNCATED!)"; } s.setContent(srcVal); if (StringUtils.isNotBlank(dbxref.getSubrefAndDescription())) { s.setSubRef(dbxref.getSubrefAndDescription()); } prop.getSourceAsReference().add(s); if (abb == null) { abb = new OBOAbbreviation(); abb.abbreviation = srcVal; abb.genericURL = srcVal; } addSource(abb); } } } }
From source file:org.globus.security.gridmap.GridMap.java
/** * Returns all globus IDs associated with the * specified local user name./* ww w. j a va 2 s . co m*/ * * @param userID local user name * @return associated globus ID, null * if there is not any. */ public String[] getAllGlobusID(String userID) { if (userID == null) { throw new IllegalArgumentException("userID is null"); } if (this.map == null) { return null; } Vector v = new Vector(); Iterator iter = this.map.entrySet().iterator(); Map.Entry mapEntry; GridMapEntry entry; while (iter.hasNext()) { mapEntry = (Map.Entry) iter.next(); entry = (GridMapEntry) mapEntry.getValue(); if (entry.containsUserID(userID)) { v.add(entry.getGlobusID()); } } // create array of strings and add values back in if (v.size() == 0) { return null; } String idS[] = new String[v.size()]; for (int ctr = 0; ctr < v.size(); ctr++) { idS[ctr] = (String) v.elementAt(ctr); } return idS; }
From source file:org.bench4Q.agent.rbe.EB.java
/** * @param state// www .java 2 s .c o m * @param url * @return bolean */ public boolean getHTML(int state, String url) { double tolerance = tolerance(curState); html = ""; int statusCode; GetMethod httpget = new GetMethod(url); httpget.getParams().setCookiePolicy(CookiePolicy.IGNORE_COOKIES); if (tolerance != 0) { httpget.getParams().setSoTimeout((int) (tolerance * 1000)); } try { statusCode = HttpClientFactory.getInstance().executeMethod(httpget); if (statusCode != HttpStatus.SC_OK) { EBStats.getEBStats().error(state, "HTTP response ERROR: " + statusCode, url); return false; } BufferedReader bin = new BufferedReader(new InputStreamReader(httpget.getResponseBodyAsStream())); StringBuilder result = new StringBuilder(); String s; while ((s = bin.readLine()) != null) { result.append(s); } html = new String(result); } catch (Exception e) { EBStats.getEBStats().error(state, "get methed ERROR.", url); return false; } finally { // always release the connection after we're done httpget.releaseConnection(); } if (!m_args.isGetImage()) { return true; } Vector<ImageReader> imageRd = new Vector<ImageReader>(0); URL u; try { u = new URL(url); } catch (MalformedURLException e) { EBStats.getEBStats().error(state, "get image ERROR.", url); return false; } findImg(html, u, imgPat, srcPat, quotePat, imageRd); findImg(html, u, inputPat, srcPat, quotePat, imageRd); while (imageRd.size() > 0) { int max = imageRd.size(); int min = Math.max(max - RBEUtil.maxImageRd, 0); int i; try { for (i = min; i < max; i++) { ImageReader rd = (ImageReader) imageRd.elementAt(i); if (!rd.readImage(state)) { imageRd.removeElementAt(i); i--; max--; } } } catch (InterruptedException inte) { EBStats.getEBStats().error(state, "get image ERROR.", url); return true; } } return true; }
From source file:alice.tuprolog.lib.OOLibrary.java
private static Constructor<?> mostSpecificConstructor(Vector<Constructor<?>> constructors) throws NoSuchMethodException { for (int i = 0; i != constructors.size(); i++) { for (int j = 0; j != constructors.size(); j++) { if ((i != j) && (moreSpecific(constructors.elementAt(i), constructors.elementAt(j)))) { constructors.removeElementAt(j); if (i > j) i--;/*from ww w . j a va 2s .co m*/ j--; } } } if (constructors.size() == 1) return constructors.elementAt(0); else throw new NoSuchMethodException(">1 most specific constructor"); }
From source file:net.aepik.alasca.core.ldap.Schema.java
/** * Retourne l'ensemble des syntaxes connues, qui sont * contenues dans le package 'ldap.syntax'. * @return String[] L'ensemble des noms de classes de syntaxes. *///from ww w.j av a 2 s.c o m public static String[] getSyntaxes() { String[] result = null; try { String packageName = getSyntaxPackageName(); URL url = Schema.class.getResource("/" + packageName.replace('.', '/')); if (url == null) { return null; } if (url.getProtocol().equals("jar")) { Vector<String> vectTmp = new Vector<String>(); int index = url.getPath().indexOf('!'); String path = URLDecoder.decode(url.getPath().substring(index + 1), "UTF-8"); JarFile jarFile = new JarFile(URLDecoder.decode(url.getPath().substring(5, index), "UTF-8")); if (path.charAt(0) == '/') { path = path.substring(1); } Enumeration<JarEntry> jarFiles = jarFile.entries(); while (jarFiles.hasMoreElements()) { JarEntry tmp = jarFiles.nextElement(); // // Pour chaque fichier dans le jar, on regarde si c'est un // fichier de classe Java. // if (!tmp.isDirectory() && tmp.getName().substring(tmp.getName().length() - 6).equals(".class") && tmp.getName().startsWith(path)) { int i = tmp.getName().lastIndexOf('/'); String classname = tmp.getName().substring(i + 1, tmp.getName().length() - 6); vectTmp.add(classname); } } jarFile.close(); result = new String[vectTmp.size()]; for (int i = 0; i < vectTmp.size(); i++) { result[i] = vectTmp.elementAt(i); } } else if (url.getProtocol().equals("file")) { // // On cr le fichier associ pour parcourir son contenu. // En l'occurence, c'est un dossier. // File[] files = (new File(url.toURI())).listFiles(); // // On liste tous les fichiers qui sont dedans. // On les stocke dans un vecteur ... // Vector<File> vectTmp = new Vector<File>(); for (File f : files) { if (!f.isDirectory()) { vectTmp.add(f); } } // // ... pour ensuite les mettres dans le tableau de resultat. // result = new String[vectTmp.size()]; for (int i = 0; i < vectTmp.size(); i++) { String name = vectTmp.elementAt(i).getName(); int a = name.indexOf('.'); name = name.substring(0, a); result[i] = name; } } } catch (Exception e) { e.printStackTrace(); } if (result != null) { Arrays.sort(result); } return result; }
From source file:com.duroty.utils.mail.MessageUtilities.java
public static void attach(MimeMultipart multipart, Vector attachments, String charset) throws MessagingException { for (int xindex = 0; xindex < attachments.size(); xindex++) { Object xobject = attachments.elementAt(xindex); // attach based on type of object if (xobject instanceof Part) { attach(multipart, (Part) xobject, charset); } else if (xobject instanceof File) { attach(multipart, (File) xobject, charset); } else if (xobject instanceof String) { attach(multipart, (String) xobject, charset, Part.ATTACHMENT, false); } else if (xobject instanceof vCard) { attach(multipart, (vCard) xobject, charset); } else {//from w ww . j a va 2 s . c o m throw new MessagingException("Cannot attach objects of type " + xobject.getClass().getName()); } } }
From source file:org.ecoinformatics.seek.datasource.EcogridCompressedDataCacheItem.java
/** * This method will get a file path which matches the given file extension * in unzipped file list. If no match, null will be returned * /* ww w .ja va 2 s .com*/ * @param fileExtension * String * @return String[] */ public String[] getUnzippedFilePath(String fileExtension) { String[] result = null; if (unCompressedFileList == null || fileExtension == null) { return result; } int length = unCompressedFileList.length; Vector tmp = new Vector(); for (int i = 0; i < length; i++) { String fileName = (String) unCompressedFileList[i]; if (fileName != null) { log.debug("file name in file list is " + fileName); int dotPosition = fileName.lastIndexOf(FILEEXTENSIONSEP); String extension = fileName.substring(dotPosition + 1, fileName.length()); log.debug("The file extension for file name " + fileName + " in file list is " + extension); if (extension.equals(fileExtension)) { // store the file path into a tmp array tmp.add(unCompressedFilePath + File.separator + fileName); } } } // transfer vector in array if (!tmp.isEmpty()) { int len = tmp.size(); result = new String[len]; for (int j = 0; j < len; j++) { result[j] = (String) tmp.elementAt(j); log.debug("The file path which math file extension " + fileExtension + " is " + result[j]); } } return result; }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetSubjectsIdListener.java
@Override public void handleEvent(Event event) { // TODO Auto-generated method stub Vector<String> values = this.setSubjectsIdUI.getValues(); Vector<String> samples = this.setSubjectsIdUI.getSamples(); for (String v : values) { if (v.compareTo("") == 0) { this.setSubjectsIdUI.displayMessage("All identifiers have to be set"); return; }/* ww w. j a v a 2 s . com*/ } File file = new File(this.dataType.getPath().toString() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping.tmp"); try { FileWriter fw = new FileWriter(file); BufferedWriter out = new BufferedWriter(fw); out.write( "study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n"); File stsmf = ((GeneExpressionData) this.dataType).getStsmf(); if (stsmf == null) { for (int i = 0; i < samples.size(); i++) { out.write(this.dataType.getStudy().toString() + "\t" + "\t" + values.elementAt(i) + "\t" + samples.elementAt(i) + "\t" + "\t" + "\t" + "\t" + "\t" + "\n"); } } else { try { BufferedReader br = new BufferedReader(new FileReader(stsmf)); String line = br.readLine(); while ((line = br.readLine()) != null) { String[] fields = line.split("\t", -1); String sample = fields[3]; String subject; if (samples.contains(sample)) { subject = values.get(samples.indexOf(sample)); } else { br.close(); return; } out.write(fields[0] + "\t" + fields[1] + "\t" + subject + "\t" + sample + "\t" + fields[4] + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n"); } br.close(); } catch (Exception e) { this.setSubjectsIdUI.displayMessage("File error: " + e.getLocalizedMessage()); out.close(); e.printStackTrace(); } } out.close(); try { File fileDest; if (stsmf != null) { String fileName = stsmf.getName(); stsmf.delete(); fileDest = new File(this.dataType.getPath() + File.separator + fileName); } else { fileDest = new File(this.dataType.getPath() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping"); } FileUtils.moveFile(file, fileDest); ((GeneExpressionData) this.dataType).setSTSMF(fileDest); } catch (IOException ioe) { this.setSubjectsIdUI.displayMessage("File error: " + ioe.getLocalizedMessage()); return; } } catch (Exception e) { this.setSubjectsIdUI.displayMessage("Error: " + e.getLocalizedMessage()); e.printStackTrace(); } this.setSubjectsIdUI.displayMessage("Subject to sample mapping file updated"); WorkPart.updateSteps(); WorkPart.updateFiles(); UsedFilesPart.sendFilesChanged(dataType); }
From source file:org.globus.gsi.gridmap.GridMap.java
/** * Returns all globus IDs associated with the * specified local user name.//from w w w . jav a 2 s .c om * * @param userID local user name * @return associated globus ID, null * if there is not any. */ public String[] getAllGlobusID(String userID) { if (userID == null) { throw new IllegalArgumentException(i18n.getMessage("userIdNull")); } if (this.map == null) { return null; } Vector v = new Vector(); Iterator iter = this.map.entrySet().iterator(); Map.Entry mapEntry; GridMapEntry entry; while (iter.hasNext()) { mapEntry = (Map.Entry) iter.next(); entry = (GridMapEntry) mapEntry.getValue(); if (entry.containsUserID(userID)) { v.add(entry.getGlobusID()); } } // create array of strings and add values back in if (v.size() == 0) { return null; } String idS[] = new String[v.size()]; for (int ctr = 0; ctr < v.size(); ctr++) { idS[ctr] = (String) v.elementAt(ctr); } return idS; }
From source file:edu.umd.cfar.lamp.viper.util.StringHelp.java
/** * Split using a separator, but allow for the separator to occur * in nested parentheses without splitting. * E.g. //www . j a va 2s .c o m * <pre> * 1, (2,3), 4 * </pre> * would split into * <UL> * <li> 1 </li> * <li> (2,3) (Doesn't get split, even though it has comma) </li> * <li> 4 </li> * </ul> * * @param line The String to be seperated. * @param sep The seperator character, eg a comma * @return An array of Strings containing the seperated data. * @see #splitBySeparator(String line, char c) */ public static String[] splitBySeparatorAndParen(String line, char sep) { boolean withinQuotes = false; String newLine = new String(line); Vector temp = new Vector(); int startIndex = 0; int nesting = 0; for (int i = 0; i < newLine.length(); i++) { char c = newLine.charAt(i); if (c == '"') { withinQuotes = !withinQuotes; } else if (!withinQuotes) { if (c == '(') { nesting++; } else if (c == ')') { nesting--; } else { if ((nesting == 0) && (c == sep)) { String s = newLine.substring(startIndex, i); temp.addElement(s); startIndex = i + 1; } } } } String s = newLine.substring(startIndex); temp.addElement(s); String[] result = new String[temp.size()]; for (int i = 0; i < result.length; i++) { result[i] = (String) temp.elementAt(i); } return (result); }