List of usage examples for org.apache.commons.lang StringUtils remove
public static String remove(String str, char remove)
Removes all occurrences of a character from within the source string.
From source file:edu.cornell.med.icb.goby.R.FisherExact.java
/** * Pass the fisher expression to R for computation. * * @param rengine The R engine to use to calcuate the results. * @param fisherExpression The string representing the expression to evaluate. * @param is2x2matrix Whether or not the data being evaluated represents a 2x2 matrix * @return The results of the evaluation (may be null if an exception interrupts the calculation) *///from w w w . j a v a2 s. c o m private static Result evaluateFisherExpression(final Rengine rengine, final String fisherExpression, final boolean is2x2matrix) { // evaluate the R expression if (LOG.isDebugEnabled()) { LOG.debug("About to evaluate: " + fisherExpression); } final REXP fisherResultExpression = rengine.eval(fisherExpression); if (LOG.isDebugEnabled()) { LOG.debug(fisherResultExpression); } if (fisherResultExpression == null) { return null; } // the result from R is a vector/map of values final RVector fisherResultVector = fisherResultExpression.asVector(); if (LOG.isDebugEnabled()) { LOG.debug(fisherResultVector); } // extract the p-value final REXP pValueExpression = fisherResultVector.at("p.value"); final double pValue; if (pValueExpression != null) { pValue = pValueExpression.asDouble(); } else { pValue = Double.NaN; } // extract the alternative hypothesis final REXP alternativeExpression = fisherResultVector.at("alternative"); final String alternative = alternativeExpression.asString(); if (LOG.isDebugEnabled()) { LOG.debug("alternative: " + alternative); } final AlternativeHypothesis alternativeHypothesis = AlternativeHypothesis .valueOf(StringUtils.remove(alternative, '.')); // some values are only returned when the input was a 2x2 matrix final double estimate; final double[] confidenceInterval; final double oddsRatio; if (is2x2matrix) { final REXP estimateExpression = fisherResultVector.at("estimate"); if (estimateExpression != null) { estimate = estimateExpression.asDouble(); } else { estimate = Double.NaN; } if (LOG.isDebugEnabled()) { LOG.debug(estimateExpression); LOG.debug("estimate: " + estimate); } final REXP confidenceIntervalExpression = fisherResultVector.at("conf.int"); if (confidenceIntervalExpression != null) { confidenceInterval = confidenceIntervalExpression.asDoubleArray(); } else { confidenceInterval = ArrayUtils.EMPTY_DOUBLE_ARRAY; } if (LOG.isDebugEnabled()) { LOG.debug(confidenceIntervalExpression); LOG.debug("confidenceInterval: " + ArrayUtils.toString(confidenceInterval)); } final REXP oddsRatioExpression = fisherResultVector.at("null.value"); if (oddsRatioExpression != null) { oddsRatio = oddsRatioExpression.asDouble(); } else { oddsRatio = Double.NaN; } if (LOG.isDebugEnabled()) { LOG.debug(oddsRatioExpression); LOG.debug("oddsRatio: " + ArrayUtils.toString(oddsRatio)); } } else { // these values are not present in the 2xN case estimate = Double.NaN; confidenceInterval = ArrayUtils.EMPTY_DOUBLE_ARRAY; oddsRatio = Double.NaN; } return new Result(pValue, confidenceInterval, estimate, oddsRatio, alternativeHypothesis); }
From source file:edu.ku.brc.specify.dbsupport.cleanuptools.GeoCleanupFuzzySearch.java
/** * @param name//from ww w . ja v a2s. c om * @return */ protected static String stripExtrasFromName(final String name) { String sName = name; for (int i = 0; i < replaceNames.length; i += 2) { sName = StringUtils.replace(sName.trim(), replaceNames[i], replaceNames[i + 1]); } for (String extraStr : removeStrs) { sName = StringUtils.remove(sName.trim(), extraStr); } for (String replStr : replaceStrs) { sName = StringUtils.replace(sName.trim(), replStr, " "); } sName = kSpecialCharsPattern.matcher(sName).replaceAll(" ").trim(); while (sName.contains(" ")) { sName = StringUtils.replace(sName.trim(), " ", " "); } return sName; }
From source file:com.doculibre.constellio.wicket.panels.results.DefaultSearchResultPanel.java
public DefaultSearchResultPanel(String id, SolrDocument doc, final SearchResultsDataProvider dataProvider) { super(id);/*from w w w. j a va 2s.com*/ RecordCollectionServices collectionServices = ConstellioSpringUtils.getRecordCollectionServices(); RecordServices recordServices = ConstellioSpringUtils.getRecordServices(); SearchInterfaceConfigServices searchInterfaceConfigServices = ConstellioSpringUtils .getSearchInterfaceConfigServices(); String collectionName = dataProvider.getSimpleSearch().getCollectionName(); RecordCollection collection = collectionServices.get(collectionName); Record record = recordServices.get(doc); if (record != null) { SearchInterfaceConfig searchInterfaceConfig = searchInterfaceConfigServices.get(); IndexField uniqueKeyField = collection.getUniqueKeyIndexField(); IndexField defaultSearchField = collection.getDefaultSearchIndexField(); IndexField urlField = collection.getUrlIndexField(); IndexField titleField = collection.getTitleIndexField(); if (urlField == null) { urlField = uniqueKeyField; } if (titleField == null) { titleField = urlField; } final String recordURL = record.getUrl(); final String displayURL; if (record.getDisplayUrl().startsWith("/get?file=")) { HttpServletRequest req = ((WebRequest) getRequest()).getHttpServletRequest(); displayURL = ContextUrlUtils.getContextUrl(req) + record.getDisplayUrl(); } else { displayURL = record.getDisplayUrl(); } String title = record.getDisplayTitle(); final String protocol = StringUtils.substringBefore(displayURL, ":"); boolean linkEnabled = isLinkEnabled(protocol); // rcupration des champs highlight partir de la cl unique // du document, dans le cas de Nutch c'est l'URL QueryResponse response = dataProvider.getQueryResponse(); Map<String, Map<String, List<String>>> highlighting = response.getHighlighting(); Map<String, List<String>> fieldsHighlighting = highlighting.get(recordURL); String titleHighlight = getTitleFromHighlight(titleField.getName(), fieldsHighlighting); if (titleHighlight != null) { title = titleHighlight; } String excerpt = null; String description = getDescription(record); String summary = getSummary(record); if (StringUtils.isNotBlank(description) && searchInterfaceConfig.isDescriptionAsExcerpt()) { excerpt = description; } else { excerpt = getExcerptFromHighlight(defaultSearchField.getName(), fieldsHighlighting); if (excerpt == null) { excerpt = description; } } toggleSummaryLink = new WebMarkupContainer("toggleSummaryLink"); add(toggleSummaryLink); toggleSummaryLink.setVisible(StringUtils.isNotBlank(summary)); toggleSummaryLink.add(new AttributeModifier("onclick", new LoadableDetachableModel() { @Override protected Object load() { return "toggleSearchResultSummary('" + summaryLabel.getMarkupId() + "')"; } })); summaryLabel = new Label("summary", summary); add(summaryLabel); summaryLabel.setOutputMarkupId(true); summaryLabel.setVisible(StringUtils.isNotBlank(summary)); ExternalLink titleLink; if (displayURL.startsWith("file://")) { HttpServletRequest req = ((WebRequest) getRequest()).getHttpServletRequest(); String newDisplayURL = ContextUrlUtils.getContextUrl(req) + "app/getSmbFile?" + SmbServletPage.RECORD_ID + "=" + record.getId() + "&" + SmbServletPage.COLLECTION + "=" + collectionName; titleLink = new ExternalLink("titleLink", newDisplayURL); } else { titleLink = new ExternalLink("titleLink", displayURL); } final RecordModel recordModel = new RecordModel(record); AttributeModifier computeClickAttributeModifier = new AttributeModifier("onmousedown", true, new LoadableDetachableModel() { @Override protected Object load() { Record record = recordModel.getObject(); SimpleSearch simpleSearch = dataProvider.getSimpleSearch(); WebRequest webRequest = (WebRequest) RequestCycle.get().getRequest(); HttpServletRequest httpRequest = webRequest.getHttpServletRequest(); return ComputeSearchResultClickServlet.getCallbackJavascript(httpRequest, simpleSearch, record); } }); titleLink.add(computeClickAttributeModifier); titleLink.setEnabled(linkEnabled); boolean resultsInNewWindow; PageParameters params = RequestCycle.get().getPageParameters(); if (params != null && params.getString(POPUP_LINK) != null) { resultsInNewWindow = params.getBoolean(POPUP_LINK); } else { resultsInNewWindow = searchInterfaceConfig.isResultsInNewWindow(); } titleLink.add(new SimpleAttributeModifier("target", resultsInNewWindow ? "_blank" : "_self")); // Add title title = StringUtils.remove(title, "\n"); title = StringUtils.remove(title, "\r"); if (StringUtils.isEmpty(title)) { title = StringUtils.defaultString(displayURL); title = StringUtils.substringAfterLast(title, "/"); title = StringUtils.substringBefore(title, "?"); try { title = URLDecoder.decode(title, "UTF-8"); } catch (UnsupportedEncodingException e) { // TODO Auto-generated catch block e.printStackTrace(); } if (title.length() > 120) { title = title.substring(0, 120) + " ..."; } } Label titleLabel = new Label("title", title); titleLink.add(titleLabel.setEscapeModelStrings(false)); add(titleLink); Label excerptLabel = new Label("excerpt", excerpt); add(excerptLabel.setEscapeModelStrings(false)); // add(new ExternalLink("url", url, // url).add(computeClickAttributeModifier).setEnabled(linkEnabled)); if (displayURL.startsWith("file://")) { // Creates a Windows path for file URLs String urlLabel = StringUtils.substringAfter(displayURL, "file:"); urlLabel = StringUtils.stripStart(urlLabel, "/"); urlLabel = "\\\\" + StringUtils.replace(urlLabel, "/", "\\"); try { urlLabel = URLDecoder.decode(urlLabel, "UTF-8"); } catch (UnsupportedEncodingException e) { // TODO Auto-generated catch block e.printStackTrace(); } add(new Label("url", urlLabel)); } else { add(new Label("url", displayURL)); } final ReloadableEntityModel<RecordCollection> collectionModel = new ReloadableEntityModel<RecordCollection>( collection); add(new ListView("searchResultFields", new LoadableDetachableModel() { @Override protected Object load() { RecordCollection collection = collectionModel.getObject(); return collection.getSearchResultFields(); } /** * Detaches from the current request. Implement this method with * custom behavior, such as setting the model object to null. */ protected void onDetach() { recordModel.detach(); collectionModel.detach(); } }) { @Override protected void populateItem(ListItem item) { SearchResultField searchResultField = (SearchResultField) item.getModelObject(); IndexFieldServices indexFieldServices = ConstellioSpringUtils.getIndexFieldServices(); Record record = recordModel.getObject(); IndexField indexField = searchResultField.getIndexField(); Locale locale = getLocale(); String indexFieldTitle = indexField.getTitle(locale); if (StringUtils.isBlank(indexFieldTitle)) { indexFieldTitle = indexField.getName(); } StringBuffer fieldValueSb = new StringBuffer(); List<Object> fieldValues = indexFieldServices.extractFieldValues(record, indexField); Map<String, String> defaultLabelledValues = indexFieldServices .getDefaultLabelledValues(indexField, locale); for (Object fieldValue : fieldValues) { if (fieldValueSb.length() > 0) { fieldValueSb.append("\n"); } String fieldValueLabel = indexField.getLabelledValue("" + fieldValue, locale); if (fieldValueLabel == null) { fieldValueLabel = defaultLabelledValues.get("" + fieldValue); } if (fieldValueLabel == null) { fieldValueLabel = "" + fieldValue; } fieldValueSb.append(fieldValueLabel); } item.add(new Label("indexField", indexFieldTitle)); item.add(new MultiLineLabel("indexFieldValue", fieldValueSb.toString())); item.setVisible(fieldValueSb.length() > 0); } @SuppressWarnings("unchecked") @Override public boolean isVisible() { boolean visible = super.isVisible(); if (visible) { List<SearchResultField> searchResultFields = (List<SearchResultField>) getModelObject(); visible = !searchResultFields.isEmpty(); } return visible; } }); // md5 ConstellioSession session = ConstellioSession.get(); ConstellioUser user = session.getUser(); // TODO Provide access to unauthenticated users ? String md5 = ""; if (user != null) { IntelliGIDServiceInfo intelligidServiceInfo = ConstellioSpringUtils.getIntelliGIDServiceInfo(); if (intelligidServiceInfo != null) { Collection<Object> md5Coll = doc.getFieldValues(IndexField.MD5); if (md5Coll != null) { for (Object md5Obj : md5Coll) { try { String md5Str = new String(Hex.encodeHex(Base64.decodeBase64(md5Obj.toString()))); InputStream is = HttpClientHelper .get(intelligidServiceInfo.getIntelligidUrl() + "/connector/checksum", "md5=" + URLEncoder.encode(md5Str, "ISO-8859-1"), "username=" + URLEncoder.encode(user.getUsername(), "ISO-8859-1"), "password=" + URLEncoder.encode(Base64.encodeBase64String( ConstellioSession.get().getPassword().getBytes())), "ISO-8859-1"); try { Document xmlDocument = new SAXReader().read(is); Element root = xmlDocument.getRootElement(); for (Iterator<Element> it = root.elementIterator("fichier"); it.hasNext();) { Element fichier = it.next(); String url = fichier.attributeValue("url"); md5 += "<a href=\"" + url + "\">" + url + "</a> "; } } finally { IOUtils.closeQuietly(is); } } catch (Exception e) { e.printStackTrace(); } } } } } Label md5Label = new Label("md5", md5) { public boolean isVisible() { boolean visible = super.isVisible(); if (visible) { visible = StringUtils.isNotBlank(this.getModelObjectAsString()); } return visible; } }; md5Label.setEscapeModelStrings(false); add(md5Label); add(new ElevatePanel("elevatePanel", record, dataProvider.getSimpleSearch())); } else { setVisible(false); } }
From source file:hydrograph.ui.expression.editor.jar.util.BuildExpressionEditorDataSturcture.java
private void loadClassesFromSettingsFolder() { Properties properties = new Properties(); IFolder folder = getCurrentProject().getFolder(PathConstant.PROJECT_RESOURCES_FOLDER); IFile file = folder.getFile(PathConstant.EXPRESSION_EDITOR_EXTERNAL_JARS_PROPERTIES_FILES); try {/*from w ww . j ava2s. com*/ LOGGER.debug("Loading property file"); if (file.getLocation().toFile().exists()) { FileInputStream inStream = new FileInputStream(file.getLocation().toString()); properties.load(inStream); for (Object key : properties.keySet()) { String packageName = StringUtils.remove((String) key, Constants.DOT + Constants.ASTERISK); if (StringUtils.isNotBlank(properties.getProperty((String) key)) && StringUtils.isNotBlank(packageName)) { loadUserDefinedClassesInClassRepo(properties.getProperty((String) key), packageName); } } } } catch (IOException | RuntimeException exception) { LOGGER.error("Exception occurred while loading jar files from projects setting folder", exception); } }
From source file:io.ecarf.core.utils.LogParser.java
private double extractAndGetTimer(String line, String after, boolean ignoreMillis) { String timer = StringUtils.substringAfter(line, after); timer = StringUtils.remove(timer, ':'); timer = StringUtils.trim(timer);// ww w.j a va 2 s . co m return this.parseStopwatchTime(timer, ignoreMillis); }
From source file:edu.ku.brc.specify.plugins.HostTaxonPlugin.java
/** * @return/*from w ww. ja va2 s .c o m*/ */ protected ViewBasedSearchQueryBuilderIFace createSearchQueryBuilder() { return new ViewBasedSearchQueryBuilderIFace() { /* (non-Javadoc) * @see edu.ku.brc.af.ui.db.ViewBasedSearchQueryBuilderIFace#buildSQL(java.lang.String, boolean) */ @Override public String buildSQL(String searchText, boolean isForCount) { String cols = isForCount ? "COUNT(*)" : "tx.fullName, tx.id"; String sql = String.format( "SELECT %s FROM Taxon tx INNER JOIN tx.definition ttd WHERE ttd.id = %d AND LOWER(tx.fullName) LIKE '%c%s%c' ORDER BY tx.fullName", cols, taxonTreeDef.getId(), '%', searchText, '%'); //System.out.println("adjustSQLTemplate: "+sql.toString()); return sql; } /* (non-Javadoc) * @see edu.ku.brc.af.ui.db.ViewBasedSearchQueryBuilderIFace#buildSQL(java.util.Map, java.util.List) */ @Override public String buildSQL(Map<String, Object> dataMap, List<String> fieldNames) { String orderBy = ""; String fullName = (String) dataMap.get("taxon.FullName"); if (StringUtils.isNotEmpty(fullName)) { fullName = StringUtils.remove(fullName, '#'); fullName = StringUtils.remove(fullName, '*'); if (StringUtils.isNotEmpty(fullName)) { orderBy = "FullName"; fullName = String.format("LOWER(FullName) LIKE '%c%s%c'", '%', fullName.toLowerCase(), '%'); } } String common = (String) dataMap.get("taxon.CommonName"); if (StringUtils.isNotEmpty(common)) { common = StringUtils.remove(common, '#'); common = StringUtils.remove(common, '*'); if (StringUtils.isNotEmpty(common)) { common = (StringUtils.isNotEmpty(fullName) ? " OR " : "") + String.format("LOWER(CommonName) LIKE '%c%s%c'", '%', common.toLowerCase(), '%'); if (StringUtils.isEmpty(orderBy)) { orderBy = "CommonName"; } } } if ("".equals(orderBy)) { orderBy = "FullName"; } String where = (fullName == null ? "" : fullName) + " " + (common == null ? "" : common); if (!"".equals(where.trim())) { where = " AND (" + where + ")"; } else { where = ""; } String sql = String.format( "SELECT TaxonID, FullName, CommonName FROM taxon tx INNER JOIN taxontreedef ttd ON tx.TaxonTreeDefID = ttd.TaxonTreeDefID WHERE ttd.TaxonTreeDefID = %d %s ORDER BY %s", taxonTreeDef.getId(), where, orderBy); //System.out.println(sql); return sql; } /* (non-Javadoc) * @see edu.ku.brc.af.ui.db.ViewBasedSearchQueryBuilderIFace#createQueryForIdResults() */ @Override public QueryForIdResultsIFace createQueryForIdResults() { ExpressResultsTableInfo esTblInfo = ExpressSearchConfigCache.getTableInfoByName("TaxonSearch"); return new TableSearchResults( DBTableIdMgr.getInstance().getInfoById(CollectionObject.getClassTableId()), esTblInfo.getCaptionInfo()); //true => is HQL } }; }
From source file:com.linkedin.pinot.index.writer.FixedByteWidthRowColDataFileWriterTest.java
@Test public void testSpecialPaddingCharsForStringReaderWriter() throws Exception { for (int iter = 0; iter < 2; iter++) { char paddingChar = (iter == 0) ? '%' : '\0'; final byte[] bytes1 = new byte[] { -17, -65, -67, -17, -65, -67, 32, 69, 120, 101, 99, 117, 116, 105, 118, 101 };//from w ww . ja v a2 s. c o m final byte[] bytes2 = new byte[] { -17, -65, -68, 32, 99, 97, 108, 103, 97, 114, 121, 32, 106, 117, 110, 107, 32, 114, 101, 109, 111, 118, 97, 108 }; File file = new File("test_single_col_writer.dat"); file.delete(); int rows = 100; int cols = 1; String testString1 = new String(bytes1); String testString2 = new String(bytes2); System.out.println(Arrays.toString(bytes2)); int stringColumnMaxLength = Math.max(testString1.getBytes().length, testString2.getBytes().length); int[] columnSizes = new int[] { stringColumnMaxLength }; FixedByteSingleValueMultiColWriter writer = new FixedByteSingleValueMultiColWriter(file, rows, cols, columnSizes); String[] data = new String[rows]; for (int i = 0; i < rows; i++) { String toPut = (i % 2 == 0) ? testString1 : testString2; final int padding = stringColumnMaxLength - toPut.getBytes().length; final StringBuilder bld = new StringBuilder(); bld.append(toPut); for (int j = 0; j < padding; j++) { bld.append(paddingChar); } data[i] = bld.toString(); writer.setString(i, 0, data[i]); } writer.close(); PinotDataBuffer mmapBuffer = PinotDataBuffer.fromFile(file, ReadMode.mmap, FileChannel.MapMode.READ_ONLY, "testing"); FixedByteSingleValueMultiColReader dataFileReader = new FixedByteSingleValueMultiColReader(mmapBuffer, rows, 1, new int[] { stringColumnMaxLength }); for (int i = 0; i < rows; i++) { String stringInFile = dataFileReader.getString(i, 0); Assert.assertEquals(stringInFile, data[i]); Assert.assertEquals(StringUtils.remove(stringInFile, String.valueOf(paddingChar)), StringUtils.remove(data[i], String.valueOf(paddingChar))); } file.delete(); } }
From source file:com.hangum.tadpole.rdb.core.dialog.dbconnect.composite.AbstractLoginComposite.java
/** * db ?? ? ./*from w w w. ja va 2 s .c om*/ * * @param userDB * @param isTest * @return */ private boolean checkDatabase(final UserDBDAO userDB, boolean isTest) { try { if (userDB.getDBDefine() == DBDefine.MONGODB_DEFAULT) { MongoConnectionManager.getInstance(userDB); } else if (userDB.getDBDefine() == DBDefine.TAJO_DEFAULT) { new TajoConnectionManager().connectionCheck(userDB); } else if (userDB.getDBDefine() == DBDefine.SQLite_DEFAULT) { String strFileLoc = StringUtils.difference( StringUtils.remove(userDB.getDBDefine().getDB_URL_INFO(), "%s"), userDB.getUrl()); File fileDB = new File(strFileLoc); if (fileDB.exists()) { List<String> strArr = FileUtils.readLines(fileDB); if (!StringUtils.contains(strArr.get(0), "SQLite format")) { throw new SQLException("Doesn't SQLite files."); } } } else { SqlMapClient sqlClient = TadpoleSQLManager.getInstance(userDB); sqlClient.queryForList("connectionCheck", userDB.getDb()); //$NON-NLS-1$ } return true; } catch (Exception e) { String errMsg = e.getMessage(); // driver ? . try { Throwable cause = e.getCause().getCause(); if (cause instanceof ClassNotFoundException) { errMsg = String.format(Messages.get().TadpoleTableComposite_driverMsg, userDB.getDbms_type(), e.getMessage()); } } catch (Exception ee) { // igonre exception } logger.error("DB Connecting... [url]" + userDB.getUrl(), e); //$NON-NLS-1$ // If UserDBDao is not invalid, remove UserDBDao at internal cache TadpoleSQLManager.removeInstance(userDB); // mssql ??? ? ?? ?. . // https://github.com/hangum/TadpoleForDBTools/issues/512 if (!isTest) {// && loginInfo.getDBDefine() != DBDefine.MSSQL_DEFAULT) { TDBYesNoErroDialog dialog = new TDBYesNoErroDialog(getShell(), userDB.getDb() + " Test", String.format(Messages.get().AbstractLoginComposite_3, errMsg)); if (dialog.open() == IDialogConstants.OK_ID) return true; } else { TDBInfoDialog dialog = new TDBInfoDialog(getShell(), userDB.getDb() + " Test", errMsg); dialog.open(); } return false; } }
From source file:edu.scripps.fl.pubchem.promiscuity.PCPromiscuityOutput.java
public void compoundPromiscuityToXML(Map<Long, CompoundPromiscuityInfo> map, PCPromiscuityParameters params, File file) throws Exception { jsp = new JSProcessor(); jsp.init();/*from w w w . j a va2 s . c om*/ try { InputStream is = getClass().getResourceAsStream("/compress.txt"); jsp.setCodeSource(new InputStreamReader(is)); String[] descriptorColumns = descriptorNames; List<Long> ids = params.getIds(); URL url = getClass().getClassLoader().getResource("Result.xml"); Document doc = new XMLDocument().readDocFromURL(url); Element root = doc.getRootElement(); String db = params.getDatabase(); String idString = "SID"; if (db.equalsIgnoreCase("pccompound")) idString = "CID"; for (Long id : ids) { Element result = root.addElement("Result"); result.addElement(idString).addText(id.toString()); CompoundPromiscuityInfo cpInfo = map.get(id); if (cpInfo == null) result.addElement("NoResults").addText("Error Processing this compound."); else { if (cpInfo.getOnHold()) result.addElement("OnHold").addText("True"); else { if (db.equalsIgnoreCase("pcsubstance")) { Element CIDe = result.addElement("CID"); if (cpInfo.getCID() != null) CIDe.addText(cpInfo.getCID().toString()); } Map<String, Object> descriptors = cpInfo.getDescriptors(); Map<String, CategorizedFunctionalGroups> categorizedFGMap = cpInfo .getCategorizedFunctionalGroupsMap(); Element descriptorsE = result.addElement("Descriptors"); for (String category : functionalGroupCategories) { Element fgCategoryE = descriptorsE.addElement(category); CategorizedFunctionalGroups cFGs = categorizedFGMap.get(category); if (cFGs != null) { List<FunctionalGroup> fgs = cFGs.getFunctionalGroups(); List<String> groups = new ArrayList<String>(); for (FunctionalGroup group : fgs) { groups.add(group.getName()); } fgCategoryE.addText(StringUtils.join(groups, ", ")); } } Element possibleFalse = descriptorsE.addElement("PossibleFalseAromaticityDetection"); if (cpInfo.isPossibleFalseAromaticityDetection()) possibleFalse.addText("true"); for (String cc : descriptorColumns) { Element descriptorCC = descriptorsE.addElement(StringUtils.remove(cc, " ")); if (descriptors.get(cc) != null) descriptorCC.addText(descriptors.get(cc).toString()); } Element proteinsE = result.addElement("Proteins"); if (params.getPerProteinMode()) { Map<Protein, Map<String, PromiscuityCount<?>>> proteinCounts = cpInfo .getPerProteinCounts(); Set<Protein> proteins = proteinCounts.keySet(); for (Protein protein : proteins) { Element proteinE = proteinsE.addElement("Protein"); proteinE.addElement("Name").addText(protein.getName()); Element promiscuityCountsE = proteinE.addElement("PromiscuityCounts"); addCounts(promiscuityCountsE, proteinCounts.get(protein), id, db); } Map<String, PromiscuityCount<?>> noProteinCounts = cpInfo.getNoProteinCounts(); Element noProtein = proteinsE.addElement("Protein"); noProtein.addElement("Name").addText(""); Element noProteinCountsE = noProtein.addElement("PromiscuityCounts"); addCounts(noProteinCountsE, noProteinCounts, id, db); root.addAttribute("format", "protein"); } else { Map<String, PromiscuityCount<?>> counts = cpInfo.getCounts(); Element allProteins = proteinsE.addElement("Protein"); allProteins.addElement("Name").addText("All Proteins"); Element allProteinCountsE = allProteins.addElement("PromiscuityCounts"); addCounts(allProteinCountsE, counts, id, db); root.addAttribute("format", "compound"); } } } } new XMLDocument().write(doc, file); log.info("Finished writing xml to: " + file.getAbsolutePath()); } finally { jsp.exit(); } }
From source file:io.ecarf.core.utils.LogParser.java
/** * - Processing file: /tmp/wordnet_links.nt.gz.kryo.gz, dictionary items: 49382611, memory usage: 14.336268931627274GB, timer: 290.0 ms * /tmp/wikipedia_links_en.nt.gz.kryo.gz, dictionary items: 44, memory usage: 0.013648882508277893GB, timer: 2.636 s * START: Downloading file: interlanguage_links_chapters_en.nt.gz.kryo.gz, memory usage: 0.0GB * @param line/* w ww .ja v a2 s. com*/ * @param after * @return */ private double[] extractAndGetMemoryDictionaryItems(String line) { double memory = 0; double items = 0; String memoryStr = null; if (line.contains(TIMER_PREFIX)) { memoryStr = StringUtils.substringBetween(line, MEM_USE, TIMER_PREFIX); if (line.contains(DIC_ITEMS)) { String itemsStr = StringUtils.trim(StringUtils.substringBetween(line, DIC_ITEMS, MEM_USE)); items = Double.parseDouble(itemsStr); } } else { memoryStr = StringUtils.substringAfter(line, MEM_USE); } if (memoryStr != null) { memoryStr = StringUtils.remove(memoryStr, "GB"); memoryStr = StringUtils.strip(memoryStr); } memory = Double.parseDouble(memoryStr); double[] values = new double[] { memory, items }; return values; }