List of usage examples for java.util Collection toArray
Object[] toArray();
From source file:com.ephesoft.dcma.util.EphesoftStringUtil.java
/** * Joins the collection values passed as a parameter separated by the delimiter passed as a parameter. * //ww w . j a v a 2 s .com * @param collection {@link Collection} collection whose values needs to be joined. * @param separator delimiter to be used as a separator between values. * @return {@link String} joined string. */ public static <E> String join(final Collection<E> collection, final char separator) { String joinString = null; if (!CollectionUtil.isEmpty(collection) && 0 != separator) { joinString = StringUtils.join(collection.toArray(), separator); } return joinString; }
From source file:sep.gaia.resources.poi.POILoaderWorker.java
/** * Generates a POI from a way by adopting its attributes and picking one of the positions it consists of * as the POIs position./*from w w w . j av a 2 s .c om*/ * @param way The way to convert. * @return The POI generated. */ private static PointOfInterest wayToPoi(Way way) { Map<String, String> tags = way.getAttributes(); String name = tags.get("name"); Collection<FloatVector3D> nodePositions = way.getNodePositions(); if (name != null && nodePositions.size() > 0) { int index = nodePositions.size() / 2; FloatVector3D position = (FloatVector3D) nodePositions.toArray()[index]; PointOfInterest poi = new PointOfInterest(name, position.getX(), position.getY()); poi.setAttributes(tags); return poi; } return null; }
From source file:gov.nist.healthcare.ttt.parsing.Parsing.java
public static boolean isValidDirectDisposition(String mtom) throws MessagingException, IOException { SOAPWithAttachment swa = Parsing.parseMtom(mtom); Collection<byte[]> documents = swa.getAttachment(); if (documents == null || documents.size() == 0) { return false; }/*from w ww. ja va 2 s.c o m*/ String directDis = new String((byte[]) documents.toArray()[0]); return DirectDisposition.isValidDirectDisposition(directDis); }
From source file:com.vmware.bdd.manager.SoftwareManagerCollector.java
/** * TODO this method has to be reverted:/*from ww w.j av a 2 s .c o m*/ * because if the target path is not accessible, it will load cert from the default keystore in java home, * but still try to write it to the non accessible path. * @param certificate * @param keyStorePath */ protected static void saveSslCertificate(String certificate, String keyStorePath) { Certificate[] certs; //parse certificates try { if (CommonUtil.isBlank(certificate)) { throw SoftwareManagerCollectorException.BAD_CERT(null); } byte[] certBytes = Base64.decodeBase64(certificate.replaceAll("-----BEGIN CERTIFICATE-----", "") .replaceAll("-----END CERTIFICATE-----", "").getBytes()); CertificateFactory cf = CertificateFactory.getInstance("X.509"); Collection c = cf.generateCertificates(new ByteArrayInputStream(certBytes)); certs = new Certificate[c.toArray().length]; if (c.size() == 0) { throw SoftwareManagerCollectorException.BAD_CERT(null); } else if (c.size() == 1) { certs[0] = cf.generateCertificate(new ByteArrayInputStream(certBytes)); } else { certs = (Certificate[]) c.toArray(certs); } } catch (CertificateException e) { throw SoftwareManagerCollectorException.BAD_CERT(e); } //load & save keystore OutputStream out = null; try { KeyStore keyStore = CommonUtil.loadAppMgrKeyStore(keyStorePath); if (keyStore == null) { logger.error(Messages.getString("SW_MGR_COLLECTOR.CANNT_READ_KEYSTORE")); throw new SWMgrCollectorInternalException( Messages.getString("SW_MGR_COLLECTOR.CANNT_READ_KEYSTORE")); } MessageDigest md5 = MessageDigest.getInstance("MD5"); String md5Fingerprint = ""; for (Certificate cert : certs) { md5.update(cert.getEncoded()); md5Fingerprint = CommonUtil.toHexString(md5.digest()); logger.debug("md5 finger print: " + md5Fingerprint); logger.debug("added cert: " + cert); keyStore.setCertificateEntry(md5Fingerprint, cert); } out = new FileOutputStream(keyStorePath + Constants.APPMANAGER_KEYSTORE_FILE); keyStore.store(new BufferedOutputStream(out), Constants.APPMANAGER_KEYSTORE_PASSWORD); } catch (CertificateException | NoSuchAlgorithmException | IOException | KeyStoreException e) { logger.error(Messages.getString("SW_MGR_COLLECTOR.FAIL_SAVE_CERT"), e); throw new SWMgrCollectorInternalException(e, Messages.getString("SW_MGR_COLLECTOR.FAIL_SAVE_CERT")); } finally { if (out != null) { try { out.close(); } catch (IOException e) { logger.warn("Output stream of appmanagers.jks close failed."); } } } }
From source file:com.sunchenbin.store.feilong.core.bean.ConvertUtil.java
/** * ? <code>collection</code>??. * // w w w. ja va 2 s .co m * <h3>:</h3> * * <blockquote> * * <pre> * List<String> list = new ArrayList<String>(); * list.add("feilong"); * list.add(""); * list.add("xinge"); * * ToStringConfig toStringConfig = new ToStringConfig(","); * toStringConfig.setIsJoinNullOrEmpty(false); * * assertEquals("feilong,xinge", ConvertUtil.toString(toStringConfig, list)); * </pre> * * </blockquote> * * @param toStringConfig * * @param collection * ?, ?,collection * @return collection isNullOrEmpty,null<br> * toStringConfig null, {@link ToStringConfig#DEFAULT_CONNECTOR} <br> * ?null,,toStringConfig.getConnector() * @see #toString(ToStringConfig, Object...) * @since 1.4.0 */ public static String toString(ToStringConfig toStringConfig, final Collection<?> collection) { if (Validator.isNullOrEmpty(collection)) { return StringUtils.EMPTY; } Object[] array = collection.toArray(); return toString(toStringConfig, array); }
From source file:gov.nih.nci.rembrandt.web.xml.FTestReport.java
public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations) { DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /*// w w w . ja v a 2 s .com * this is for filtering, we will want a p-value filter for CC */ ArrayList filter_string = new ArrayList(); // hashmap of genes | reporters | cytobands String filter_type = "show"; // show | hide String filter_element = "none"; // none | gene | reporter | cytoband if (filterMapParams.containsKey("filter_string") && filterMapParams.get("filter_string") != null) filter_string = (ArrayList) filterMapParams.get("filter_string"); if (filterMapParams.containsKey("filter_type") && filterMapParams.get("filter_type") != null) filter_type = (String) filterMapParams.get("filter_type"); if (filterMapParams.containsKey("filter_element") && filterMapParams.get("filter_element") != null) filter_element = (String) filterMapParams.get("filter_element"); String defaultV = "--"; String delim = " | "; Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Class Comparison"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Class Comparison")); //lets flag this as Ftest report.addAttribute("reportSubType", "FTEST"); //fudge these for now report.addAttribute("groupBy", "none"); String queryName = "none"; queryName = finding.getTaskId(); //set the queryName to be unique for session/cache access report.addAttribute("queryName", queryName); report.addAttribute("sessionId", "the session id"); report.addAttribute("creationTime", "right now"); StringBuffer sb = new StringBuffer(); int recordCount = 0; int totalSamples = 0; //TODO: instance of FTestFinding ccf = (FTestFinding) finding; //process the query details ArrayList<String> queryDetails = new ArrayList(); ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO(); if (ccdto != null) { String tmp = ""; tmp = ccdto.getQueryName() != null ? ccdto.getQueryName() : ""; queryDetails.add("Query Name: " + tmp); tmp = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValue().toString() : ""; queryDetails.add("Array Platform: " + tmp); tmp = ""; List<ClinicalQueryDTO> grps = ccdto.getComparisonGroups() != null ? ccdto.getComparisonGroups() : new ArrayList(); Collection grs = new ArrayList(); for (ClinicalQueryDTO cdto : grps) { if (cdto.getQueryName() != null) grs.add(cdto.getQueryName()); } tmp += StringUtils.join(grs.toArray(), ", ") + " (baseline)"; queryDetails.add("Groups: " + tmp); tmp = ccdto.getExprFoldChangeDE() != null ? ccdto.getExprFoldChangeDE().getValue().toString() : ""; queryDetails.add("Fold Change: " + tmp); //queryDetails.add("Institutions: " + ccdto.getInstitutionDEs()); tmp = ccdto.getMultiGroupComparisonAdjustmentTypeDE() != null ? ccdto.getMultiGroupComparisonAdjustmentTypeDE().getValue().toString() : ""; queryDetails.add("Multi Group: " + tmp); tmp = ccdto.getStatisticalSignificanceDE() != null ? ccdto.getStatisticalSignificanceDE().getValue().toString() : ""; queryDetails.add("Stat Sig.: " + tmp); tmp = ccdto.getStatisticTypeDE() != null ? ccdto.getStatisticTypeDE().getValue().toString() : ""; queryDetails.add("Stat Type: " + tmp); } String qd = ""; for (String q : queryDetails) { qd += q + " ||| "; } if (ccf != null) { Element details = report.addElement("Query_details"); cell = details.addElement("Data"); cell.addText(qd); cell = null; Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Reporter"); data = null; cell = null; //pvalue is fixed in the second column, essential for XSL cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); String isAdj = ccf.arePvaluesAdjusted() ? " (Adjusted) " : ""; data = cell.addElement("Data").addAttribute("type", "header") .addText(RembrandtConstants.PVALUE + isAdj); data = null; cell = null; //one col for each group in the comparison List<String> groupNames = ccf.getGroupNames(); for (String n : groupNames) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(n + " Group Avg"); data = null; cell = null; } cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Fold Change"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Gene Symbol"); data = null; cell = null; //starting annotations...get them only if allAnnotations == true if (allAnnotations) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GenBank Acc"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Locus link"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GO Id"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Pathways"); data = null; cell = null; } /* done with the headerRow and SampleRow Elements, time to add data rows */ List<FTestResultEntry> fTestResultEntrys = ccf.getResultEntries(); List<String> reporterIds = new ArrayList<String>(); for (FTestResultEntry fTestResultEntry : fTestResultEntrys) { if (fTestResultEntry.getReporterId() != null) { reporterIds.add(fTestResultEntry.getReporterId()); } } ArrayPlatformType arrayPlatform = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValueObjectAsArrayPlatformType() : ArrayPlatformType.AFFY_OLIGO_PLATFORM; Map reporterResultsetMap = null; if (allAnnotations) { //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getAllAnnotationsFor(reporterIds, arrayPlatform); } catch (Exception e) { e.printStackTrace(); } } else { //Map<String, String> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getGeneSymbolsFor(reporterIds, arrayPlatform); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } for (FTestResultEntry ccre : ccf.getResultEntries()) { dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(ccre.getReporterId()); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "pval").addAttribute("class", "data") .addAttribute("group", "data"); //String pv = (ccre.getPvalue() == null) ? String.valueOf(ccre.getPvalue()) : "N/A"; BigDecimal bigd = new BigDecimal(ccre.getPvalue()); data = cell.addElement("Data").addAttribute("type", "header").addText(bigd.toPlainString()); data = null; cell = null; //one col for each group for (int i = 0; i < ccre.getGroupMeans().length; i++) { cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(resultFormat.format(ccre.getGroupMeans()[i])); data = null; cell = null; } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(String.valueOf(resultFormat.format(ccre.getMaximumFoldChange()))); data = null; cell = null; //if only showing genes if (!allAnnotations && reporterResultsetMap != null) { String reporterId = ccre.getReporterId(); String genes = reporterResultsetMap.get(reporterId) != null ? (String) reporterResultsetMap.get(reporterId) : defaultV; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; } else { //get the gene symbols for this reporter //ccre.getReporterId() String genes = defaultV; //start annotations String accIds = defaultV; String llink = defaultV; String go = defaultV; String pw = defaultV; if (reporterResultsetMap != null) { // && reporterIds != null //int count = 0; String reporterId = ccre.getReporterId(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotations ra = (ReporterAnnotations) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); String geneSymbols = ra.getGeneSymbol(); if (geneSymbols != null) genes = geneSymbols; /* if(geneSymbols != null){ genes = StringUtils.join(geneSymbols.toArray(), delim); } */ Collection<String> genBank_AccIDS = (Collection<String>) ra.getAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinks(); if (locusLinkIDs != null) { llink = StringUtils.join(locusLinkIDs.toArray(), delim); } Collection<String> goIds = (Collection<String>) ra.getGoIDS(); if (goIds != null) { go = StringUtils.join(goIds.toArray(), delim); } Collection<String> pathways = (Collection<String>) ra.getPathways(); if (pathways != null) { pw = StringUtils.join(pathways.toArray(), delim); } } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(accIds); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(llink); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(go); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(pw); data = null; cell = null; } } } else { //TODO: handle this error sb.append("<br/><br/>Class Comparison is empty<br/>"); } logger.info(document.toString()); return document; }
From source file:gov.nih.nci.ispy.web.xml.ClassComparisonReport.java
public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations) { allAnnotations = true; //force this for now ISPY prerelease - RCL 3/2 DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /*//from w w w .j ava2 s . c o m * this is for filtering, we will want a p-value filter for CC */ ArrayList filter_string = new ArrayList(); // hashmap of genes | reporters | cytobands String filter_type = "show"; // show | hide String filter_element = "none"; // none | gene | reporter | cytoband if (filterMapParams.containsKey("filter_string") && filterMapParams.get("filter_string") != null) filter_string = (ArrayList) filterMapParams.get("filter_string"); if (filterMapParams.containsKey("filter_type") && filterMapParams.get("filter_type") != null) filter_type = (String) filterMapParams.get("filter_type"); if (filterMapParams.containsKey("filter_element") && filterMapParams.get("filter_element") != null) filter_element = (String) filterMapParams.get("filter_element"); String defaultV = "--"; String delim = " | "; Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Class Comparison"); //fudge these for now report.addAttribute("groupBy", "none"); String queryName = "none"; queryName = finding.getTaskId(); //set the queryName to be unique for session/cache access report.addAttribute("queryName", queryName); report.addAttribute("sessionId", "the session id"); report.addAttribute("creationTime", "right now"); StringBuffer sb = new StringBuffer(); int recordCount = 0; int totalSamples = 0; //TODO: instance of ClassComparisonFinding ccf = (ClassComparisonFinding) finding; //process the query details ArrayList<String> queryDetails = new ArrayList(); ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO(); String reporterType = ccdto.getArrayPlatformDE().getValueObject(); if (ccdto != null) { String tmp = ""; tmp = ccdto.getQueryName() != null ? ccdto.getQueryName() : ""; queryDetails.add("Query Name: " + tmp); tmp = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValue().toString() : ""; queryDetails.add("Array Platform: " + tmp); tmp = ""; List<ClinicalQueryDTO> grps = ccdto.getComparisonGroups() != null ? ccdto.getComparisonGroups() : new ArrayList(); Collection grs = new ArrayList(); for (ClinicalQueryDTO cdto : grps) { if (cdto.getQueryName() != null) grs.add(cdto.getQueryName()); } tmp += StringUtils.join(grs.toArray(), ", ") + " (baseline)"; queryDetails.add("Groups: " + tmp); /* noHTMLString = noHTMLString.replaceAll("<", "{"); noHTMLString = noHTMLString.replaceAll(">", "}"); noHTMLString = noHTMLString.replaceAll(" ", " "); */ tmp = ccdto.getExprFoldChangeDE() != null ? ccdto.getExprFoldChangeDE().getValue().toString() : ""; queryDetails.add("Fold Change: " + tmp); //queryDetails.add("Institutions: " + ccdto.getInstitutionDEs()); tmp = ccdto.getMultiGroupComparisonAdjustmentTypeDE() != null ? ccdto.getMultiGroupComparisonAdjustmentTypeDE().getValue().toString() : ""; queryDetails.add("Multi Group: " + tmp); tmp = ccdto.getStatisticalSignificanceDE() != null ? ccdto.getStatisticalSignificanceDE().getValue().toString() : ""; queryDetails.add("Stat Sig.: " + tmp); tmp = ccdto.getStatisticTypeDE() != null ? ccdto.getStatisticTypeDE().getValue().toString() : ""; queryDetails.add("Stat Type: " + tmp); } /* queryDetails.add("Analysis Result name: " + ccform.getAnalysisResultName()); queryDetails.add("Array Platform: " + ccform.getArrayPlatform()); queryDetails.add("Baseline group: " + ccform.getBaselineGroup()); queryDetails.add("Comparison Groups: " + ccform.getSelectedGroups()[0].toString()); queryDetails.add("Comparison Adjustment: " + ccform.getComparisonAdjustment()); //queryDetails.add("Comp. Adj. Coll: " + ccform.getComparisonAdjustmentCollection()); //queryDetails.add("Existing Groups: " + ccform.getExistingGroups()); //queryDetails.add("Existing group list: " + ccform.getExistingGroupsList()); //queryDetails.add("Fold Change: " + ccform.getFoldChange()); queryDetails.add("Fold Change auto: " + ccform.getFoldChangeAuto()); //queryDetails.add("Fold change auto list: " + ccform.getFoldChangeAutoList()); //queryDetails.add("Fold change manual: " + ccform.getFoldChangeManual()); queryDetails.add("Stastic: " + ccform.getStatistic()); queryDetails.add("Stastical method: " + ccform.getStatisticalMethod()); //queryDetails.add("Stastical method coll.: " + ccform.getStatisticalMethodCollection()); queryDetails.add("Stastical significance: " + ccform.getStatisticalSignificance()); */ String qd = ""; for (String q : queryDetails) { qd += q + " ||| "; } if (ccf != null) { Element details = report.addElement("Query_details"); cell = details.addElement("Data"); cell.addText(qd); cell = null; Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Reporter"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Group Avg"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); String isAdj = ccf.arePvaluesAdjusted() ? " (Adjusted) " : ""; data = cell.addElement("Data").addAttribute("type", "header").addText("P-Value" + isAdj); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Fold Change"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Gene Symbol"); data = null; cell = null; //starting annotations...get them only if allAnnotations == true if (allAnnotations) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GenBank Acc"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Locus link"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GO Id"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Pathways"); data = null; cell = null; } /* done with the headerRow and SampleRow Elements, time to add data rows */ /* Map<String,ReporterResultset> reporterResultsetMap = null; reporterResultsetMap = ccf.getReporterAnnotationsMap(); */ List<ClassComparisonResultEntry> classComparisonResultEntrys = ccf.getResultEntries(); List<String> reporterIds = new ArrayList<String>(); for (ClassComparisonResultEntry classComparisonResultEntry : classComparisonResultEntrys) { if (classComparisonResultEntry.getReporterId() != null) { reporterIds.add(classComparisonResultEntry.getReporterId()); } } Map reporterResultsetMap = null; try { GeneExprAnnotationService geService = GeneExprAnnotationServiceFactory.getInstance(); reporterResultsetMap = geService.getAnnotationsMapForReporters(reporterIds); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } /* //new stuff AnnotationHandler h = new AnnotationHandler(); Map reporterResultsetMap = null; if(allAnnotations){ //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = h.getAllAnnotationsFor(reporterIds); } catch (Exception e) { e.printStackTrace(); } } else { //Map<String, String> reporterResultsetMap = null; try { reporterResultsetMap = h.getGeneSymbolsFor(reporterIds); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } */ /* //this looks like a failsafe for the old method if(reporterResultsetMap == null) { try { reporterResultsetMap = GeneExprAnnotationService.getAnnotationsMapForReporters(reporterIds); } catch(Exception e){} } */ for (ClassComparisonResultEntry ccre : ccf.getResultEntries()) { dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", reporterType).addText(ccre.getReporterId()); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(resultFormat.format(ccre.getMeanGrp1()) + " / " + resultFormat.format(ccre.getMeanBaselineGrp())); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "pval").addAttribute("class", "data") .addAttribute("group", "data"); //String pv = (ccre.getPvalue() == null) ? String.valueOf(ccre.getPvalue()) : "N/A"; String pv = defaultV; BigDecimal bigd; try { bigd = new BigDecimal(ccre.getPvalue()); pv = bigd.toPlainString(); } catch (Exception e) { //missing value } data = cell.addElement("Data").addAttribute("type", "header").addText(pv); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(String.valueOf(resultFormat.format(ccre.getFoldChange()))); data = null; cell = null; //if only showing genes if (!allAnnotations && reporterResultsetMap != null) { String reporterId = ccre.getReporterId().toUpperCase().trim(); String genes = reporterResultsetMap.get(reporterId) != null ? (String) reporterResultsetMap.get(reporterId) : defaultV; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; } else { //get the gene symbols for this reporter //ccre.getReporterId() String genes = defaultV; //start annotations String accIds = defaultV; String llink = defaultV; String go = defaultV; String pw = defaultV; if (reporterResultsetMap != null) { // && reporterIds != null //int count = 0; String reporterId = ccre.getReporterId().toUpperCase().trim(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotation ra = (ReporterAnnotation) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); if (ra != null) { List geneSymbols = ra.getGeneSymbols(); //if(geneSymbols != null) // genes = geneSymbols.toString(); if (geneSymbols != null) { genes = StringUtils.join(geneSymbols.toArray(), delim); } Collection<String> genBank_AccIDS = (Collection<String>) ra.getGenbankAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinkIds(); if (locusLinkIDs != null) { llink = StringUtils.join(locusLinkIDs.toArray(), delim); } Collection<String> goIds = (Collection<String>) ra.getGOIds(); if (goIds != null) { go = StringUtils.join(goIds.toArray(), delim); } Collection<String> pathways = (Collection<String>) ra.getPathwayIds(); if (pathways != null) { pw = StringUtils.join(pathways.toArray(), delim); } } } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(accIds); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(llink); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(go); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(pw); data = null; cell = null; } } } else { //TODO: handle this error sb.append("<br><Br>Class Comparison is empty<br>"); } return document; }
From source file:com.l2jfree.util.L2Collections.java
public static <T> T random(Collection<? extends T> c) { if (c instanceof RandomAccess) { final List<? extends T> list = (List<? extends T>) c; return list.isEmpty() ? null : (T) list.get(Rnd.get(list.size())); } else {// w w w.j av a 2 s . co m final Object[] array = c.toArray(); return array.length == 0 ? null : (T) array[Rnd.get(array.length)]; } }
From source file:edu.ku.brc.af.ui.forms.BaseBusRules.java
/** * Removed an Object from a Collection by Id. * @param collection the Java Collection * @param dataObj the data object to be removed *///ww w . j av a2s . c o m public static void removeById(final Collection<?> collection, final FormDataObjIFace dataObj) { for (Object obj : collection.toArray()) { if (obj instanceof FormDataObjIFace) { FormDataObjIFace colObj = (FormDataObjIFace) obj; if (obj == colObj || (colObj.getId() != null && dataObj.getId() != null && dataObj.getId().equals(colObj.getId()))) { collection.remove(obj); break; } } } }
From source file:gov.nih.nci.rembrandt.web.xml.ClassComparisonReport.java
public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations, ArrayList reporterIdFilter) { DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /*/*from www . ja va2s.c om*/ * this is for filtering, we will want a p-value filter for CC */ ArrayList filter_string = new ArrayList(); // hashmap of genes | reporters | cytobands String filter_type = "show"; // show | hide String filter_element = "none"; // none | gene | reporter | cytoband if (filterMapParams.containsKey("filter_string") && filterMapParams.get("filter_string") != null) filter_string = (ArrayList) filterMapParams.get("filter_string"); if (filterMapParams.containsKey("filter_type") && filterMapParams.get("filter_type") != null) filter_type = (String) filterMapParams.get("filter_type"); if (filterMapParams.containsKey("filter_element") && filterMapParams.get("filter_element") != null) filter_element = (String) filterMapParams.get("filter_element"); String defaultV = "--"; String delim = " | "; Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Class Comparison"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Class Comparison")); //fudge these for now report.addAttribute("groupBy", "none"); String queryName = "none"; queryName = finding.getTaskId(); //set the queryName to be unique for session/cache access report.addAttribute("queryName", queryName); report.addAttribute("sessionId", "the session id"); report.addAttribute("creationTime", "right now"); StringBuffer sb = new StringBuffer(); int recordCount = 0; int totalSamples = 0; //TODO: instance of ClassComparisonFinding ccf = (ClassComparisonFinding) finding; //process the query details ArrayList<String> queryDetails = new ArrayList(); ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO(); if (ccdto != null) { String tmp = ""; tmp = ccdto.getQueryName() != null ? ccdto.getQueryName() : ""; queryDetails.add("Query Name: " + tmp); tmp = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValue().toString() : ""; queryDetails.add("Array Platform: " + tmp); tmp = ""; List<ClinicalQueryDTO> grps = ccdto.getComparisonGroups() != null ? ccdto.getComparisonGroups() : new ArrayList(); Collection grs = new ArrayList(); for (ClinicalQueryDTO cdto : grps) { if (cdto.getQueryName() != null) grs.add(cdto.getQueryName()); } tmp += StringUtils.join(grs.toArray(), ", ") + " (baseline)"; queryDetails.add("Groups: " + tmp); /* noHTMLString = noHTMLString.replaceAll("<", "{"); noHTMLString = noHTMLString.replaceAll(">", "}"); noHTMLString = noHTMLString.replaceAll(" ", " "); */ tmp = ccdto.getExprFoldChangeDE() != null ? ccdto.getExprFoldChangeDE().getValue().toString() : ""; queryDetails.add("Fold Change: " + tmp); //queryDetails.add("Institutions: " + ccdto.getInstitutionDEs()); tmp = ccdto.getMultiGroupComparisonAdjustmentTypeDE() != null ? ccdto.getMultiGroupComparisonAdjustmentTypeDE().getValue().toString() : ""; queryDetails.add("Multi Group: " + tmp); tmp = ccdto.getStatisticalSignificanceDE() != null ? ccdto.getStatisticalSignificanceDE().getValue().toString() : ""; queryDetails.add("Stat Sig.: " + tmp); tmp = ccdto.getStatisticTypeDE() != null ? ccdto.getStatisticTypeDE().getValue().toString() : ""; queryDetails.add("Stat Type: " + tmp); } /* queryDetails.add("Analysis Result name: " + ccform.getAnalysisResultName()); queryDetails.add("Array Platform: " + ccform.getArrayPlatform()); queryDetails.add("Baseline group: " + ccform.getBaselineGroup()); queryDetails.add("Comparison Groups: " + ccform.getSelectedGroups()[0].toString()); queryDetails.add("Comparison Adjustment: " + ccform.getComparisonAdjustment()); //queryDetails.add("Comp. Adj. Coll: " + ccform.getComparisonAdjustmentCollection()); //queryDetails.add("Existing Groups: " + ccform.getExistingGroups()); //queryDetails.add("Existing group list: " + ccform.getExistingGroupsList()); //queryDetails.add("Fold Change: " + ccform.getFoldChange()); queryDetails.add("Fold Change auto: " + ccform.getFoldChangeAuto()); //queryDetails.add("Fold change auto list: " + ccform.getFoldChangeAutoList()); //queryDetails.add("Fold change manual: " + ccform.getFoldChangeManual()); queryDetails.add("Stastic: " + ccform.getStatistic()); queryDetails.add("Stastical method: " + ccform.getStatisticalMethod()); //queryDetails.add("Stastical method coll.: " + ccform.getStatisticalMethodCollection()); queryDetails.add("Stastical significance: " + ccform.getStatisticalSignificance()); */ String qd = ""; for (String q : queryDetails) { qd += q + " ||| "; } if (ccf != null) { Element details = report.addElement("Query_details"); cell = details.addElement("Data"); cell.addText(qd); cell = null; Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Reporter"); data = null; cell = null; //pvalue is fixed in the second column, essential for XSL cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); String isAdj = ccf.arePvaluesAdjusted() ? " (Adjusted) " : ""; data = cell.addElement("Data").addAttribute("type", "header") .addText(RembrandtConstants.PVALUE + isAdj); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Group Avg"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Fold Change"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Gene Symbol"); data = null; cell = null; //starting annotations...get them only if allAnnotations == true if (allAnnotations) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GenBank Acc"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Locus link"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GO Id"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Pathways"); data = null; cell = null; } /* done with the headerRow and SampleRow Elements, time to add data rows */ /* Map<String,ReporterResultset> reporterResultsetMap = null; reporterResultsetMap = ccf.getReporterAnnotationsMap(); */ List<ClassComparisonResultEntry> classComparisonResultEntrys = ccf.getResultEntries(); List<String> reporterIds = new ArrayList<String>(); HashSet<String> reporterIdSet = null; if (reporterIdFilter != null) { reporterIdSet = new HashSet<String>(reporterIdFilter); } int index = 0; if (reporterIdFilter == null) { for (ClassComparisonResultEntry classComparisonResultEntry : classComparisonResultEntrys) { if (classComparisonResultEntry.getReporterId() != null) { reporterIds.add(classComparisonResultEntry.getReporterId()); } } } else { reporterIds = reporterIdFilter; } Map reporterResultsetMap = null; ArrayPlatformType arrayPlatform = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValueObjectAsArrayPlatformType() : ArrayPlatformType.AFFY_OLIGO_PLATFORM; if (allAnnotations) { //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getAllAnnotationsFor(reporterIds, arrayPlatform); } catch (Exception e) { e.printStackTrace(); } } else { try { reporterResultsetMap = AnnotationHandler.getGeneSymbolsFor(reporterIds, arrayPlatform); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } /* //this looks like a failsafe for the old method if(reporterResultsetMap == null) { try { reporterResultsetMap = GeneExprAnnotationService.getAnnotationsMapForReporters(reporterIds); } catch(Exception e){} } */ boolean found = false; for (ClassComparisonResultEntry ccre : ccf.getResultEntries()) { if (reporterIdFilter != null) { found = reporterIdSet.contains(ccre.getReporterId()); //not found, then skip if (!found) continue; } dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(ccre.getReporterId()); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "pval").addAttribute("class", "data") .addAttribute("group", "data"); //String pv = (ccre.getPvalue() == null) ? String.valueOf(ccre.getPvalue()) : "N/A"; BigDecimal bigd = new BigDecimal(ccre.getPvalue()); data = cell.addElement("Data").addAttribute("type", "header").addText(bigd.toPlainString()); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(resultFormat.format(ccre.getMeanGrp1()) + " / " + resultFormat.format(ccre.getMeanBaselineGrp())); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(String.valueOf(resultFormat.format(ccre.getFoldChange()))); data = null; cell = null; //if only showing genes if (!allAnnotations && reporterResultsetMap != null) { String reporterId = ccre.getReporterId(); String genes = reporterResultsetMap.get(reporterId) != null ? (String) reporterResultsetMap.get(reporterId) : defaultV; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; } else { //get the gene symbols for this reporter //ccre.getReporterId() String genes = defaultV; //start annotations String accIds = defaultV; String llink = defaultV; String go = defaultV; String pw = defaultV; if (reporterResultsetMap != null) { // && reporterIds != null //int count = 0; String reporterId = ccre.getReporterId(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotations ra = (ReporterAnnotations) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); String geneSymbols = ra.getGeneSymbol(); if (geneSymbols != null) genes = geneSymbols; /* if(geneSymbols != null){ genes = StringUtils.join(geneSymbols.toArray(), delim); } */ Collection<String> genBank_AccIDS = (Collection<String>) ra.getAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinks(); if (locusLinkIDs != null) { llink = StringUtils.join(locusLinkIDs.toArray(), delim); } Collection<String> goIds = (Collection<String>) ra.getGoIDS(); if (goIds != null) { go = StringUtils.join(goIds.toArray(), delim); } Collection<String> pathways = (Collection<String>) ra.getPathways(); if (pathways != null) { pw = StringUtils.join(pathways.toArray(), delim); } } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(accIds); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(llink); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(go); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(pw); data = null; cell = null; } } } else { //TODO: handle this error sb.append("<br/><br/>Class Comparison is empty<br/>"); } return document; }