List of usage examples for java.util Vector indexOf
public int indexOf(Object o)
From source file:com.ricemap.spateDB.operations.RangeQuery.java
public static void main(String[] args) throws IOException { CommandLineArguments cla = new CommandLineArguments(args); final QueryInput query = cla.getQuery(); final Path[] paths = cla.getPaths(); if (paths.length == 0 || (cla.getPrism() == null && cla.getSelectionRatio() < 0.0f)) { printUsage();/* w ww . jav a2 s.co m*/ throw new RuntimeException("Illegal parameters"); } JobConf conf = new JobConf(FileMBR.class); final Path inputFile = paths[0]; final FileSystem fs = inputFile.getFileSystem(conf); if (!fs.exists(inputFile)) { printUsage(); throw new RuntimeException("Input file does not exist"); } final Path outputPath = paths.length > 1 ? paths[1] : null; final Prism[] queryRanges = cla.getPrisms(); int concurrency = cla.getConcurrency(); final Shape stockShape = cla.getShape(true); final boolean overwrite = cla.isOverwrite(); final long[] results = new long[queryRanges.length]; final Vector<Thread> threads = new Vector<Thread>(); final BooleanWritable exceptionHappened = new BooleanWritable(); Thread.UncaughtExceptionHandler h = new Thread.UncaughtExceptionHandler() { public void uncaughtException(Thread th, Throwable ex) { ex.printStackTrace(); exceptionHappened.set(true); } }; for (int i = 0; i < queryRanges.length; i++) { Thread t = new Thread() { @Override public void run() { try { int thread_i = threads.indexOf(this); long result_count = rangeQueryMapReduce(fs, inputFile, outputPath, queryRanges[thread_i], stockShape, overwrite, false, query); results[thread_i] = result_count; } catch (IOException e) { throw new RuntimeException(e); } } }; t.setUncaughtExceptionHandler(h); threads.add(t); } long t1 = System.currentTimeMillis(); do { // Ensure that there is at least MaxConcurrentThreads running int i = 0; while (i < concurrency && i < threads.size()) { Thread.State state = threads.elementAt(i).getState(); if (state == Thread.State.TERMINATED) { // Thread already terminated, remove from the queue threads.remove(i); } else if (state == Thread.State.NEW) { // Start the thread and move to next one threads.elementAt(i++).start(); } else { // Thread is still running, skip over it i++; } } if (!threads.isEmpty()) { try { // Sleep for 10 seconds or until the first thread terminates threads.firstElement().join(10000); } catch (InterruptedException e) { e.printStackTrace(); } } } while (!threads.isEmpty()); long t2 = System.currentTimeMillis(); if (exceptionHappened.get()) throw new RuntimeException("Not all jobs finished correctly"); System.out.println("Time for " + queryRanges.length + " jobs is " + (t2 - t1) + " millis"); System.out.print("Result size: ["); for (long result : results) { System.out.print(result + ", "); } System.out.println("]"); }
From source file:com.seer.datacruncher.profiler.spring.ProfilerInfoController.java
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { @SuppressWarnings("unchecked") Hashtable<String, String> dbParams = (Hashtable<String, String>) request.getSession(true) .getAttribute("dbConnectionData"); if (dbParams != null) { request.setAttribute("serverName", CommonUtil.notNullValue(dbParams.get("Database_DSN"))); }/*from w w w .j a v a 2s . c om*/ String selectedValue = CommonUtil.notNullValue(request.getParameter("selectedValue")); request.setAttribute("selectedValue", selectedValue); String parentNodeValue = CommonUtil.notNullValue(request.getParameter("parent")); request.setAttribute("parentValue", parentNodeValue); ObjectMapper mapper = new ObjectMapper(); if (CommonUtil.notNullValue(request.getParameter("action")).equals("minMaxValues")) { InfoBL ibl = new InfoBL(); String data = mapper.writeValueAsString( ibl.generateMinMaxValueGrid(CommonUtil.notNullValue(dbParams.get("Database_DSN")), parentNodeValue, selectedValue.split(":")[0])); PrintWriter out = response.getWriter(); out.println(data); return null; } else if (CommonUtil.notNullValue(request.getParameter("tab")).equals("analysis")) { String queryString = CommonUtil.notNullValue(request.getParameter("queryString")); Vector vector = RdbmsConnection.getTable(); String s = parentNodeValue; int i = vector.indexOf(s); Vector avector[] = (Vector[]) null; avector = TableMetaInfo.populateTable(5, i, i + 1, avector); QueryDialog querydialog = new QueryDialog(1, s, avector); List<String> listPrimaryKeys = new ArrayList<String>(); try { RdbmsConnection.openConn(); DatabaseMetaData dbmd = RdbmsConnection.getMetaData(); ResultSet resultset = dbmd.getPrimaryKeys(null, null, s); while (resultset.next()) { listPrimaryKeys.add(resultset.getString("COLUMN_NAME")); } RdbmsConnection.closeConn(); } catch (Exception ex) { ex.printStackTrace(); } try { querydialog.executeAction(queryString); } catch (Exception e) { e.printStackTrace(); } request.setAttribute("rowCount", querydialog.getRowCount()); GridUtil gridUtil = new GridUtil(); gridUtil.generateGridData(querydialog.getTableGridDTO(), false, listPrimaryKeys); request.setAttribute("gridColumns", gridUtil.getColumnNames()); GridUtil gridUtilEdit = new GridUtil(); gridUtilEdit.generateGridData(querydialog.getTableGridDTO(), true, listPrimaryKeys); request.setAttribute("gridColumnsEdit", gridUtilEdit.getColumnNames()); request.setAttribute("gridFields", gridUtil.getFieldNames()); request.setAttribute("gridData", gridUtil.getData()); request.setAttribute("systemDate", new Date(System.currentTimeMillis()).toString()); return new ModelAndView("jsp/profiler/analysis.jsp"); } else if (CommonUtil.notNullValue(request.getParameter("isLeaf")).equals("true")) { String s = dbParams.get("Database_DSN"); String s1 = parentNodeValue; String s2 = selectedValue.split(":")[0]; QueryBuilder querybuilder = new QueryBuilder(s, s1, s2, RdbmsConnection.getDBType()); Double profileValues[] = FirstInformation.getProfileValues(querybuilder); Vector patternValues[] = FirstInformation.getPatternValues(querybuilder); Vector distValues[] = getDistributionValues(querybuilder, request); // showBar(ad); // showPatternChart(avector); String pieChartData = ChartUtil.getChartDataForPieChart(distValues); String barChartData = ChartUtil.getChartDataForBarChart(profileValues); String patternChartData = ChartUtil.getChartDataForPieChart(patternValues); request.setAttribute("pieChartData", pieChartData); request.setAttribute("barChartData", barChartData); request.setAttribute("patternChartData", patternChartData); return new ModelAndView("jsp/profiler/charts.jsp"); } else { Vector vector = RdbmsConnection.getTable(); String s = selectedValue; int i = vector.indexOf(s); Vector avector[] = (Vector[]) null; avector = TableMetaInfo.populateTable(5, i, i + 1, avector); QueryDialog querydialog = new QueryDialog(1, s, avector); try { querydialog.executeAction(""); } catch (Exception e) { e.printStackTrace(); } request.setAttribute("rowCount", querydialog.getRowCount()); GridUtil gridUtil = new GridUtil(); gridUtil.generateGridData(querydialog.getTableGridDTO(), false, null); request.setAttribute("gridColumns", gridUtil.getColumnNames()); request.setAttribute("colCount", querydialog.getTableGridDTO().getColumnNames().length); request.setAttribute("gridFields", gridUtil.getFieldNames()); request.setAttribute("gridData", gridUtil.getData()); return new ModelAndView("jsp/profiler/info.jsp"); } }
From source file:com.seer.datacruncher.profiler.spring.ProfilerInfoUpdateController.java
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { ServletOutputStream out = null;//from w w w . j ava 2 s.c o m response.setContentType("application/json"); out = response.getOutputStream(); @SuppressWarnings("unchecked") Hashtable<String, String> dbParams = (Hashtable<String, String>) request.getSession(true) .getAttribute("dbConnectionData"); if (dbParams != null) { request.setAttribute("serverName", CommonUtil.notNullValue(dbParams.get("Database_DSN"))); } String selectedValue = CommonUtil.notNullValue(request.getParameter("selectedValue")); request.setAttribute("selectedValue", selectedValue); String tableName = CommonUtil.notNullValue(request.getParameter("parent")); request.setAttribute("parentValue", tableName); ObjectMapper mapper = new ObjectMapper(); Vector vector = RdbmsConnection.getTable(); int i = vector.indexOf(tableName); Vector avector[] = (Vector[]) null; avector = TableMetaInfo.populateTable(5, i, i + 1, avector); QueryDialog querydialog = new QueryDialog(1, tableName, avector); try { querydialog.executeAction(""); } catch (Exception e) { e.printStackTrace(); } String strColumnName = ""; List<String> listPrimaryKeys = new ArrayList<String>(); Map<String, Integer> mapColumnNames = new HashMap<String, Integer>(); try { RdbmsConnection.openConn(); DatabaseMetaData dbmd = RdbmsConnection.getMetaData(); ResultSet resultset = dbmd.getPrimaryKeys(null, null, tableName); while (resultset.next()) { listPrimaryKeys.add(resultset.getString("COLUMN_NAME")); } resultset = dbmd.getColumns(null, null, tableName, null); while (resultset.next()) { strColumnName = resultset.getString(4); mapColumnNames.put(strColumnName, resultset.getInt(5)); } RdbmsConnection.closeConn(); } catch (Exception ex) { ex.printStackTrace(); } Map<String, Integer> mapPrimaryKeys = new HashMap<String, Integer>(); if (strColumnName.trim().length() > 0) { try { JSONArray array = new JSONArray(request.getParameter("data")); for (int count = 0; count < array.length(); count++) { JSONObject jsonObject = new JSONObject(array.get(count).toString()); StringBuilder queryString = new StringBuilder(); Iterator<String> keyIterator = jsonObject.keys(); while (keyIterator.hasNext()) { String strKey = keyIterator.next(); if (listPrimaryKeys.contains(strKey)) { mapPrimaryKeys.put(strKey, ((int) Double.parseDouble(jsonObject.get(strKey).toString()))); continue; } if (jsonObject.get(strKey) != null) { if (mapColumnNames.get(strKey) == 4 || mapColumnNames.get(strKey) == 5 || mapColumnNames.get(strKey) == -6) { queryString.append( strKey + "=" + Integer.parseInt(jsonObject.get(strKey).toString()) + ","); } else if (mapColumnNames.get(strKey) == 2 || mapColumnNames.get(strKey) == 3 || mapColumnNames.get(strKey) == 7 || mapColumnNames.get(strKey) == 6 || mapColumnNames.get(strKey) == -5) { queryString.append(strKey + "=" + jsonObject.get(strKey) + ","); } else if (mapColumnNames.get(strKey) == 91 || mapColumnNames.get(strKey) == 92 || mapColumnNames.get(strKey) == 93) { queryString.append(strKey + "=" + jsonObject.get(strKey) + ","); } else if (mapColumnNames.get(strKey) == -7 || mapColumnNames.get(strKey) == 16 || mapColumnNames.get(strKey) == -3 || mapColumnNames.get(strKey) == -4) { queryString.append(strKey + "=" + jsonObject.get(strKey) + ","); } else if (mapColumnNames.get(strKey) == -1 || mapColumnNames.get(strKey) == 1 || mapColumnNames.get(strKey) == 12) { queryString.append(strKey + "=\"" + jsonObject.get(strKey) + "\","); } } } StringBuilder whereClause = new StringBuilder(" where "); for (String primaryKey : listPrimaryKeys) { whereClause.append(primaryKey + "=" + mapPrimaryKeys.get(primaryKey).intValue()); whereClause.append(" and "); } String strWhereClause = whereClause.toString(); strWhereClause = strWhereClause.substring(0, strWhereClause.lastIndexOf("and")); queryString = new StringBuilder("UPDATE " + tableName + " SET ") .append(queryString.toString().substring(0, queryString.toString().length() - 1)); queryString.append(strWhereClause); RdbmsConnection.openConn(); RdbmsConnection.executeUpdate(queryString.toString()); RdbmsConnection.closeConn(); } } catch (Exception ex) { ex.printStackTrace(); } } Update update = new Update(); update.setSuccess(true); GridUtil gridUtil = new GridUtil(); gridUtil.generateGridData(querydialog.getTableGridDTO(), false, null); update.setResults(gridUtil.getData()); out.write(mapper.writeValueAsBytes(update)); out.flush(); out.close(); return null; }
From source file:edu.ku.brc.af.ui.forms.MenuSwitcherPanel.java
/** * @param value/*from w w w .j a va 2 s . c om*/ */ public void set(final AltViewIFace altView) { if (cardLayout != null) { cardLayout.show(this, altView.getSelectorValue()); } String value = isSelector ? altView.getSelectorValue() : "0"; Vector<AltViewIFace> avList = selectorValHash.get(value); DropDownButtonStateful dds = switcherHash.get(value); if (dds != null && avList != null) { dds.setCurrentIndex(avList.indexOf(altView)); } }
From source file:net.aepik.alasca.gui.util.LoadFileFrame.java
/** * Load a file./* w w w .ja va 2s. co m*/ */ public boolean loadFile(String filename, String syntaxe) { if (!(new File(filename)).exists()) { this.errorMessage = "Le fichier n'existe pas."; return false; } try { SchemaSyntax syntax = Schema.getSyntax(syntaxe); SchemaFile schemaFile = Schema.createAndLoad(syntax, filename, true); Schema schema = schemaFile.getSchema(); if (schema == null) { String message = ""; if (schemaFile.isError()) { message += "\n\n" + "Line " + schemaFile.getErrorLine() + ":\n" + schemaFile.getErrorMessage(); } this.errorMessage = "Le format du fichier est incorrect." + message; return false; } if (manager.isSchemaIdExists((new File(filename)).getName())) { this.errorMessage = "Le fichier est dj ouvert."; return false; } Vector<String> files = Pref.getVector(Pref.PREF_LASTOPENFILES); Vector<String> syntaxes = Pref.getVector(Pref.PREF_LASTOPENSYNTAXES); int index = files.indexOf(filename); if (index >= 0) { files.removeElementAt(index); syntaxes.removeElementAt(index); } files.add(filename); syntaxes.add(syntaxe); if (files.size() > 10) { files.removeElementAt(0); syntaxes.removeElementAt(0); } Pref.set(Pref.PREF_LASTOPENFILES, files.toArray(new String[0])); Pref.set(Pref.PREF_LASTOPENSYNTAXES, syntaxes.toArray(new String[0])); manager.addSchema((new File(filename)).getName(), schema); } catch (Exception e) { e.printStackTrace(); this.errorMessage = "Une erreur inattendue est survenue."; return false; } return true; }
From source file:edu.ku.brc.specify.tasks.subpane.security.UserAgentVSQBldr.java
/** * @param dataMap/*from www .j ava 2 s .c o m*/ * @param fieldNames * @return */ @Override public String buildSQL(final Map<String, Object> dataMap, final List<String> fieldNames) { Vector<Object> disciplineIds = BasicSQLUtils .querySingleCol("SELECT DisciplineID FROM discipline ORDER BY Name"); if (disciplineIds.size() > 1) { Vector<Object> divisionNames = BasicSQLUtils .querySingleCol("SELECT Name FROM discipline ORDER BY Name"); ToggleButtonChooserDlg<Object> divDlg = new ToggleButtonChooserDlg<Object>((Dialog) null, UIRegistry.getResourceString("SEC_PK_SRCH"), divisionNames, ToggleButtonChooserPanel.Type.RadioButton); divDlg.setUseScrollPane(true); divDlg.createUI(); divDlg.getCancelBtn().setVisible(false); divDlg.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); UIHelper.centerAndShow(divDlg); int inx = divisionNames.indexOf(divDlg.getSelectedObject()); disciplineID = (Integer) disciplineIds.get(inx); } else { disciplineID = (Integer) disciplineIds.get(0); } String searchName = cbx.getSearchName(); if (searchName != null) { esTblInfo = ExpressSearchConfigCache.getTableInfoByName(searchName); if (esTblInfo != null) { String sqlStr = esTblInfo.getViewSql(); return buildSearchString(dataMap, fieldNames, StringUtils.replace(sqlStr, "DSPLNID", disciplineID.toString())); } } return null; }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.snpData.SetPlatformListener.java
@Override public void handleEvent(Event event) { Vector<String> values = this.ui.getValues(); Vector<String> samples = this.ui.getSamples(); File file = new File(this.dataType.getPath().toString() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping.tmp"); File mappingFile = ((SnpData) this.dataType).getMappingFile(); if (mappingFile == null) { this.ui.displayMessage("Error: no subject to sample mapping file"); }/*from w w w. ja va2 s. c om*/ try { FileWriter fw = new FileWriter(file); BufferedWriter out = new BufferedWriter(fw); try { BufferedReader br = new BufferedReader(new FileReader(mappingFile)); String line; while ((line = br.readLine()) != null) { String[] fields = line.split("\t", -1); String sample = fields[3]; String platform; if (samples.contains(sample)) { platform = values.get(samples.indexOf(sample)); } else { br.close(); return; } out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n"); } br.close(); } catch (Exception e) { this.ui.displayMessage("Error: " + e.getLocalizedMessage()); out.close(); e.printStackTrace(); } out.close(); try { File fileDest; if (mappingFile != null) { String fileName = mappingFile.getName(); mappingFile.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); ((SnpData) this.dataType).setMappingFile(fileDest); } catch (IOException ioe) { this.ui.displayMessage("File error: " + ioe.getLocalizedMessage()); return; } } catch (Exception e) { this.ui.displayMessage("Error: " + e.getLocalizedMessage()); e.printStackTrace(); } this.ui.displayMessage("Subject to sample mapping file updated"); WorkPart.updateSteps(); WorkPart.updateFiles(); }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.snpData.SetTissueListener.java
@Override public void handleEvent(Event event) { Vector<String> values = this.ui.getValues(); Vector<String> samples = this.ui.getSamples(); File file = new File(this.dataType.getPath().toString() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping.tmp"); File mappingFile = ((SnpData) this.dataType).getMappingFile(); if (mappingFile == null) { this.ui.displayMessage("Error: no subject to sample mapping file"); }// ww w .java 2 s . c o m try { FileWriter fw = new FileWriter(file); BufferedWriter out = new BufferedWriter(fw); try { BufferedReader br = new BufferedReader(new FileReader(mappingFile)); String line; while ((line = br.readLine()) != null) { String[] fields = line.split("\t", -1); String sample = fields[3]; String tissueType; if (samples.contains(sample)) { tissueType = values.get(samples.indexOf(sample)); } else { br.close(); return; } out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + fields[4] + "\t" + tissueType + "\t" + fields[6] + "\t" + fields[7] + "\t" + "PLATFORM+TISSUETYPE" + "\n"); } br.close(); } catch (Exception e) { this.ui.displayMessage("File error: " + e.getLocalizedMessage()); out.close(); e.printStackTrace(); } out.close(); try { File fileDest; if (mappingFile != null) { String fileName = mappingFile.getName(); mappingFile.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); ((SnpData) this.dataType).setMappingFile(fileDest); } catch (IOException ioe) { this.ui.displayMessage("File error: " + ioe.getLocalizedMessage()); return; } } catch (Exception e) { this.ui.displayMessage("Error: " + e.getLocalizedMessage()); e.printStackTrace(); } this.ui.displayMessage("Subject to sample mapping file updated"); WorkPart.updateSteps(); WorkPart.updateFiles(); }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetSiteIdListener.java
@Override public void handleEvent(Event event) { // TODO Auto-generated method stub Vector<String> values = this.setSiteIdUI.getValues(); Vector<String> samples = this.setSiteIdUI.getSamples(); File file = new File(this.dataType.getPath().toString() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping.tmp"); File stsmf = ((GeneExpressionData) this.dataType).getStsmf(); if (stsmf == null) { this.setSiteIdUI.displayMessage("Error: no subject to sample mapping file"); }// w ww. j ava2s .c o m 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"); 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 site; if (samples.contains(sample)) { site = values.get(samples.indexOf(sample)); } else { br.close(); return; } out.write(fields[0] + "\t" + site + "\t" + fields[2] + "\t" + sample + "\t" + fields[4] + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n"); } br.close(); } catch (Exception e) { this.setSiteIdUI.displayMessage("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.setSiteIdUI.displayMessage("File error: " + ioe.getLocalizedMessage()); return; } } catch (Exception e) { this.setSiteIdUI.displayMessage("Error: " + e.getLocalizedMessage()); e.printStackTrace(); } this.setSiteIdUI.displayMessage("Subject to sample mapping file updated"); WorkPart.updateSteps(); WorkPart.updateFiles(); }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.SetPlatformsListener.java
@Override public void handleEvent(Event event) { // TODO Auto-generated method stub Vector<String> values = this.setPlatformsUI.getValues(); Vector<String> samples = this.setPlatformsUI.getSamples(); File file = new File(this.dataType.getPath().toString() + File.separator + this.dataType.getStudy().toString() + ".subject_mapping.tmp"); File stsmf = ((GeneExpressionData) this.dataType).getStsmf(); if (stsmf == null) { this.setPlatformsUI.displayMessage("Error: no subject to sample mapping file"); }//from ww w . j a v a 2 s. co m 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"); 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 platform; if (samples.contains(sample)) { platform = values.get(samples.indexOf(sample)); } else { br.close(); return; } out.write(fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform + "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8] + "\n"); } br.close(); } catch (Exception e) { this.setPlatformsUI.displayMessage("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.setPlatformsUI.displayMessage("File error: " + ioe.getLocalizedMessage()); return; } } catch (Exception e) { this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage()); e.printStackTrace(); } this.setPlatformsUI.displayMessage("Subject to sample mapping file updated"); WorkPart.updateSteps(); WorkPart.updateFiles(); }