PEAK LIST file\\n\\t\\t\\t\\t\\t\\t\\t\\tprideXMLFileMapping.addRelationship(peakListFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t// RAW file -> PEAK LIST file\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping rawFileMapping : rawFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\trawFileMapping.addRelationship(peakListFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\n\\t\\t\\t\\t\\t\\t\\t\\t// prideXMLFileMapping\\n\\t\\t\\t\\t\\t\\t\\t\\t// .addRelationship(peakListFileMapping\\n\\t\\t\\t\\t\\t\\t\\t\\t// .getId());\\n\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t}\\n\\n\\t\\t\\t\\t\\t// MIAPE MS REPORTS\\n\\t\\t\\t\\t\\tfinal List miapeMSReportFiles = getMiapeMSReportFiles(replicate);\\n\\t\\t\\t\\t\\tif (miapeMSReportFiles != null)\\n\\t\\t\\t\\t\\t\\tfor (final PexFile miapeMSReportFile : miapeMSReportFiles) {\\n\\t\\t\\t\\t\\t\\t\\tif (!fileLocationsMapping.containsKey(miapeMSReportFile.getFileLocation())) {\\n\\t\\t\\t\\t\\t\\t\\t\\tfinal PexFileMapping miapeReportFileMapping = new PexFileMapping(\\\"other\\\", fileCounter++,\\n\\t\\t\\t\\t\\t\\t\\t\\t\\t\\tmiapeMSReportFile.getFileLocation(), null);\\n\\t\\t\\t\\t\\t\\t\\t\\tmiapeReportFileMappings.add(miapeReportFileMapping);\\n\\t\\t\\t\\t\\t\\t\\t\\tfileLocationsMapping.put(miapeMSReportFile.getFileLocation(), miapeReportFileMapping);\\n\\n\\t\\t\\t\\t\\t\\t\\t\\t// PRIDE XML -> MIAPE MS report\\n\\t\\t\\t\\t\\t\\t\\t\\tprideXMLFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t// RAW file -> MIAPE MS report\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping rawFileMapping : rawFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\trawFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t\\t// PEAK LIST file -> MIAPE MS report\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping peakListFileMapping : replicatePeakListFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\tpeakListFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t}\\n\\n\\t\\t\\t\\t\\t// SEARCH ENGINE OUTPUT FILES\\n\\t\\t\\t\\t\\tfinal List searchEngineOutputFiles = getSearchEngineOutputFiles(replicate);\\n\\t\\t\\t\\t\\tfinal List replicatesearchEngineOutputFilesMappings = new ArrayList();\\n\\t\\t\\t\\t\\tif (searchEngineOutputFiles != null) {\\n\\t\\t\\t\\t\\t\\tfor (final PexFile peakList : searchEngineOutputFiles) {\\n\\t\\t\\t\\t\\t\\t\\tif (!fileLocationsMapping.containsKey(peakList.getFileLocation())) {\\n\\t\\t\\t\\t\\t\\t\\t\\tfinal PexFileMapping searchEngineOutputFileMapping = new PexFileMapping(\\\"search\\\",\\n\\t\\t\\t\\t\\t\\t\\t\\t\\t\\tfileCounter++, peakList.getFileLocation(), null);\\n\\t\\t\\t\\t\\t\\t\\t\\toutputSearchEngineFileMappings.add(searchEngineOutputFileMapping);\\n\\t\\t\\t\\t\\t\\t\\t\\treplicatesearchEngineOutputFilesMappings.add(searchEngineOutputFileMapping);\\n\\t\\t\\t\\t\\t\\t\\t\\tfileLocationsMapping.put(peakList.getFileLocation(), searchEngineOutputFileMapping);\\n\\t\\t\\t\\t\\t\\t\\t\\t// PRIDE XML -> SEARCH ENGINE OUTPUT file\\n\\t\\t\\t\\t\\t\\t\\t\\tprideXMLFileMapping.addRelationship(searchEngineOutputFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t// RAW file -> SEARCH ENGINE OUTPUT file\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping rawFileMapping : rawFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\trawFileMapping.addRelationship(searchEngineOutputFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t\\t// PEAK LIST FILE -> SEARCH ENGINE OUTPUT file\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping peakListFileMapping : replicatePeakListFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\tpeakListFileMapping.addRelationship(searchEngineOutputFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t}\\n\\n\\t\\t\\t\\t\\t// MIAPE MSI REPORTS\\n\\t\\t\\t\\t\\tfinal List miapeMSIReportFiles = getMiapeMSIReportFiles(replicate);\\n\\t\\t\\t\\t\\tif (miapeMSIReportFiles != null)\\n\\t\\t\\t\\t\\t\\tfor (final PexFile miapeMSIReportFile : miapeMSIReportFiles) {\\n\\t\\t\\t\\t\\t\\t\\tif (!fileLocationsMapping.containsKey(miapeMSIReportFile.getFileLocation())) {\\n\\t\\t\\t\\t\\t\\t\\t\\tfinal PexFileMapping miapeReportFileMapping = new PexFileMapping(\\\"other\\\", fileCounter++,\\n\\t\\t\\t\\t\\t\\t\\t\\t\\t\\tmiapeMSIReportFile.getFileLocation(), null);\\n\\t\\t\\t\\t\\t\\t\\t\\tmiapeReportFileMappings.add(miapeReportFileMapping);\\n\\t\\t\\t\\t\\t\\t\\t\\tfileLocationsMapping.put(miapeMSIReportFile.getFileLocation(), miapeReportFileMapping);\\n\\n\\t\\t\\t\\t\\t\\t\\t\\t// PRIDE XML -> MIAPE MSI report\\n\\t\\t\\t\\t\\t\\t\\t\\tprideXMLFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t// RAW file -> MIAPE MSI report\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping rawFileMapping : rawFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\trawFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t\\t// PEAK LIST FILE -> MIAPE MSI report\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping peakListFileMapping : replicatePeakListFileMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\tpeakListFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t\\t\\t// SEARCH ENGINE OUTPUT file -> MIAPE MSI report\\n\\t\\t\\t\\t\\t\\t\\t\\tfor (final PexFileMapping searchEngineOutputFileMapping : replicatesearchEngineOutputFilesMappings) {\\n\\t\\t\\t\\t\\t\\t\\t\\t\\tsearchEngineOutputFileMapping.addRelationship(miapeReportFileMapping.getId());\\n\\t\\t\\t\\t\\t\\t\\t\\t}\\n\\n\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t// Add all to the same list and then sort by id\\n\\t\\t\\t\\t\\ttotalFileList.addAll(outputSearchEngineFileMappings);\\n\\t\\t\\t\\t\\ttotalFileList.addAll(miapeReportFileMappings);\\n\\t\\t\\t\\t\\ttotalFileList.addAll(peakListFileMappings);\\n\\t\\t\\t\\t\\ttotalFileList.addAll(rawFileMappings);\\n\\t\\t\\t\\t}\\n\\t\\t\\t}\\n\\t\\t}\\n\\n\\t\\t// Sort the list of files\\n\\t\\tCollections.sort(totalFileList, new Comparator() {\\n\\n\\t\\t\\t@Override\\n\\t\\t\\tpublic int compare(PexFileMapping o1, PexFileMapping o2) {\\n\\n\\t\\t\\t\\treturn Integer.valueOf(o1.getId()).compareTo(Integer.valueOf(o2.getId()));\\n\\n\\t\\t\\t}\\n\\n\\t\\t});\\n\\t\\tfor (final PexFileMapping pexFileMapping : totalFileList) {\\n\\t\\t\\tret.add(pexFileMapping.toString());\\n\\t\\t}\\n\\t\\treturn ret;\\n\\t}\",\n \"public void readDocument() throws FileNotFoundException{\\r\\n\\t\\t// Initialize 2 empty read document collections, one without duplicate words.\\r\\n\\t\\treadDocument = new LinkedBag();\\r\\n\\t\\treadDocumentNoDuplicates = new LinkedSet();\\r\\n\\t\\t\\r\\n\\t\\t// Prompt user for name of read document file.\\r\\n\\t\\tScanner input = new Scanner(System.in);\\r\\n\\t\\tSystem.out.print(\\\"Enter the file you would like checked with extension: \\\");\\r\\n\\t\\tString readDocFileName = input.nextLine();\\r\\n\\t\\t\\r\\n\\t\\t// If exists, open file specified by user. Then add words to both collections.\\r\\n\\t\\ttry {\\r\\n\\t\\t\\tFile file = new File(readDocFileName);\\r\\n\\t\\t\\tScanner scanner = new Scanner(file);\\r\\n\\t\\t\\twhile (scanner.hasNextLine()) {\\r\\n\\t\\t\\t\\tString word = scanner.next();\\r\\n\\t\\t\\t\\treadDocument.add(word.replaceFirst(\\\"^[^a-zA-Z]+\\\",\\\"\\\").replaceAll(\\\"[^a-zA-Z]+$\\\", \\\"\\\"));\\r\\n\\t\\t\\t\\treadDocumentNoDuplicates.add(word.replaceFirst(\\\"^[^a-zA-Z]+\\\",\\\"\\\").replaceAll(\\\"[^a-zA-Z]+$\\\", \\\"\\\"));\\r\\n\\t\\t\\t}\\r\\n\\t\\t\\tscanner.close();\\r\\n\\t\\t\\tSystem.out.println(\\\"Document read\\\");\\r\\n\\r\\n\\t\\t\\t// Get initial list of incorrect words.\\r\\n\\t\\t\\tincorrectWords = readDocumentNoDuplicates.difference(dictionary);\\r\\n\\t\\t\\t\\r\\n\\t\\t\\t// Display message showing how many words were in the read document.\\r\\n\\t\\t\\tSystem.out.println(\\\"This document contains \\\" + readDocument.size() + \\\" words.\\\");\\r\\n\\t\\t}\\r\\n\\t\\tcatch (FileNotFoundException e) {\\r\\n\\t\\t\\treadDocument = null;\\r\\n\\t\\t\\treadDocumentNoDuplicates = null;\\r\\n\\t\\t\\tSystem.out.println(\\\"Error: File '\\\" + readDocFileName + \\\"' not found. Please try again.\\\");\\r\\n\\t\\t}\\r\\n\\t}\",\n \"private static void loadFiles(String[] files) throws IOException {\\n\\t\\tfor(String file : files){\\n\\n\\t\\t\\t//Create reader for the file\\n\\t\\t\\tBufferedReader fileReader = new BufferedReader(new FileReader(file));\\n\\n\\t\\t\\t//Create HashMap to store words and counts\\n\\t\\t\\tHashMap fileWordCounts = new HashMap();\\n\\t\\t\\tArrayList sentences = new ArrayList();\\n\\n\\t\\t\\t//While the file still has more lines to be read from\\n\\t\\t\\twhile(fileReader.ready()){\\n\\n\\t\\t\\t\\t//Read a line from the file\\n\\t\\t\\t\\tString fileLine = fileReader.readLine();\\n\\t\\t\\t\\t//Add the line to file sentences\\n\\t\\t\\t\\tsentences.add(fileLine);\\n\\t\\t\\t\\t//Split the file and remove punctuation from words\\n\\t\\t\\t\\tString[] fileWords = fileLine.replaceAll(\\\"[^a-zA-Z ]\\\", \\\"\\\").toLowerCase().split(\\\"\\\\\\\\s+\\\");\\n\\n\\t\\t\\t\\t//iterate through all words in each line\\n\\t\\t\\t\\tfor (String word : fileWords)\\n\\t\\t\\t\\t{\\n\\t\\t\\t\\t\\tWordCount count = fileWordCounts.get(word);\\n\\t\\t\\t\\t\\t//If word is not in file, add it \\n\\t\\t\\t\\t\\tif (count == null) {\\n\\t\\t\\t\\t\\t\\tfileWordCounts.put(word,new WordCount(word));\\n\\t\\t\\t\\t\\t} else {\\n\\t\\t\\t\\t\\t\\tcount.inc(); //If not, increment it\\n\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t} \\n\\t\\t\\t}\\n\\n\\t\\t\\t//Add file to fileDatabase \\n\\t\\t\\tfileDatabase.map.put(file, new FileObject(file, fileWordCounts, sentences));\\n\\n\\t\\t\\tfileReader.close(); // Close File\\n\\n\\t\\t}//End of For Loop reading from all files\\n\\t}\",\n \"public Map NextDocument() throws IOException {\\n\\t\\tMap map = new HashMap<>();\\n\\t\\tStringBuffer content = new StringBuffer();\\n\\t\\tString line = inputStream.readLine();\\n\\t\\tif(line==null) {\\n\\t\\t\\tinputStream.close();\\n\\t\\t\\treturn null;\\n\\t\\t} else {\\n\\t\\t\\tmap.put(\\\"DOCNO\\\", line);\\n\\t\\t\\tmap.put(\\\"CONTENT\\\", inputStream.readLine());\\n\\t\\t\\treturn map;\\n\\t\\t}\\n\\t}\",\n \"private void processMetadataFromLoader() {\\n\\n int recordCount = mdi.readInt();\\n\\n long currentTime = System.currentTimeMillis();\\n synchronized (entities) {\\n clearOldTempIndexes(currentTime);\\n\\n for (int i = 0; i < recordCount; i++) {\\n int tempIndex = mdi.readInt();\\n assert DirectProtocol.isValidTempIndex(tempIndex);\\n String symbol = mdi.readCharSequence().toString().intern();\\n\\n ConstantIdentityKey key;\\n int entityIndex = entities.get(symbol, NOT_FOUND_VALUE);\\n if (entityIndex == NOT_FOUND_VALUE) {\\n entityIndex = entities.size();\\n key = new ConstantIdentityKey(symbol);\\n entities.put(key, entityIndex);\\n } else {\\n key = entities.getKeyObject(symbol);\\n }\\n\\n // Note: key is guarantied to be same object as in \\\"entities\\\" field\\n tempIndexes.put(tempIndex, key);\\n\\n sendMetadata(symbol, entityIndex);\\n }\\n if (recordCount > 0) {\\n lastTempIndexAdded = currentTime;\\n }\\n }\\n }\",\n \"@android.annotation.SuppressLint({\\\"NewApi\\\"})\\n private void listRoots() {\\n /*\\n r23 = this;\\n r21 = 0;\\n r0 = r21;\\n r1 = r23;\\n r1.currentDir = r0;\\n r0 = r23;\\n r0 = r0.items;\\n r21 = r0;\\n r21.clear();\\n r17 = new java.util.HashSet;\\n r17.();\\n r21 = android.os.Environment.getExternalStorageDirectory();\\n r5 = r21.getPath();\\n r12 = android.os.Environment.isExternalStorageRemovable();\\n r6 = android.os.Environment.getExternalStorageState();\\n r21 = \\\"mounted\\\";\\n r0 = r21;\\n r21 = r6.equals(r0);\\n if (r21 != 0) goto L_0x003c;\\n L_0x0031:\\n r21 = \\\"mounted_ro\\\";\\n r0 = r21;\\n r21 = r6.equals(r0);\\n if (r21 == 0) goto L_0x0084;\\n L_0x003c:\\n r8 = new org.telegram.ui.DocumentSelectActivity$ListItem;\\n r21 = 0;\\n r0 = r23;\\n r1 = r21;\\n r8.();\\n r21 = android.os.Environment.isExternalStorageRemovable();\\n if (r21 == 0) goto L_0x02ae;\\n L_0x004d:\\n r21 = \\\"SdCard\\\";\\n r22 = 2131494825; // 0x7f0c07a9 float:1.861317E38 double:1.0530983673E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\n r0 = r21;\\n r8.title = r0;\\n r21 = 2131165433; // 0x7f0700f9 float:1.7945083E38 double:1.052935626E-314;\\n r0 = r21;\\n r8.icon = r0;\\n L_0x0062:\\n r0 = r23;\\n r21 = r0.getRootSubtitle(r5);\\n r0 = r21;\\n r8.subtitle = r0;\\n r21 = android.os.Environment.getExternalStorageDirectory();\\n r0 = r21;\\n r8.file = r0;\\n r0 = r23;\\n r0 = r0.items;\\n r21 = r0;\\n r0 = r21;\\n r0.add(r8);\\n r0 = r17;\\n r0.add(r5);\\n L_0x0084:\\n r3 = 0;\\n r4 = new java.io.BufferedReader;\\t Catch:{ Exception -> 0x0302 }\\n r21 = new java.io.FileReader;\\t Catch:{ Exception -> 0x0302 }\\n r22 = \\\"/proc/mounts\\\";\\n r21.(r22);\\t Catch:{ Exception -> 0x0302 }\\n r0 = r21;\\n r4.(r0);\\t Catch:{ Exception -> 0x0302 }\\n L_0x0094:\\n r14 = r4.readLine();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r14 == 0) goto L_0x02dd;\\n L_0x009a:\\n r21 = \\\"vfat\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x00b0;\\n L_0x00a5:\\n r21 = \\\"/mnt\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 == 0) goto L_0x0094;\\n L_0x00b0:\\n r21 = org.telegram.messenger.BuildVars.LOGS_ENABLED;\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 == 0) goto L_0x00b7;\\n L_0x00b4:\\n org.telegram.messenger.FileLog.d(r14);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n L_0x00b7:\\n r19 = new java.util.StringTokenizer;\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = \\\" \\\";\\n r0 = r19;\\n r1 = r21;\\n r0.(r14, r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r20 = r19.nextToken();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r16 = r19.nextToken();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r0 = r17;\\n r1 = r16;\\n r21 = r0.contains(r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x00d5:\\n r21 = \\\"/dev/block/vold\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 == 0) goto L_0x0094;\\n L_0x00e0:\\n r21 = \\\"/mnt/secure\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x00eb:\\n r21 = \\\"/mnt/asec\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x00f6:\\n r21 = \\\"/mnt/obb\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x0101:\\n r21 = \\\"/dev/mapper\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x010c:\\n r21 = \\\"tmpfs\\\";\\n r0 = r21;\\n r21 = r14.contains(r0);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0094;\\n L_0x0117:\\n r21 = new java.io.File;\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r0 = r21;\\n r1 = r16;\\n r0.(r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = r21.isDirectory();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 != 0) goto L_0x0163;\\n L_0x0126:\\n r21 = 47;\\n r0 = r16;\\n r1 = r21;\\n r11 = r0.lastIndexOf(r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = -1;\\n r0 = r21;\\n if (r11 == r0) goto L_0x0163;\\n L_0x0136:\\n r21 = new java.lang.StringBuilder;\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21.();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r22 = \\\"/storage/\\\";\\n r21 = r21.append(r22);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r22 = r11 + 1;\\n r0 = r16;\\n r1 = r22;\\n r22 = r0.substring(r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = r21.append(r22);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r15 = r21.toString();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = new java.io.File;\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r0 = r21;\\n r0.(r15);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r21 = r21.isDirectory();\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n if (r21 == 0) goto L_0x0163;\\n L_0x0161:\\n r16 = r15;\\n L_0x0163:\\n r0 = r17;\\n r1 = r16;\\n r0.add(r1);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n r13 = new org.telegram.ui.DocumentSelectActivity$ListItem;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r21 = 0;\\n r0 = r23;\\n r1 = r21;\\n r13.();\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r21 = r16.toLowerCase();\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r22 = \\\"sd\\\";\\n r21 = r21.contains(r22);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n if (r21 == 0) goto L_0x02c5;\\n L_0x0182:\\n r21 = \\\"SdCard\\\";\\n r22 = 2131494825; // 0x7f0c07a9 float:1.861317E38 double:1.0530983673E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r21;\\n r13.title = r0;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n L_0x0190:\\n r21 = 2131165433; // 0x7f0700f9 float:1.7945083E38 double:1.052935626E-314;\\n r0 = r21;\\n r13.icon = r0;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r23;\\n r1 = r16;\\n r21 = r0.getRootSubtitle(r1);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r21;\\n r13.subtitle = r0;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r21 = new java.io.File;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r21;\\n r1 = r16;\\n r0.(r1);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r21;\\n r13.file = r0;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r23;\\n r0 = r0.items;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r21 = r0;\\n r0 = r21;\\n r0.add(r13);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n goto L_0x0094;\\n L_0x01bd:\\n r7 = move-exception;\\n org.telegram.messenger.FileLog.e(r7);\\t Catch:{ Exception -> 0x01c3, all -> 0x02d5 }\\n goto L_0x0094;\\n L_0x01c3:\\n r7 = move-exception;\\n r3 = r4;\\n L_0x01c5:\\n org.telegram.messenger.FileLog.e(r7);\\t Catch:{ all -> 0x0300 }\\n if (r3 == 0) goto L_0x01cd;\\n L_0x01ca:\\n r3.close();\\t Catch:{ Exception -> 0x02ec }\\n L_0x01cd:\\n r9 = new org.telegram.ui.DocumentSelectActivity$ListItem;\\n r21 = 0;\\n r0 = r23;\\n r1 = r21;\\n r9.();\\n r21 = \\\"/\\\";\\n r0 = r21;\\n r9.title = r0;\\n r21 = \\\"SystemRoot\\\";\\n r22 = 2131495071; // 0x7f0c089f float:1.8613668E38 double:1.053098489E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\n r0 = r21;\\n r9.subtitle = r0;\\n r21 = 2131165426; // 0x7f0700f2 float:1.7945069E38 double:1.0529356226E-314;\\n r0 = r21;\\n r9.icon = r0;\\n r21 = new java.io.File;\\n r22 = \\\"/\\\";\\n r21.(r22);\\n r0 = r21;\\n r9.file = r0;\\n r0 = r23;\\n r0 = r0.items;\\n r21 = r0;\\n r0 = r21;\\n r0.add(r9);\\n r18 = new java.io.File;\\t Catch:{ Exception -> 0x02f7 }\\n r21 = android.os.Environment.getExternalStorageDirectory();\\t Catch:{ Exception -> 0x02f7 }\\n r22 = \\\"Telegram\\\";\\n r0 = r18;\\n r1 = r21;\\n r2 = r22;\\n r0.(r1, r2);\\t Catch:{ Exception -> 0x02f7 }\\n r21 = r18.exists();\\t Catch:{ Exception -> 0x02f7 }\\n if (r21 == 0) goto L_0x0254;\\n L_0x0223:\\n r10 = new org.telegram.ui.DocumentSelectActivity$ListItem;\\t Catch:{ Exception -> 0x02f7 }\\n r21 = 0;\\n r0 = r23;\\n r1 = r21;\\n r10.();\\t Catch:{ Exception -> 0x02f7 }\\n r21 = \\\"Telegram\\\";\\n r0 = r21;\\n r10.title = r0;\\t Catch:{ Exception -> 0x02fd }\\n r21 = r18.toString();\\t Catch:{ Exception -> 0x02fd }\\n r0 = r21;\\n r10.subtitle = r0;\\t Catch:{ Exception -> 0x02fd }\\n r21 = 2131165426; // 0x7f0700f2 float:1.7945069E38 double:1.0529356226E-314;\\n r0 = r21;\\n r10.icon = r0;\\t Catch:{ Exception -> 0x02fd }\\n r0 = r18;\\n r10.file = r0;\\t Catch:{ Exception -> 0x02fd }\\n r0 = r23;\\n r0 = r0.items;\\t Catch:{ Exception -> 0x02fd }\\n r21 = r0;\\n r0 = r21;\\n r0.add(r10);\\t Catch:{ Exception -> 0x02fd }\\n r9 = r10;\\n L_0x0254:\\n r9 = new org.telegram.ui.DocumentSelectActivity$ListItem;\\n r21 = 0;\\n r0 = r23;\\n r1 = r21;\\n r9.();\\n r21 = \\\"Gallery\\\";\\n r22 = 2131493847; // 0x7f0c03d7 float:1.8611186E38 double:1.053097884E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\n r0 = r21;\\n r9.title = r0;\\n r21 = \\\"GalleryInfo\\\";\\n r22 = 2131493848; // 0x7f0c03d8 float:1.8611188E38 double:1.0530978846E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\n r0 = r21;\\n r9.subtitle = r0;\\n r21 = 2131165529; // 0x7f070159 float:1.7945278E38 double:1.0529356735E-314;\\n r0 = r21;\\n r9.icon = r0;\\n r21 = 0;\\n r0 = r21;\\n r9.file = r0;\\n r0 = r23;\\n r0 = r0.items;\\n r21 = r0;\\n r0 = r21;\\n r0.add(r9);\\n r0 = r23;\\n r0 = r0.listView;\\n r21 = r0;\\n org.telegram.messenger.AndroidUtilities.clearDrawableAnimation(r21);\\n r21 = 1;\\n r0 = r21;\\n r1 = r23;\\n r1.scrolling = r0;\\n r0 = r23;\\n r0 = r0.listAdapter;\\n r21 = r0;\\n r21.notifyDataSetChanged();\\n return;\\n L_0x02ae:\\n r21 = \\\"InternalStorage\\\";\\n r22 = 2131493929; // 0x7f0c0429 float:1.8611352E38 double:1.0530979246E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\n r0 = r21;\\n r8.title = r0;\\n r21 = 2131165528; // 0x7f070158 float:1.7945276E38 double:1.052935673E-314;\\n r0 = r21;\\n r8.icon = r0;\\n goto L_0x0062;\\n L_0x02c5:\\n r21 = \\\"ExternalStorage\\\";\\n r22 = 2131493730; // 0x7f0c0362 float:1.8610948E38 double:1.0530978263E-314;\\n r21 = org.telegram.messenger.LocaleController.getString(r21, r22);\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n r0 = r21;\\n r13.title = r0;\\t Catch:{ Exception -> 0x01bd, all -> 0x02d5 }\\n goto L_0x0190;\\n L_0x02d5:\\n r21 = move-exception;\\n r3 = r4;\\n L_0x02d7:\\n if (r3 == 0) goto L_0x02dc;\\n L_0x02d9:\\n r3.close();\\t Catch:{ Exception -> 0x02f2 }\\n L_0x02dc:\\n throw r21;\\n L_0x02dd:\\n if (r4 == 0) goto L_0x0305;\\n L_0x02df:\\n r4.close();\\t Catch:{ Exception -> 0x02e5 }\\n r3 = r4;\\n goto L_0x01cd;\\n L_0x02e5:\\n r7 = move-exception;\\n org.telegram.messenger.FileLog.e(r7);\\n r3 = r4;\\n goto L_0x01cd;\\n L_0x02ec:\\n r7 = move-exception;\\n org.telegram.messenger.FileLog.e(r7);\\n goto L_0x01cd;\\n L_0x02f2:\\n r7 = move-exception;\\n org.telegram.messenger.FileLog.e(r7);\\n goto L_0x02dc;\\n L_0x02f7:\\n r7 = move-exception;\\n L_0x02f8:\\n org.telegram.messenger.FileLog.e(r7);\\n goto L_0x0254;\\n L_0x02fd:\\n r7 = move-exception;\\n r9 = r10;\\n goto L_0x02f8;\\n L_0x0300:\\n r21 = move-exception;\\n goto L_0x02d7;\\n L_0x0302:\\n r7 = move-exception;\\n goto L_0x01c5;\\n L_0x0305:\\n r3 = r4;\\n goto L_0x01cd;\\n */\\n throw new UnsupportedOperationException(\\\"Method not decompiled: org.telegram.ui.DocumentSelectActivity.listRoots():void\\\");\\n }\",\n \"public static void startup() {\\n\\t\\tString thisLine;\\n\\t\\tString currentName = \\\"\\\";\\n\\t\\tboolean next = true;\\n\\n\\t\\t// DEBUG\\n\\t\\t// System.out.println(\\\"entered here\\\");\\n\\n\\t\\t// Loop across the arguments\\n\\n\\t\\t// Open the file for reading\\n\\t\\ttry {\\n\\t\\t\\tBufferedReader br = new BufferedReader(new FileReader(GIGA_WORD));\\n\\t\\t\\twhile ((thisLine = br.readLine()) != null) {\\n\\t\\t\\t\\tString str = thisLine.trim();// .replaceAll(\\\"(\\\\\\\\r|\\\\\\\\n)\\\", \\\"\\\");\\n\\t\\t\\t\\tString[] wordNumber = str.split(\\\"[ ]{2,}\\\");\\n\\t\\t\\t\\tString word = wordNumber[0].toLowerCase();\\n\\t\\t\\t\\tint cnt = Integer.parseInt(wordNumber[1]);\\n\\t\\t\\t\\tgigaMap.put(word, cnt);\\n\\t\\t\\t}\\n\\t\\t\\tbr.close();\\n\\t\\t\\tbr = null;\\n\\t\\t\\tbr = new BufferedReader(new FileReader(FILE_NAME));\\n\\t\\t\\twhile ((thisLine = br.readLine()) != null) {\\n\\t\\t\\t\\tString str = thisLine.trim();// replaceAll(\\\"(\\\\\\\\r|\\\\\\\\n)\\\", \\\"\\\");\\n\\t\\t\\t\\tif (str.equals(\\\"[Term]\\\")) {\\n\\t\\t\\t\\t\\tnext = true;\\n\\t\\t\\t\\t}\\n\\t\\t\\t\\tif (str.startsWith(\\\"name:\\\")) {\\n\\t\\t\\t\\t\\tif (next) {\\n\\t\\t\\t\\t\\t\\tcurrentName = str.replaceAll(\\\"name: \\\", \\\"\\\");\\n\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t}\\n\\t\\t\\t\\tif (str.startsWith(\\\"synonym:\\\")) {\\n\\t\\t\\t\\t\\tif (str.contains(\\\"EXACT\\\") || str.contains(\\\"NARROW\\\")) {\\n\\t\\t\\t\\t\\t\\t// synonym..\\n\\t\\t\\t\\t\\t\\tPattern pattern = Pattern\\n\\t\\t\\t\\t\\t\\t\\t\\t.compile(\\\"synonym:.*\\\\\\\"(.*)\\\\\\\".*\\\");\\n\\t\\t\\t\\t\\t\\tMatcher matcher = pattern.matcher(str);\\n\\t\\t\\t\\t\\t\\t// DEBUG\\n\\t\\t\\t\\t\\t\\t// System.err.println(str);\\n\\t\\t\\t\\t\\t\\tif (matcher.find()) {\\n\\t\\t\\t\\t\\t\\t\\tString syno = matcher.group(1);\\n\\t\\t\\t\\t\\t\\t\\tif (!currentName.equals(\\\"\\\")) {\\n\\t\\t\\t\\t\\t\\t\\t\\t// System.err.format(\\\"%s:%s.\\\\n\\\", currentName,\\n\\t\\t\\t\\t\\t\\t\\t\\t// syno);\\n\\n\\t\\t\\t\\t\\t\\t\\t\\tadd(currentName, syno);\\n\\t\\t\\t\\t\\t\\t\\t\\tadd(syno, currentName);\\n\\t\\t\\t\\t\\t\\t\\t\\trecursiveAddSyno(currentName, syno);\\n\\t\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t\\t}\\n\\t\\t\\t\\t}\\n\\t\\t\\t}\\n\\t\\t\\tbr.close();\\n\\t\\t\\tbr = null;\\n\\t\\t} catch (IOException e) {\\n\\t\\t\\tSystem.err.println(\\\"Error: \\\" + e);\\n\\t\\t}\\n\\t}\",\n \"public void start(){\\n\\t\\tboolean readFromFile = readFromIndex();\\r\\n\\t\\tif (!readFromFile){\\t\\r\\n\\t\\t\\tfor (int i = 0;i<1000;++i){\\r\\n\\t\\t\\t\\tString file = \\\"../crawler/pages/page\\\"+i+\\\".html\\\";\\r\\n\\t\\t\\t\\taddFile(file);\\r\\n\\t\\t\\t}\\r\\n\\t\\t}\\r\\n\\t}\",\n \"public static void testDictionary() throws IOException {\\n String wnhome=\\\"c:\\\\\\\\Users\\\\\\\\Katherine\\\\\\\\Documents\\\\\\\\2nd sem\\\\\\\\IR\\\\\\\\project\\\\\\\\WordNet_3.1\\\";\\n String path = wnhome + File.separator + \\\"dict\\\";\\n\\n\\n URL url = new URL(\\\"file\\\", null, path);\\n\\n IDictionary dictionary = new Dictionary(url);\\n dictionary.open();\\n // /Users/Ward/Downloads\\n IIndexWord indexWord = dictionary.getIndexWord(\\\"use\\\", POS.VERB);\\n\\n for (IWordID wordID : indexWord.getWordIDs()) {\\n\\n IWord word = dictionary.getWord(wordID);\\n for (IWord word1 : word.getSynset().getWords()) {\\n System.out.println(word1.getLemma());\\n }\\n// System.out.println(\\\"Id = \\\" + wordID);\\n// System.out.println(\\\" Lemma = \\\" + word.getLemma());\\n// System.out.println(\\\" Gloss = \\\" + word.getSynset().getGloss());\\n\\n List hypernyms =\\n word.getSynset().getRelatedSynsets(Pointer.HYPERNYM);\\n // print out each h y p e r n y m s id and synonyms\\n List words;\\n for (ISynsetID sid : hypernyms) {\\n words = dictionary.getSynset(sid).getWords();\\n System.out.print(sid + \\\" {\\\");\\n for (Iterator i = words.iterator(); i.hasNext(); ) {\\n System.out.print(i.next().getLemma());\\n if (i.hasNext())\\n System.out.print(\\\", \\\");\\n }\\n System.out.println(\\\"}\\\");\\n }\\n }\\n }\",\n \"@SuppressWarnings(\\\"unchecked\\\")\\r\\n private void newMap() throws IOException, ClassNotFoundException {\\r\\n this.music_map.clear();\\r\\n if (needNewMap()) {\\r\\n if (!save_file.exists()) {\\r\\n System.out.println(\\\"DIZIONARIO NON PRESENTE\\\");\\r\\n System.out.println(\\\"CREAZIONE NUOVO DIZIONARIO IN CORSO...\\\");\\r\\n\\r\\n this.setTarget();\\r\\n\\r\\n this.recoursiveMapCreation(this.music_root);\\r\\n this.saveMap();\\r\\n } else {\\r\\n System.out.println(\\\"DIZIONARIO NON AGGIORNATO\\\");\\r\\n if (!UtilFunctions.newDictionaryRequest(this.save_file, this.music_root)) {\\r\\n System.out.println(\\\"AGGIORNAMENTO DIZIONARIO RIFIUTATO\\\");\\r\\n FileInputStream f = new FileInputStream(this.save_file);\\r\\n ObjectInputStream o = new ObjectInputStream(f);\\r\\n this.music_map.putAll((Map) o.readObject());\\r\\n current.set(ProgressDialog.TOTAL.get());\\r\\n } else {\\r\\n System.out.println(\\\"CREAZIONE NUOVO DIZIONARIO IN CORSO...\\\");\\r\\n this.setTarget();\\r\\n this.recoursiveMapCreation(this.music_root);\\r\\n this.saveMap();\\r\\n }\\r\\n }\\r\\n } else {\\r\\n System.out.println(\\\"DIZIONARIO GIA' PRESENTE\\\");\\r\\n FileInputStream f = new FileInputStream(this.save_file);\\r\\n ObjectInputStream o = new ObjectInputStream(f);\\r\\n this.music_map.putAll((Map) o.readObject());\\r\\n current.set(ProgressDialog.TOTAL.get());\\r\\n }\\r\\n }\",\n \"private static void searchMemo() {\\n\\t\\t\\n\\t}\",\n \"private static Positional_inverted_index posindexCorpus(DocumentCorpus corpus) throws ClassNotFoundException, InstantiationException, IllegalAccessException, FileNotFoundException, IOException {\\n\\n NewTokenProcessor processor = new NewTokenProcessor();\\n Iterable docs = corpus.getDocuments(); //call registerFileDocumentFactory first?\\n\\n List Doc_length = new ArrayList<>();\\n Positional_inverted_index index = new Positional_inverted_index();\\n\\n double token_count = 0;\\n\\n // Iterate through the documents, and:\\n for (Document d : docs) {\\n //File f = new File(path + \\\"\\\\\\\\\\\" + d.getTitle());\\n File f = new File(path + \\\"\\\\\\\\\\\" + d.getFileName().toString());\\n double Filesize = f.length();\\n //edited by bhavya\\n double doc_weight = 0; //first entry in docweights.bin\\n double doc_tokens = 0;\\n double doc_length = 0;\\n HashMap tftd = new HashMap<>();\\n // Tokenize the document's content by constructing an EnglishTokenStream around the document's content.\\n Reader reader = d.getContent();\\n EnglishTokenStream stream = new EnglishTokenStream(reader); //can access tokens through this stream\\n N++;\\n // Iterate through the tokens in the document, processing them using a BasicTokenProcessor,\\n //\\t\\tand adding them to the HashSet vocabulary.\\n Iterable tokens = stream.getTokens();\\n int i = 0;\\n\\n for (String token : tokens) {\\n\\n //adding token in index\\n List word = new ArrayList();\\n word = processor.processToken(token);\\n //System.out.println(word.get(0));\\n if (word.get(0).matches(\\\"\\\")) {\\n continue;\\n } else {\\n\\n index.addTerm(word.get(0), i, d.getId());\\n\\n }\\n i = i + 1;\\n\\n //we check if token already exists in hashmap or not. \\n //if it exists, increase its freq by 1 else make a new entry.\\n if (tftd.containsKey(word.get(0))) {\\n doc_tokens++;\\n int count = tftd.get(word.get(0));\\n tftd.replace(word.get(0), count + 1);\\n } else {\\n doc_tokens++;\\n// token_count++; //gives total number of tokens.\\n tftd.put(word.get(0), 1);\\n }\\n\\n }\\n double length = 0;\\n double wdt = 0;\\n\\n double total_tftd = 0;\\n for (Map.Entry entry : tftd.entrySet()) {\\n\\n wdt = 1 + log(entry.getValue());\\n\\n length = length + pow(wdt, 2);\\n total_tftd = total_tftd + entry.getValue();\\n }\\n token_count = token_count + doc_tokens;\\n doc_weight = pow(length, 0.5);\\n double avg_tftd = total_tftd / (double) tftd.size();\\n\\n Doc_length.add(doc_weight);\\n Doc_length.add(avg_tftd);\\n Doc_length.add(doc_tokens);\\n Doc_length.add(Filesize);\\n }\\n Doc_length.add(token_count / N);\\n\\n DiskIndexWriter d = new DiskIndexWriter();\\n d.write_doc(path, Doc_length);\\n\\n return index;\\n }\",\n \"@Override\\n public void processCas(CAS aCas) throws ResourceProcessException {\\nSystem.out.println(\\\"Retrival evaluator...\\\");\\n JCas jcas;\\n try {\\n jcas = aCas.getJCas();\\n } catch (CASException e) {\\n throw new ResourceProcessException(e);\\n }\\n\\n FSIterator it = jcas.getAnnotationIndex(Document.type).iterator();\\n \\n// if (it.hasNext()) {\\n// Document doc = (Document) it.next();\\n// cnt++;\\n// }\\n// log(cnt);\\n it = jcas.getAnnotationIndex(Document.type).iterator();\\n\\n if (it.hasNext()) {\\n Document doc = (Document) it.next();\\n int queryid = doc.getQueryID();\\n int rel = doc.getRelevanceValue();\\n // Make sure that your previous annotators have populated this in CAS\\n FSList fsTokenList = doc.getTokenList();\\n ArrayList tokenList = Utils.fromFSListToCollection(fsTokenList, Token.class);\\n Map queryVector = new HashMap();\\n Map docVector = new HashMap();\\n if (rel == 99) {\\n for (Token t : tokenList) {\\n queryVector.put(t.getText(), t.getFrequency());\\n }\\n queryVectorlist.add(queryVector);\\n } else {\\n for (Token t : tokenList) {\\n docVector.put(t.getText(), t.getFrequency());\\n }\\n double cos = computeCosineSimilarity(queryVectorlist.get(queryid - 1), docVector);\\n coslist.add(cos);\\n\\n if (rel == 1) {\\n gold = lines;\\n goldcos = cos;\\n System.out.println(\\\"goldcos\\\"+goldcos);\\n }\\n }\\n \\n if (qIdList.size() >= 1 && qIdList.get(qIdList.size() - 1) != queryid) {\\n// System.out.println(\\\"lines:\\\"+lines);\\n sortSimilarity(coslist);\\n log(coslist);\\n int rank=findRank(coslist,goldcos);\\n rankList.add(rank);\\n coslist = new ArrayList();\\n }\\n\\n qIdList.add(doc.getQueryID());// 有啥用？？？\\n relList.add(doc.getRelevanceValue());\\n\\n // Do something useful here\\n lines++;\\n }\\n //log(coslist);\\n\\n }\",\n \"public IndexDatabase(String index_path, String genomes_path_file, int K_size, SequenceDatabase genomeDb) {\\n int cores = Runtime.getRuntime().availableProcessors() / 2 + 1;\\n int k;\\n long p;\\n IndexPointer null_pointer = new IndexPointer();\\n try {\\n Files.createDirectory(Paths.get(index_path));\\n System.out.println(\\\"Running KMC2... \\\");\\n executeCommand(\\\"kmc -r -k\\\" + K_size + \\\" -t\\\" + cores + \\\" -m\\\" + \\n (Runtime.getRuntime().maxMemory() / 1073741824L) + \\\" -ci1 -fm \\\" + \\n (genomeDb.num_genomes > 1 ? \\\"@\\\" + genomes_path_file.trim() : genomeDb.genome_names[1]) + \\\" \\\" + index_path + \\\"/kmers \\\" + index_path);\\n String output = executeCommand(\\\"kmc_tools sort \\\" + index_path + \\\"/kmers \\\" + index_path + \\\"/sorted\\\");\\n if (output.startsWith(\\\"This database contains sorted k-mers already!\\\")) {\\n new File(index_path + \\\"/kmers.kmc_pre\\\").renameTo(new File(index_path + \\\"/sorted.kmc_pre\\\"));\\n new File(index_path + \\\"/kmers.kmc_suf\\\").renameTo(new File(index_path + \\\"/sorted.kmc_suf\\\"));\\n //Files.copy(Paths.get(path+\\\"/kmers.kmc_pre\\\"), Paths.get(path+\\\"/sorted.kmc_pre\\\"));\\n //Files.copy(Paths.get(path+\\\"/kmers.kmc_suf\\\"), Paths.get(path+\\\"/sorted.kmc_suf\\\"));\\n } else {\\n new File(index_path + \\\"/kmers.kmc_pre\\\").delete();\\n new File(index_path + \\\"/kmers.kmc_suf\\\").delete();\\n }\\n pre_file = new RandomAccessFile(index_path + \\\"/sorted.kmc_pre\\\", \\\"r\\\");\\n pre_file.seek(pre_file.length() - 8);\\n header_pos = read_int(pre_file);\\n pre_file.seek(pre_file.length() - 8 - header_pos);\\n // read the index properties \\n K = read_int(pre_file);\\n mode = read_int(pre_file);\\n ctr_size = read_int(pre_file);\\n pre_len = read_int(pre_file);\\n min_count = read_int(pre_file);\\n max_count = read_int(pre_file);\\n kmers_num = read_long(pre_file);\\n suf_len = K - pre_len;\\n key = new kmer(K, pre_len, suf_len);\\n System.out.println(\\\"Indexing \\\" + kmers_num + \\\" kmers... \\\");\\n // load the prefix file into the memory \\n pre_file.seek(4);\\n int q, len = 1 << (2 * pre_len);\\n prefix_ptr = new long[len];\\n MappedByteBuffer pre_buff;\\n for (q = 0, p = 0; p < 8; ++p) {\\n pre_buff = pre_file.getChannel().map(FileChannel.MapMode.READ_ONLY, 4 + p * len, len);\\n for (k = 0; k < len / 8; ++k, ++q) {\\n prefix_ptr[q] = read_long(pre_buff);\\n }\\n pre_buff = null;\\n }\\n pre_file.close();\\n\\n // mapping suffix file into the memory\\n suf_rec_size = ctr_size + suf_len / 4;\\n MAX_BYTE_COUNT = MAX_BYTE_COUNT / suf_rec_size * suf_rec_size;\\n suf_parts_num = (int) ((kmers_num * suf_rec_size) % MAX_BYTE_COUNT == 0 ? (kmers_num * suf_rec_size) / MAX_BYTE_COUNT : (kmers_num * suf_rec_size) / MAX_BYTE_COUNT + 1);\\n suf_parts_size = new long[suf_parts_num];\\n suf_file = new RandomAccessFile(index_path + \\\"/sorted.kmc_suf\\\", \\\"r\\\");\\n suf_buff = new MappedByteBuffer[suf_parts_num];\\n for (k = 0; k < suf_parts_num; ++k) {\\n suf_parts_size[k] = (int) (k == suf_parts_num - 1 ? (kmers_num * suf_rec_size) % MAX_BYTE_COUNT : MAX_BYTE_COUNT);\\n suf_buff[k] = suf_file.getChannel().map(FileChannel.MapMode.READ_ONLY, 4 + k * suf_parts_size[0], suf_parts_size[k]);\\n }\\n // mapping pointers file into the memory\\n MAX_BYTE_COUNT = MAX_BYTE_COUNT / POINTER_LENGTH * POINTER_LENGTH;\\n ptr_parts_num = (int) ((kmers_num * POINTER_LENGTH) % MAX_BYTE_COUNT == 0 ? (kmers_num * POINTER_LENGTH) / MAX_BYTE_COUNT : (kmers_num * POINTER_LENGTH) / MAX_BYTE_COUNT + 1);\\n ptr_parts_size = new long[ptr_parts_num];\\n ptr_file = new RandomAccessFile(index_path + \\\"/pointers.db\\\", \\\"rw\\\");\\n ptr_buff = new MappedByteBuffer[ptr_parts_num];\\n for (k = 0; k < ptr_parts_num; ++k) {\\n ptr_parts_size[k] = (int) (k == ptr_parts_num - 1 ? (kmers_num * POINTER_LENGTH) % MAX_BYTE_COUNT : MAX_BYTE_COUNT);\\n ptr_buff[k] = ptr_file.getChannel().map(FileChannel.MapMode.READ_WRITE, k * ptr_parts_size[0], ptr_parts_size[k]);\\n }\\n for (p = 0; p < kmers_num; ++p) {\\n put_pointer(null_pointer, p);\\n }\\n } catch (IOException e) {\\n System.out.println(e.getMessage());\\n System.exit(1);\\n }\\n }\",\n \"String prepareLegalDocuments();\",\n \"public void map(Object key, Text value, Context context\\n\\t\\t ) throws IOException, InterruptedException {\\n\\n\\t\\t\\t\\n\\t\\t\\t\\n\\t\\t\\t \\n\\t\\t\\t String curr_string=value.toString();\\n\\t\\t\\t /// splitting based on \\\"*\\\" as a delimiter...\\n\\t\\t\\t String [] parts=curr_string.split(\\\"\\\\\\\\*\\\");\\n\\t\\t\\t String curr_key=parts[0];\\n\\t\\t\\t // Removing spaces from both left and right part of the string..\\n\\t\\t\\t String curr_value=parts[1].trim();\\n\\t\\t\\t String [] small_parts=curr_value.split(\\\",\\\");\\n\\t\\t\\t // Taking the count of unique files which are present in the input given to tfidf\\n\\t\\t\\t int no_of_unique_files=Integer.parseInt(small_parts[small_parts.length-1]);\\n\\t\\t\\t /// The formula to compute idf is log((1+no_of_files)/no_of_unique_files))....\\n\\t\\t\\t Configuration conf=context.getConfiguration();\\n\\t\\t\\t String value_count=conf.get(\\\"test\\\");\\n\\t\\t\\t if(!value_count.isEmpty())\\n\\t\\t\\t {\\n\\t\\t\\t int total_no_files=Integer.parseInt(value_count);\\n\\t\\t\\t double x=(total_no_files/no_of_unique_files);\\n\\t\\t\\t // Formula fo rcomputing the idf value....\\n\\t\\t\\t double idf_value=Math.log10(1+x);\\n\\t\\t\\t for(int i=0;i entry : this.index.entrySet()) {\n saveJSON(\"postings/t\"+hash(entry.getKey())+\".json\", entry.getValue());\n System.err.println(\"postings/t\"+hash(entry.getKey())+\".json\");\n count++;\n if (count%1000==0)\n System.err.println(\"storing \"+ count);\n }\n // Store mapping ID<->document names mapping\n this.saveJSON(\"postings/docIDs.json\", this.docIDs);\n this.saveJSON(\"postings/docLengths.json\", this.docLengths);\n }"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["private void saveToken() throws IOException {\n\t\t\n\t\tFileWriter termIdx = new FileWriter(StoragePath+Path.termIdxDir);\n\t\t\n\t\tfor(Entry term: termDic.entrySet()){\n\t\t\ttermIdx.append(term.getKey() + \"\\n\" + term.getValue() + \"\\n\");\n\t\t}\n\t\t\n\t\ttermIdx.close();\n\t\t\n\t}","public static void generateInvertedIndex(Map> stemMap, List documentIds)\n {\n long lineCounter = 0;\n int documentCounter = -1;\n String currentDocId = \"\";\n String currentDocTitle = \"\";\n Scanner scanner = new Scanner(System.in);\n\n while (scanner.hasNext())\n {\n String line = scanner.nextLine();\n lineCounter++;\n \n if (line.startsWith(\"$DOC\"))\n {\n String[] wordStems = line.split(\" \");\n currentDocId = wordStems[1];\n documentCounter++;\n }\n else if (line.startsWith(\"$TITLE\"))\n {\n /* Save document titles for documentId list */\n long docLineNumber = lineCounter - 1;\n currentDocTitle = \"\";\n \n while (scanner.hasNext())\n {\n String nextTitleLine = scanner.nextLine();\n if (nextTitleLine.startsWith(\"$TEXT\"))\n {\n lineCounter++;\n documentIds.add(String.format(\"%s %d %s\\n\", currentDocId, docLineNumber, currentDocTitle));\n break;\n }\n else\n {\n lineCounter++;\n currentDocTitle += nextTitleLine;\n currentDocTitle += \" \";\n }\n }\n }\n else\n {\n String[] wordStems = line.split(\" \");\n for (String wordStem: wordStems)\n {\n if (stemMap.containsKey(wordStem))\n {\n List currentStemPostings = stemMap.get(wordStem);\n int lastElementIndex = currentStemPostings.size() - 1;\n Posting lastPosting = currentStemPostings.get(lastElementIndex);\n \n if (lastPosting.documentId == documentCounter)\n {\n lastPosting.termFrequency += 1;\n }\n else\n {\n Posting posting = new Posting(documentCounter, 1);\n currentStemPostings.add(posting);\n }\n }\n else\n {\n List postings = new ArrayList<>();\n Posting posting = new Posting(documentCounter, 1);\n postings.add(posting);\n stemMap.put(wordStem, postings);\n }\n }\n }\n }\n scanner.close();\n }","public void writeIDs() {\n try {\n FileOutputStream fileOut = new FileOutputStream(\"temp/ids.ser\");\n ObjectOutputStream out = new ObjectOutputStream(fileOut);\n out.writeObject(ids);\n out.close();\n fileOut.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n\n }","private void scanDocuments()\n{\n document_counts = new HashMap<>();\n kgram_counts = new HashMap<>();\n for (File f : root_files) {\n addDocuments(f);\n }\n}","public static void printInvertedIndexToFile(Map> stemMap, List documentIds)\n {\n try\n {\n PrintWriter dictionaryPW = new PrintWriter(DICTIONARY_OUTPUT_FILE_PATH, \"UTF-8\");\n PrintWriter postingsPW = new PrintWriter(POSTINGS_OUTPUT_FILE_PATH, \"UTF-8\");\n PrintWriter docIdsPW = new PrintWriter(DOCUMENT_ID_OUTPUT_FILE_PATH, \"UTF-8\");\n\n int numStems = stemMap.size();\n int numPostingEntries = 0;\n int numDocuments = documentIds.size();\n \n for (List posting: stemMap.values())\n {\n numPostingEntries += posting.size();\n }\n\n dictionaryPW.println(numStems);\n postingsPW.println(numPostingEntries);\n docIdsPW.println(numDocuments);\n\n for (Entry> entrySet: stemMap.entrySet())\n {\n String stem = entrySet.getKey();\n List postings = entrySet.getValue();\n\n dictionaryPW.println(String.format(\"%s %d\", stem, postings.size()));\n for (Posting posting: postings)\n {\n postingsPW.println(String.format(\"%d %d\", posting.documentId, posting.termFrequency));\n numPostingEntries++;\n }\n }\n\n for (String docId: documentIds)\n {\n docIdsPW.print(docId);\n }\n\n dictionaryPW.close();\n postingsPW.close();\n docIdsPW.close();\n }\n catch (Exception e)\n {\n System.out.println(e.getMessage());\n }\n }","private void saveIds(ArrayList idList) {\n\n\t\ttry {\n\t\t\tFileOutputStream fileOutputStream = context.openFileOutput(\n\t\t\t\t\tSAVE_FILE, Context.MODE_PRIVATE);\n\t\t\tOutputStreamWriter outputStreamWriter = new OutputStreamWriter(\n\t\t\t\t\tfileOutputStream);\n\t\t\tGsonBuilder builder = new GsonBuilder();\n\t\t\tGson gson = builder.create();\n\t\t\tgson.toJson(idList, outputStreamWriter); // Serialize to Json\n\t\t\toutputStreamWriter.flush();\n\t\t\toutputStreamWriter.close();\n\t\t} catch (IOException e) {\n\t\t\te.printStackTrace();\n\t\t}\n\t}","public static void save(String indexFileName) throws FileNotFoundException, UnsupportedEncodingException{\n\t\tHashMap sCurrentHashMap = globalHash.get(indexFileName);\n\t\t\n\t\tPrintWriter writer = new PrintWriter(indexFileName+\".txt\", \"UTF-8\");\n\n\t\tIterator it = sCurrentHashMap.entrySet().iterator();\n\t\twhile(it.hasNext()){\n\t\t\tHashMap.Entry entry = (HashMap.Entry) it.next();\n\t\t\t//if this term appear more than one doc\n\t\t\tif(entry.getValue().length()>1) {\n\t\t\t\tStringTokenizer stDocID = new StringTokenizer(entry.getValue(),\",\");\n\t\t\t\twriter.println(entry.getKey()+\",\"+stDocID.countTokens()+\":<\"+entry.getValue()+\">\");\n\t\t\t} else{\n\t\t\t\twriter.println(entry.getKey()+\",1:<\"+entry.getValue()+\">\");\n\t\t\t}\n\t\t}\n\t\twriter.close();\n\t}","public void IndexADocument(String docno, String content) throws IOException {\n\t\tdocid++;\n\t\tdoc2docid.put(docno, docid);\n\t\tdocid2doc.put(docid, docno);\n\n\t\t// Insert every term in this doc into docid2map\n\t\tString[] terms = content.trim().split(\" \");\n\t\tMap docTerm = new HashMap<>();\n\t\tint thisTermid;\n\t\tfor(String term: terms){\n\t\t\t// get termid\n\t\t\tif(term2termid.get(term)!=null) thisTermid = term2termid.get(term);\n\t\t\telse{\n\t\t\t\tthisTermid = ++termid;\n\t\t\t\tterm2termid.put(term, thisTermid);\n\t\t\t}\n\t\t\tdocTerm.put(thisTermid, docTerm.getOrDefault(thisTermid, 0)+1);\n\t\t\t// Merge this term's information into termid2map\n\t\t\tMap temp = termid2map.getOrDefault(thisTermid, new HashMap());\n\t\t\ttemp.put(docid, temp.getOrDefault(docid, 0)+1);\n\t\t\ttermid2map.put(thisTermid, temp);\n\t\t\ttermid2fre.put(thisTermid, termid2fre.getOrDefault(thisTermid, 0)+1);\n\t\t}\n\t\tdocid2map.put(docid, docTerm);\n\n//\t\t// Merge all the terms' information into termid2map\n//\t\tfor(Long tid: docTerm.keySet()){\n//\t\t\tMap temp = termid2map.getOrDefault(tid, new HashMap());\n//\t\t\ttemp.put(docid,docTerm.get(tid));\n//\t\t\ttermid2map.put(tid, temp);\n//\t\t\t// update this term's frequency\n//\t\t\ttermid2fre.put(tid, termid2fre.getOrDefault(tid,0L)+docTerm.get(tid));\n//\t\t}\n\n\t\t// When termid2map and docid2map is big enough, put it into disk\n\t\tif(docid%blockSize==0){\n\t\t\tWritePostingFile();\n\t\t\tWriteDocFile();\n\t\t}\n\t}","static private void saveSentenceTokens( final String outputDirPath,\n final String documentId, final Iterable tokenizedSentences ) {\n // Be prepared for documentId that contains directory segments, some of which may not exist\n final File outputFile = new File( outputDirPath + File.pathSeparator + documentId );\n if ( !outputFile.getParentFile().exists() && !outputFile.getParentFile().mkdirs() ) {\n LOGGER.error( outputFile.getPath() + \" is an invalid output file path\" );\n return;\n }\n try ( final BufferedWriter writer = new BufferedWriter( new FileWriter( outputFile ) ) ) {\n for ( String tokenizedSentence : tokenizedSentences ) {\n writer.write( tokenizedSentence );\n writer.newLine();\n }\n } catch ( IOException ioE ) {\n LOGGER.error( ioE.getMessage() );\n }\n }","private void writeVocabPost(FlIndexer fi) throws IOException{\n this.docNormPow = new HashMap<>();\n \n LinkedList tf;\n LinkedList files;\n String token;\n int position=0;\n File file = new File(\"CollectionIndex/VocabularyFile.txt\");\n File Postingfile = new File(\"CollectionIndex/PostingFile.txt\");\n \n\tFileWriter fw = new FileWriter(file.getAbsoluteFile());\n FileWriter fw_posting = new FileWriter(Postingfile.getAbsolutePath());\n try (BufferedWriter bw = new BufferedWriter(fw)) {\n try (BufferedWriter bw_posting = new BufferedWriter(fw_posting)){\n for (Map.Entry entry : fi.mapTerms.entrySet()){\n double idf = ((double)this.docMap.size())/entry.getValue().getDf();\n //idf=log2(idf, 2);\n bw.write(entry.getValue().getTerm()+\" \"+entry.getValue().getDf()+\" \"+idf+\" \"+position+\"\\n\");\n \n tf=entry.getValue().getTfList();\n files=entry.getValue().getFileList();\n int i=tf.size();\n for (int j=0; j bow) {\n //logger.info(\"lsm.mapDocument\");\n SparseVector vector = new SparseVector();\n\n Iterator it = bow.iterator();\n String term = null;\n int index = 0;\n int tf = 0;\n float tfIdf;\n for (int i = 0; it.hasNext(); i++) {\n //logger.info(i + \" \" + t[i]);\n term = it.next();\n index = termIndex.get(term);\n\n if (index != -1) {\n tf = bow.getFrequency(term);\n tfIdf = (float) (log2(tf)) * Iidf[index];\n\n //logger.info(term + \" ==> \" + index + \", tf.idf = \" + tf + \"(\" + (log2(tf)) + \") * \" + Iidf[index] + \" = \" + tfIdf);\n vector.add(index, tfIdf);\n\n }\n } // end for\n\n return vector;\n }","public static void main(String[] args) throws IOException{\n\t\tint termIndex = 1;\n\t\t\n\t\t// startOffset holds the start offset for each term in\n\t\t// the corpus.\n\t\tlong startOffset = 0;\n\t\t\t\n\t\t// unique_terms is true if there are atleast one more\n\t\t// unique term in corpus.\n\t\tboolean unique_terms = true;\n\t\t\n\t\t\n\t\t//load the stopwords from the HDD\n\t\tString stopwords = getStopWords();\n\t\t\n\t\t// allTokenHash contains all the terms and its termid\n\t\tHashMap allTermHash = new HashMap();\n\t\t\n\t\t// catalogHash contains the term and its position in\n\t\t// the inverted list present in the HDD.\n\t\tHashMap catalogHash = new HashMap();\n\t\t\n\t\t// finalCatalogHash contains the catalogHash for the invertedIndexHash\n\t\t// present in the HDD.\n\t\tHashMap finalCatalogHash = new HashMap();\n\t\t\n\t\t// token1000Hash contains the term and Dblocks for the first 1000\n\t\tHashMap token1000DocHash = new HashMap();\n\t\t\n\t\t// documentHash contains the doclength of all the documents in the corpus\n\t\tHashMap documentHash = new HashMap();\t\n\t\t\n\t\t// id holds the document id corresponding to the docNumber.\n\t\tint id = 1;\n\t\t\n\t\t// until all unique terms are exhausted\n\t\t// pass through the documents and index the terms.\n\t\t//while(unique_terms){\n\t\t\t\n\t\t\tFile folder = new File(\"C:/Naveen/CCS/IR/AP89_DATA/AP_DATA/ap89_collection\");\n\t\t\t//File folder = new File(\"C:/Users/Naveen/Desktop/TestFolder\");\n\t\t\tFile[] listOfFiles = folder.listFiles();\n\t\t\t\n\t\t\t//for each file in the folder \n\t\t\tfor (File file : listOfFiles) {\n\t\t\t if (file.isFile()) {\n\t\t\t \t\n\t\t\t \tString str = file.getPath().replace(\"\\\\\",\"//\");\n\t\t\t \t\n\t\t\t \t\n\t\t\t\t\t//Document doc = new Document();\n\t\t\t //System.out.println(\"\"+str);\n\t\t\t\t\t//variables to keep parse document.\n\t\t\t\t\tint docCount = 0;\n\t\t\t\t\tint docNumber = 0;\n\t\t\t\t\tint endDoc = 0;\n\t\t\t\t\tint textCount = 0;\n\t\t\t\t\tint noText = 0;\n\t\t\t\t\tPath path = Paths.get(str);\n\t\t\t\t\t\n\t\t\t\t\t//Document id and text\n\t\t\t\t\tString docID = null;\n\t\t\t\t\tString docTEXT = null;\n\t\t\t\t\t\n\t\t\t\t\t//Stringbuffer to hold the text of each document\n\t\t\t\t\tStringBuffer text = new StringBuffer();\n\t\t\t\t\t\n\t\t\t\t\tScanner scanner = new Scanner(path);\n\t\t\t\t\twhile(scanner.hasNext()){\n\t\t\t\t\t\tString line = scanner.nextLine();\n\t\t\t\t\t\tif(line.contains(\"\")){\n\t\t\t\t\t\t\t++docCount;\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t\telse if(line.contains(\" \")){\n\t\t\t\t\t\t\t++endDoc;\n\t\t\t\t\t\t\tdocTEXT = text.toString();\n\t\t\t\t\t\t\t//docTEXT = docTEXT.replaceAll(\"[\\\\n]\",\" \");\n\t\t\t\t\t\t\tSystem.out.println(\"ID: \"+id);\n\t\t\t\t\t\t\t//System.out.println(\"TEXT: \"+docTEXT);\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t// text with stop words removed\n\t\t\t\t\t\t\tPattern pattern1 = Pattern.compile(\"\\\\b(?:\"+stopwords+\")\\\\b\\\\s*\", Pattern.CASE_INSENSITIVE);\n\t\t\t\t\t\t\tMatcher matcher1 = pattern1.matcher(docTEXT);\n\t\t\t\t\t\t\tdocTEXT = matcher1.replaceAll(\"\");\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t// text with stemming\n\t\t\t\t\t\t\t//docTEXT = stemmer(docTEXT);\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\tint docLength = 1;\n\t\t\t\t\t\t\t// regex to build the tokens from the document text\n\t\t\t\t\t\t\tPattern pattern = Pattern.compile(\"\\\\w+(\\\\.?\\\\w+)*\");\n\t\t\t\t\t\t\tMatcher matcher = pattern.matcher(docTEXT.toLowerCase());\n\t\t\t\t\t\t\twhile (matcher.find()) {\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\tfor (int i = 0; i < matcher.groupCount(); i++) {\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t// alltermHash contains term and term id\n\t\t\t\t\t\t\t\t\t// if term is present in the alltermHash\n\t\t\t\t\t\t\t\t\tif(allTermHash.containsKey(matcher.group(i))){\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\tint termId = allTermHash.get(matcher.group(i));\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t//if term is present in the token1000Hash\n\t\t\t\t\t\t\t\t\t\t//then update the dblock of the term.\n\t\t\t\t\t\t\t\t\t\tif(token1000DocHash.containsKey(termId)){\n\t\t\t\t\t\t\t\t\t\t\tMultimap dBlockUpdate = token1000DocHash.get(termId);\n\t\t\t\t\t\t\t\t\t\t\t//Multimap dBlockUpdate = token1000DocHash.get(matcher.group(i));\n\t\t\t\t\t\t\t\t\t\t\tif(dBlockUpdate.containsKey(id)){\n\t\t\t\t\t\t\t\t\t\t\t\tdBlockUpdate.put(String.valueOf(id), String.valueOf(matcher.start()));\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\telse{\n\t\t\t\t\t\t\t\t\t\t\t\tdBlockUpdate.put(String.valueOf(id), String.valueOf(matcher.start()));\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t//if term is not present in the token1000hash\n\t\t\t\t\t\t\t\t\t\t//then add the token with its dBlock\n\t\t\t\t\t\t\t\t\t\telse{\n\t\t\t\t\t\t\t\t\t\t\tMultimap dBlockInsert = ArrayListMultimap.create();\n\t\t\t\t\t\t\t\t\t\t\tdBlockInsert.put(String.valueOf(id), String.valueOf(matcher.start()));\n\t\t\t\t\t\t\t\t\t\t\ttoken1000DocHash.put(termId, dBlockInsert);\t\n\t\t\t\t\t\t\t\t\t\t}\t\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t// if the term is not present I will put the term into allTermHash\n\t\t\t\t\t\t\t\t\t// put corresponding value into the token1000DocHash and increment\n\t\t\t\t\t\t\t\t\t// termIndex\n\t\t\t\t\t\t\t\t\telse{\n\t\t\t\t\t\t\t\t\t\tallTermHash.put(matcher.group(i),termIndex);\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\tMultimap dBlockInsert = ArrayListMultimap.create();\n\t\t\t\t\t\t\t\t\t\tdBlockInsert.put(String.valueOf(id), String.valueOf(matcher.start()));\n\t\t\t\t\t\t\t\t\t\ttoken1000DocHash.put(termIndex, dBlockInsert);\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\ttermIndex++;\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\tdocLength++;\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\tif(id%1000 == 0){\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t// then dump index file to HDD\n\t\t\t\t\t\t\t\t\twriteInvertedIndex(token1000DocHash,\"token1000DocHash\");\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t// update catalog file\n\t\t\t\t\t\t\t\t\t// to populate catalogHash with the offset\n\t\t\t\t\t\t\t\t\tfor(Entry entry : token1000DocHash.entrySet()){\n\t\t\t\t\t\t\t\t\t\tif(catalogHash.containsKey(entry.getKey())){\n\t\t\t\t\t\t\t\t\t\t\tint len = (entry.getKey()+\":\"+entry.getValue()).length();\n\t\t\t\t\t\t\t\t\t\t\t//String offset = String.valueOf(startOffset)+\":\"+String.valueOf(len);\n\t\t\t\t\t\t\t\t\t\t\tMultimap catUpdate = catalogHash.get(entry.getKey());\n\t\t\t\t\t\t\t\t\t\t\tcatUpdate.put(String.valueOf(startOffset), String.valueOf(len));\n\t\t\t\t\t\t\t\t\t\t\tcatalogHash.put(entry.getKey(), catUpdate);\n\t\t\t\t\t\t\t\t\t\t\tstartOffset += len+2;\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\telse{\n\t\t\t\t\t\t\t\t\t\t\tint len = (entry.getKey()+\":\"+entry.getValue()).length();\n\t\t\t\t\t\t\t\t\t\t\t//String offset = String.valueOf(startOffset)+\":\"+String.valueOf(len);\n\t\t\t\t\t\t\t\t\t\t\tMultimap catInsert = ArrayListMultimap.create();\n\t\t\t\t\t\t\t\t\t\t\tcatInsert.put(String.valueOf(startOffset), String.valueOf(len));\n\t\t\t\t\t\t\t\t\t\t\tcatalogHash.put(entry.getKey(), catInsert);//entry.getValue());\n\t\t\t\t\t\t\t\t\t\t\tstartOffset += len+2;\n\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t}\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t//clear the token1000DocHash\n\t\t\t\t\t\t\t\t\ttoken1000DocHash.clear();\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\tdocumentHash.put(docID, \"\"+id+\":\"+docLength);\n\t\t\t\t\t\t\tid++;\n\t\t\t\t\t\t\ttext = new StringBuffer();\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t\telse if(line.contains(\"\")){\n\t\t\t\t\t\t\t++docNumber;\n\t\t\t\t\t\t\tdocID = line.substring(8, 21);\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t\telse if(line.contains(\"\")){\n\t\t\t\t\t\t\t++textCount;\n\t\t\t\t\t\t}\n\t\t\t\t\t\telse if((line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\" \"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\" \"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\" \"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))||\n\t\t\t\t\t\t\t\t(line.contains(\" \"))||\n\t\t\t\t\t\t\t\t(line.contains(\" \"))||\n\t\t\t\t\t\t\t\t(line.contains(\"\"))){\n\t\t\t\t\t\t\t ++noText;\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t\telse if(endDoc == docCount - 1){\n\t\t\t\t\t\t\ttext.append(line);\n\t\t\t\t\t\t\ttext.append(\" \");\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t \t\n\t\t\t }//end of if - to check if this is a file and parse.\n\t\t\t \n\t\t\t}//end of for loop to load each file\n\t\t\t\n\t\t//}//end of while loop \n\t\t\n\t// write catalogfile to the hdd to check.\n\t\t\t\n\t\t\t// then dump index file to HDD\n\t\t\twriteInvertedIndex(token1000DocHash,\"token1000DocHash\");\n\t\t\t\n\t\t\t// update catalog file\n\t\t\t// to populate catalogHash with the offset\n\t\t\tfor(Entry entry : token1000DocHash.entrySet()){\n\t\t\t\tif(catalogHash.containsKey(entry.getKey())){\n\t\t\t\t\tint len = (entry.getKey()+\":\"+entry.getValue()).length();\n\t\t\t\t\t//String offset = String.valueOf(startOffset)+\":\"+String.valueOf(len);\n\t\t\t\t\tMultimap catUpdate = catalogHash.get(entry.getKey());\n\t\t\t\t\tcatUpdate.put(String.valueOf(startOffset), String.valueOf(len));\n\t\t\t\t\tcatalogHash.put(entry.getKey(), catUpdate);\n\t\t\t\t\tstartOffset += len+2;\n\t\t\t\t\t\n\t\t\t\t}\n\t\t\t\telse{\n\t\t\t\t\tint len = (entry.getKey()+\":\"+entry.getValue()).length();\n\t\t\t\t\t//String offset = String.valueOf(startOffset)+\":\"+String.valueOf(len);\n\t\t\t\t\tMultimap catInsert = ArrayListMultimap.create();\n\t\t\t\t\tcatInsert.put(String.valueOf(startOffset), String.valueOf(len));\n\t\t\t\t\tcatalogHash.put(entry.getKey(), catInsert);//entry.getValue());\n\t\t\t\t\tstartOffset += len+2;\n\t\t\t\t\t\n\t\t\t\t}\t\t\t\t\t\t\t\t\t\t\n\t\t\t}\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\twriteInvertedIndex(catalogHash,\"catalogHash\");\n\t\t\tprintHashMapSI(allTermHash);\n\t\t\tprintHashMapSS(documentHash);\n\t\t\t\n\t\t\tlong InvIndstartOffset = 0;\n\t\t\t\n\t\t\t//write it to file\n \n\t\t\t//change the finalcatalogHash to the form termid:startoffset:length\n\t\t\tfor (Integer name: catalogHash.keySet()){\n\t String key = name.toString();\n\t String value = catalogHash.get(name).toString(); \n\t //System.out.println(key + \" \" + value); \n\t String finalTermIndex = genInvertedIndex(key, value);\n\t finalTermIndex = key+\":\"+finalTermIndex;\n\t int indexLength = finalTermIndex.length();\n\t \n\t \n\t PrintWriter writer = new PrintWriter(new BufferedWriter\n\t \t\t(new FileWriter(\"C:/Users/Naveen/Desktop/TestRuns/LastRun/InvertedIndex\", true)));\n\t writer.println(finalTermIndex);\n\t writer.close();\n\t \n\t //update the finalcatalogHash\n\t //Multimap catInsert = ArrayListMultimap.create();\n\t\t\t\t//catInsert.put(String.valueOf(InvIndstartOffset), String.valueOf(indexLength));\n\t\t\t\tfinalCatalogHash.put(name, String.valueOf(InvIndstartOffset)+\":\"+String.valueOf(indexLength));//entry.getValue());\n\t\t\t\tInvIndstartOffset += indexLength+2;\n\t \n\t\t\t}\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\tprintHashMapIS(finalCatalogHash);\n\t\t\t\n\t}","public static TreeMap calc_tf_idf( String \tbaseFolder,\n\t\t\t\t\t\t\t\t\t\t\t\t\t String baseFolder_out,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tString \tinputFile, \n\t\t\t\t\t\t\t\t\t\t\t\t\t\tString delimiter_for_inputFile,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tint \ttoken_index_having_text,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tString \toutFile,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tboolean is_do_stemming_on_word,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tboolean is_ignore_stop_words_all_together,\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tboolean isSOPprint\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t){\n\t\tTreeMap mapOut=new TreeMap();\n\t\ttry{\n\t\t\tString line=\"\";\n\t\t\tBufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream( inputFile) ));\n\t\t\t//boolean is_do_stemming_on_word=true;\n\t\t\tStemmer stemmer=new Stemmer(); String token=\"\";\n\t\t TreeMap mapVoc_Freq=new TreeMap();\n\t\t TreeMap> map_Word_UniqueDocumentIdHavingIT=new TreeMap>();\n\t\t TreeMap > map_DocID_wordFrequency=new TreeMap>();\n\t\t\t\tint lineNumber=0; int last_doc_id=-1;\n\t\t\t\n\t\t\tFileWriter writer_voc=new FileWriter(new File(baseFolder_out+\"unique_word_vocabulary.txt\"));\n\t\t\t\t\n\t\t\tFileWriter writer=new FileWriter(new File(outFile));\n\t\t\t// files for docID wordID tf-idf output\n\t\t\tFileWriter writer_no_stopword=new FileWriter(new File(outFile+\"_noStopWord.txt\"));\t\t\t\n\t\t\tFileWriter writer_wordID=new FileWriter(new File(outFile+\"_WORD_ID.txt\"));\n\t\t\tFileWriter writer_wordID_no_stopword=new FileWriter(new File(outFile+\"_noStopWord_WORD_ID.txt\"));\n\t\t\tFileWriter writer_word_stemmedWord=new FileWriter(new File(outFile+\"_Word_stemmedWord.txt\"));\n\t\t\t\n\t\t\t// files for docID wordID frequency output\n\t\t\tFileWriter writer2=new FileWriter(new File(outFile+\"_docWordID_freq2.txt\"));\n\t\t\tFileWriter writer2_no_stopword=new FileWriter(new File(outFile+\"_noStopWord2.txt\"));\n\t\t\tFileWriter writer2_wordID=new FileWriter(new File(outFile+\"_WORD_ID2.txt\"));\n\t\t\tFileWriter writer2_wordID_no_stopword=new FileWriter(new File(outFile+\"_noStopWord_WORD_ID2.txt\"));\n\t\t\tFileWriter writer2_word_stemmedWord=new FileWriter(new File(outFile+\"_Word_stemmedWord2.txt\"));\n\t\t\t\n\n\t\t\t\n\t\t\tFileWriter writer_debug=new FileWriter(new File(outFile+\"_DEBUG.txt\"));\n\t\t\tFileWriter writer_debug_2=new FileWriter(new File(outFile+\"_DEBUG_2.txt\"));\n\t\t\t\n\t\t\tTreeMap map_already_wrote=new TreeMap();\n\t\t\t//\n\t\t\twhile ((line = reader.readLine()) != null) {\n\t\t\t\tlineNumber++;\n\t\t\t\tSystem.out.println(\"lineNumber:\"+lineNumber);\n\t\t\t\t\n\t\t\t\t//DEBUG BREAK\n//\t\t\t\tif(lineNumber>100) break;\n\t\t\t\t\n\t\t\t\t//mapVoc_Freq=new TreeMap();\n\t\t\t\tint curr_doc_id=lineNumber;\n\t\t\t\tString [] token_= line.split(delimiter_for_inputFile);\n\t\t\t\t\n\t\t\t\t //clean\n\t\t\t\t token=token_[token_index_having_text-1].replace(\"\\\"\", \" \").replace(\"'\", \" \").replace(\",\", \" \").replace(\";\",\" \").replace(\".\", \" \")\n\t\t\t\t\t\t\t\t .replace(\"‘\", \" \").replace(\"“\", \" \").replace(\"–\", \" \").replace(\")\", \" \").replace(\"(\", \" \")\n\t\t\t\t\t\t\t\t .replace(\"-\", \" \").replace(\":\", \" \").replace(\"’\", \" \").replace(\"”\", \" \").replace(\"—\", \" \")\n\t\t\t\t\t\t\t\t .replace(\"#\", \" \").replace(\"%\", \" \")//.replace(\"$\", \" \")\n\t\t\t\t\t\t\t\t .replace(\"/\",\" \")\n\t\t\t\t\t\t\t\t .replace(\" \", \" \");\n\t\t\t\t \n\t\t\t\t token=token.toLowerCase();\n\n\t\t\t\t \n\t\t\t\t // \n\t\t\t\t String [] arr_token=token.split(\" \");\n\t\t\t\t int cnt=0;\n\t\t\t\t // \n\t\t\t\t while(cnt < arr_token.length){\n\t\t\t\t\t String temp= Ltrim.ltrim( arr_token[cnt]);\n\t\t\t\t\t \n\t\t\t\t\t // ignore stop words all together\n\t\t\t\t\t if(is_ignore_stop_words_all_together==true && Stopwords.is_stopword(temp)){\n\t\t\t\t\t\t cnt++;\n\t\t\t\t\t\t continue;\n\t\t\t\t\t }\n\t\t\t\t\t \n\t\t\t\t\t // do stemming\n\t\t\t\t\t if(is_do_stemming_on_word){\n\t\t\t\t\t\t String orig_temp=temp;\n\t\t\t\t\t\t //ltrim.ltrim(\n\t\t\t\t\t\t temp= stemmer.stem(temp);\n\t\t\t\t\t\t \n\t\t\t\t\t\t if(!map_already_wrote.containsKey(orig_temp)){\n\t\t\t\t\t\t\t writer_word_stemmedWord.append(orig_temp+\"!!!\"+temp +\"\\n\");\n\t\t\t\t\t\t\t writer_word_stemmedWord.flush();\n\t\t\t\t\t\t }\n\t\t\t\t\t\t \n\t\t\t\t\t\t map_already_wrote.put(orig_temp, -1);\n\t\t\t\t\t\t \n\t\t\t\t\t }\n\t\t\t\t\t else \n\t\t\t\t\t\t temp=temp;\n\n\t\t\t\t\t\t // \n\t\t\t\t\t\t if(!mapVoc_Freq.containsKey(temp)){\n\t\t\t\t\t\t\t //vocabulary term-freq\n\t\t\t\t\t\t\t mapVoc_Freq.put(temp, 1);\t\t\t\t\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t //word-document freq- unique number of documents this word occurs.\n\t\t\t\t\t\t\t List l=new ArrayList();\n\t\t\t\t\t\t\t l.add(curr_doc_id);\n\t\t\t\t\t\t\t map_Word_UniqueDocumentIdHavingIT.put(temp, l);\n\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t //doc-wise frequency\n\t\t\t\t\t\t\t if(!map_DocID_wordFrequency.containsKey(curr_doc_id)){\n\t\t\t\t\t\t\t\t TreeMap t2=new TreeMap();\n\t\t\t\t\t\t\t\t t2.put( temp, 1 ) ;\n\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2);\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t else{\n\t\t\t\t\t\t\t\t TreeMap t2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t\t if(!t2.containsKey(temp)){\n\t\t\t\t\t\t\t\t\t TreeMap t2_2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t\t t2_2.put( temp, 1 ) ;\n\t\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2_2);\n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t else{\n\t\t\t\t\t\t\t\t\t TreeMap t2_2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t\t int sz=t2.get(temp)+1;\n\t\t\t\t\t\t\t\t\t t2_2.put( temp, sz ) ;\n\t\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2_2);\n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t \n\t\t\t\t\t\t }\n\t\t\t\t\t\t else{\n\t\t\t\t\t\t\t int freq=mapVoc_Freq.get(temp)+1;\n\t\t\t\t\t\t\t //System.out.println(\"last_doc_id!=curr_doc_id->\"+last_doc_id+\"<-->\"+curr_doc_id );\n\t\t\t\t\t\t\t //vocabulary term-freq\n\t\t\t\t\t\t\t mapVoc_Freq.put(temp, freq);\n\t\t\t\t\t\t\t // word-document freq- unique number of documents this word occurs.\n\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t\t List uniq_doc=map_Word_UniqueDocumentIdHavingIT.get(temp);\n\t\t\t\t\t\t\t\t // if this docID not contained before in list\n\t\t\t\t\t\t\t\t if(!uniq_doc.contains(curr_doc_id)){\n\t\t\t\t\t\t\t\t\t uniq_doc.add(curr_doc_id );\n\t\t\t\t\t\t\t\t\t map_Word_UniqueDocumentIdHavingIT.put(temp, uniq_doc);\n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t\t //doc-wise frequency\n\t\t\t\t\t\t\t\t if(!map_DocID_wordFrequency.containsKey(curr_doc_id)){\n\t\t\t\t\t\t\t\t\t TreeMap t2=new TreeMap();\n\t\t\t\t\t\t\t\t\t t2.put( temp, 1 ) ;\n\t\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2);\n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t else{\n\t\t\t\t\t\t\t\t\t TreeMap t2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t\t\t if(!t2.containsKey(temp)){\n\t\t\t\t\t\t\t\t\t\t TreeMap t2_2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t\t\t t2_2.put( temp, 1 ) ;\n\t\t\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2_2);\n\t\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t\t else{\n\t\t\t\t\t\t\t\t\t\t TreeMap t2_2=map_DocID_wordFrequency.get(curr_doc_id);\n\t\t\t\t\t\t\t\t\t\t int sz=t2.get(temp)+1;\n\t\t\t\t\t\t\t\t\t\t t2_2.put( temp, sz ) ;\n\t\t\t\t\t\t\t\t\t\t map_DocID_wordFrequency.put(curr_doc_id, t2_2);\n\t\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\t \n\t\t\t\t\t\t }\n\t\t\t\t\tcnt++;\n\t\t\t\t }\n\t\t\t\t \n\t\t\t\t if(isSOPprint){\n\t\t\t\t\t System.out.println(\"doc:\"+curr_doc_id+\" token-freq:\"+mapVoc_Freq.size()+\" token-doc.freq:\"+map_Word_UniqueDocumentIdHavingIT.size());\n\t\t\t\t }\n\t\t\t\t //\n\t\t\t\t last_doc_id=curr_doc_id;\n\t\t\t}\n\t\t\tSystem.out.println(\" token-freq:\"+mapVoc_Freq.size()+\" token-doc.freq:\"+map_Word_UniqueDocumentIdHavingIT.size());\n\t\t\tint uniq_word_id=1;\n\t\t\tTreeMap mapVocabulary_word_wordID= new TreeMap();\n\t\t\t// create uniq_word_id for each word in vocabulary\n\t\t\tfor(String word:mapVoc_Freq.keySet()){\n\t\t\t\tmapVocabulary_word_wordID.put(word, uniq_word_id);\n\t\t\t\t\n\t\t\t\twriter_voc.append(word+\"!!!\"+uniq_word_id+\"\\n\");\n\t\t\t\twriter_voc.flush();\n\t\t\t\t \n\t\t\t\tuniq_word_id++;\n\t\t\t}\n\t\t\tSystem.out.println(\"step 1: running docid-wordid-tf-IDF\");\n\t\t\t//step 1: calculate tf-idf (DONT COMMENT BELOW)\n\t\t\tfor(int docID:map_DocID_wordFrequency.keySet()){\n\t\t\t\t//System.out.println(\"docID:\"+docID+ \" size:\" +map_DocID_wordFrequency.get(docID).size()); //\t+\" word-freq:\"+map_DocID_wordFrequency.get(docID));\n\t\t\t\twriter_debug.append(\"docID:\"+docID+ \" size:\" +map_DocID_wordFrequency.get(docID).size()+\" word-freq:\"+map_DocID_wordFrequency.get(docID)+\"\\n\");\n\t\t\t\twriter_debug.flush();\n\t\t\t\tdouble tf_idf=0.0;\n\t\t\t\t//Iterate each word in current document\n\t\t\t\tfor(String word:map_DocID_wordFrequency.get(docID).keySet() ){\n\t\t\t\t\t//\n\t\t\t\t\tif(mapVoc_Freq.containsKey(word )){\n\t\t\t\t\t\t\n\t\t\t\t\t\t//System.out.println(\"param1,2:\"+map_DocID_wordFrequency.get(docID).get(word) +\" \"+map_Word_UniqueDocumentIdHavingIT.get(word).size() );\n\t\t\t\t\t\t// tf-idf\n\t\t\t\t\t\ttf_idf=map_DocID_wordFrequency.get(docID).get(word) * Math.log10( map_DocID_wordFrequency.size() / map_Word_UniqueDocumentIdHavingIT.get(word).size() );\n\t\t\t\t\t\t//System.out.println();\n\t\t\t\t\t\twriter.append( docID+\"!!!\"+word+\"!!!\"+tf_idf+\"\\n\");\n\t\t\t\t\t\twriter.flush();\n\t\t\t\t\t\t\n\t\t\t\t\t\twriter_wordID.append( docID+\"!!!\"+mapVocabulary_word_wordID.get(word)+\"!!!\"+tf_idf+\"\\n\");\n\t\t\t\t\t\twriter_wordID.flush();\n\t\t\t\t\t\t\n\t\t\t\t\t\t// \n\t\t\t\t\t\tif(!Stopwords.is_stopword(word.toLowerCase())){\n\t\t\t\t\t\t\twriter_no_stopword.append(docID+\"!!!\"+word+\"!!!\"+tf_idf+\"\\n\");\n\t\t\t\t\t\t\twriter_no_stopword.flush();\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\twriter_wordID_no_stopword.append(docID+\"!!!\"+ mapVocabulary_word_wordID.get(word) +\"!!!\"+tf_idf+\"\\n\");\n\t\t\t\t\t\t\twriter_wordID_no_stopword.flush();\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\telse{\n\t\t\t\t\t\twriter_debug_2.append( \"(not exist in vocab) word->\"+word+\" for doc_id->\"+docID+\"\\n\");\n\t\t\t\t\t\twriter_debug_2.flush();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} //for(int docID:map_DocID_wordFrequency.keySet()){\n\t\t\t\n\t\t\tSystem.out.println(\"step 2: running docid-wordid-frquency\");\n\t\t\t//step 2: (DOC-WORDID AND FREQUENCY)another output - writing \n\t\t\tfor(int docID:map_DocID_wordFrequency.keySet()){\n\t\t\t\t\n\t\t\t\tSystem.out.println(\"2.docID:\"+docID+ \" size:\" +map_DocID_wordFrequency.get(docID).size()); //\t+\" word-freq:\"+map_DocID_wordFrequency.get(docID));\n\t\t\t\t//writer_debug.append(\"docID:\"+docID+ \" size:\" +map_DocID_wordFrequency.get(docID).size()+\" word-freq:\"+map_DocID_wordFrequency.get(docID)+\"\\n\");\n\t\t\t\t//writer_debug.flush();\n\t\t\t\tint frequency=0;\n\t\t\t\t//Iterate each word in current document\n\t\t\t\tfor(String word:map_DocID_wordFrequency.get(docID).keySet() ){\n\t\t\t\t\t//\n\t\t\t\t\tif(mapVoc_Freq.containsKey(word )){\n\t\t\t\t\t\t\n\t\t\t\t\t\t// System.out.println(\"param1,2:\"+map_DocID_wordFrequency.get(docID).get(word) +\" \"+map_Word_UniqueDocumentIdHavingIT.get(word).size() );\n\t\t\t\t\t\t// frequency\n\t\t\t\t\t\tfrequency=map_DocID_wordFrequency.get(docID).get(word);\n\t\t\t\t\t\t//System.out.println();\n\t\t\t\t\t\twriter2.append( docID+\"!!!\"+word+\"!!!\"+frequency+\"\\n\");\n\t\t\t\t\t\twriter2.flush();\n\t\t\t\t\t\t\n\t\t\t\t\t\twriter2_wordID.append( docID+\"!!!\"+mapVocabulary_word_wordID.get(word)+\"!!!\"+frequency+\"\\n\");\n\t\t\t\t\t\twriter2_wordID.flush();\n\t\t\t\t\t\t \n\t\t\t\t\t\t// \n\t\t\t\t\t\tif(!Stopwords.is_stopword(word.toLowerCase())){\n\t\t\t\t\t\t\twriter2_no_stopword.append(docID+\"!!!\"+word+\"!!!\"+frequency+\"\\n\");\n\t\t\t\t\t\t\twriter2_no_stopword.flush();\n\t\t\t\t\t\t\t//\n\t\t\t\t\t\t\twriter2_wordID_no_stopword.append(docID+\"!!!\"+ mapVocabulary_word_wordID.get(word) +\"!!!\"+frequency+\"\\n\");\n\t\t\t\t\t\t\twriter2_wordID_no_stopword.flush();\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\telse{\n\t\t\t\t\t\twriter_debug_2.append( \"(not exist in vocab) word->\"+word+\" for doc_id->\"+docID+\"\\n\");\n\t\t\t\t\t\twriter_debug_2.flush();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} //for(int docID:map_DocID_wordFrequency.keySet()){\n\n\t\t\tSystem.out.println(\"********************************************\");\n\t\t\tSystem.out.println(\"File holding the not found words in vocabulary: \"+\"outFile+\\\"_DEBUG_2.txt\\\"\");\n\t\t\tSystem.out.println(\"Doc-wise word freq: \"+\"outFile+\\\"_DEBUG.txt\\\"\");\n\t\t\tSystem.out.println(\"******Below files are docId-wordID-tfIDF\");\n\t\t\tSystem.out.println(\"with Word->\"+outFile);\n\t\t\tSystem.out.println(\"with Word(no stopword)->\"+outFile+\"_noStopWord.txt\");\n\t\t\tSystem.out.println(\"with WordID->\"+outFile+\"_WORD_ID.txt\");\n\t\t\tSystem.out.println(\"with WordID(no stopword)->\"+outFile+\"_noStopWord_WORD_ID.txt\");\n\t\t\tSystem.out.println(\"VOC FILE ->\"+baseFolder+\"unique_word_vocabulary.txt\");\n\t\t\t//**********/\n\t\t\tSystem.out.println(\"***********Below files are docId-wordID-frequency (file ends with \\\"format2.txt\\\"\");\n\t\t\tSystem.out.println( \"\"+outFile+\"_docWordID_freq2.txt\");\n\t\t\tSystem.out.println( \"\"+outFile+\"_noStopWord2.txt\");\n\t\t\tSystem.out.println( \"\"+outFile+\"_WORD_ID2.txt\");\n\t\t\tSystem.out.println( \"\"+outFile+\"_noStopWord_WORD_ID2.txt\");\n\t\t\tSystem.out.println( \"\"+outFile+\"_Word_stemmedWord2.txt\");\n\t\t\t \n\t\t\tmapOut.put(-99, outFile+\"_noStopWord_WORD_ID.txt\");\n\t\t\t//maximum word id\n\t\t\tmapOut.put(1, String.valueOf( uniq_word_id) );\n\t\t}\n\t\tcatch(Exception e){\n\t\t\te.printStackTrace();\n\t\t}\n\t\treturn mapOut;\n\t}","public static void DocumentFrequencies() throws FileNotFoundException {\n for (Entry> entry : dictionary.entrySet()) {\n List termfrequency = new ArrayList<>();\n\n termfrequency = entry.getValue();\t// getting each word's termfrequency list\n int i = 0;\n termfrequency.add(0); \t\t\t//maintaining documentfrequency at the 57th index\n Integer documentFrequency = termfrequency.get(totaldocument+1);\n while(i<56) { //iterate 0 to 55 all speeches term frequency\n if(termfrequency.get(i)>0) {\t\t//increment document frequency of that word if termfrequency is greater than 0.0\n documentFrequency++;\t\t\t//increment document frequency\n }\n i++;\t\t//increment index\n }\n termfrequency.set(57, documentFrequency);\t//re-set the documentfrequency and save the current maintained document frequency from 0 to calculated value\n dictionary.put(entry.getKey(), termfrequency);\t\t// place the incremented final value of that word back to the same list in dictionary hashmap\n }\n //save();\n }","public void createIDMap()\n {\n IDMap = new HashMap<>();\n idFile.open(\"idpassword.txt\");\n String line = idFile.getNextLine();\n\n\n\n while(line!=null) {\n String[] fields = line.split(\",\");\n IDMap.put(fields[0], fields[1]);\n\n line = idFile.getNextLine();\n\n }\n\n }","public void indexDocument(String documentName, ArrayList documentTokens) {\n for (String token : documentTokens) {\n if (!this.index.containsKey(token)) {\n // Create a key with that token\n this.index.put(token, new HashMap<>());\n }\n\n // Get the HashMap associated with that term\n HashMap term = this.index.get(token);\n\n // Check if term has a posting for the document\n if (term.containsKey(documentName)) {\n // Increase its occurrence by 1\n int occurrences = term.get(documentName);\n term.put(documentName, ++occurrences);\n } else {\n // Create a new posting for the term\n term.put(documentName, 1);\n }\n }\n }","public void buildWordFileMap(){\n hashWords.clear();\n DirectoryResource dr = new DirectoryResource();\n for (File f : dr.selectedFiles()){ //for all the files selected make the hashWords hashmap\n addWordsFromFile(f);\n }\n \n }","private void createTokenIndex(){\n\t\tLinkedList tokens = new LinkedList<>(tokenDict.keySet());\n\t\tArrayList> vals = new ArrayList<>(tokenDict.values());\n\t\tint k = 8;\n\n\t\tKFront kf = new KFront(true);\n\t\tkf.createKFront(k, tokens);\n\n\t\tTokensIndex tIdx = new TokensIndex(k, this.dir);\n\t\ttIdx.insertData(kf.getTable(), vals, kf.getConcatString());\n\n\t\tsaveToDir(TOKEN_INDEX_FILE, tIdx);\n\t}","private static Positional_inverted_index posindexCorpus(DocumentCorpus corpus) throws ClassNotFoundException, InstantiationException, IllegalAccessException, FileNotFoundException, IOException {\n\n NewTokenProcessor processor = new NewTokenProcessor();\n Iterable docs = corpus.getDocuments(); //call registerFileDocumentFactory first?\n\n List Doc_length = new ArrayList<>();\n Positional_inverted_index index = new Positional_inverted_index();\n\n double token_count = 0;\n\n // Iterate through the documents, and:\n for (Document d : docs) {\n //File f = new File(path + \"\\\\\" + d.getTitle());\n File f = new File(path + \"\\\\\" + d.getFileName().toString());\n double Filesize = f.length();\n //edited by bhavya\n double doc_weight = 0; //first entry in docweights.bin\n double doc_tokens = 0;\n double doc_length = 0;\n HashMap tftd = new HashMap<>();\n // Tokenize the document's content by constructing an EnglishTokenStream around the document's content.\n Reader reader = d.getContent();\n EnglishTokenStream stream = new EnglishTokenStream(reader); //can access tokens through this stream\n N++;\n // Iterate through the tokens in the document, processing them using a BasicTokenProcessor,\n //\t\tand adding them to the HashSet vocabulary.\n Iterable tokens = stream.getTokens();\n int i = 0;\n\n for (String token : tokens) {\n\n //adding token in index\n List word = new ArrayList();\n word = processor.processToken(token);\n //System.out.println(word.get(0));\n if (word.get(0).matches(\"\")) {\n continue;\n } else {\n\n index.addTerm(word.get(0), i, d.getId());\n\n }\n i = i + 1;\n\n //we check if token already exists in hashmap or not. \n //if it exists, increase its freq by 1 else make a new entry.\n if (tftd.containsKey(word.get(0))) {\n doc_tokens++;\n int count = tftd.get(word.get(0));\n tftd.replace(word.get(0), count + 1);\n } else {\n doc_tokens++;\n// token_count++; //gives total number of tokens.\n tftd.put(word.get(0), 1);\n }\n\n }\n double length = 0;\n double wdt = 0;\n\n double total_tftd = 0;\n for (Map.Entry entry : tftd.entrySet()) {\n\n wdt = 1 + log(entry.getValue());\n\n length = length + pow(wdt, 2);\n total_tftd = total_tftd + entry.getValue();\n }\n token_count = token_count + doc_tokens;\n doc_weight = pow(length, 0.5);\n double avg_tftd = total_tftd / (double) tftd.size();\n\n Doc_length.add(doc_weight);\n Doc_length.add(avg_tftd);\n Doc_length.add(doc_tokens);\n Doc_length.add(Filesize);\n }\n Doc_length.add(token_count / N);\n\n DiskIndexWriter d = new DiskIndexWriter();\n d.write_doc(path, Doc_length);\n\n return index;\n }","static void idlize() throws IOException {\r\n\t\t/**give mid who has name a id, for other mid, keep using mid to identify them*/\r\n\t\t//\t\tHashMap namedmid2name = new HashMap(20000000);\r\n\t\t//\t\tHashMap relationname2id = new HashMap(1000000);\r\n\t\t//\t\tDelimitedWriter dw = new DelimitedWriter(Main.dir + \"/visible_idize\");\r\n\t\t//\t\tDelimitedWriter dw_debug = new DelimitedWriter(Main.dir + \"/visible_debug\");\r\n\t\t//\t\t{\r\n\t\t//\t\t\tDelimitedReader dr = new DelimitedReader(Main.file_fbenglishname);\r\n\t\t//\t\t\tString[] l;\r\n\t\t//\t\t\twhile ((l = dr.read()) != null) {\r\n\t\t//\t\t\t\tnamedmid2name.put(l[0], namedmid2name.size());\r\n\t\t//\t\t\t}\r\n\t\t//\t\t\tD.p(\"load mid2name finished\");\r\n\t\t//\t\t\tdr.close();\r\n\t\t//\t\t}\r\n\t\t//\t\t{\r\n\t\t//\t\t\tDelimitedReader dr = new DelimitedReader(Main.file_visible_str);\r\n\t\t//\t\t\tString[] l;\r\n\t\t//\t\t\twhile ((l = dr.read()) != null) {\r\n\t\t//\t\t\t\tString mid = l[0];\r\n\t\t//\t\t\t\tInteger gid = namedmid2name.get(mid);\r\n\t\t//\t\t\t\tif (gid == null) {\r\n\t\t//\t\t\t\t\tdw_debug.write(l);\r\n\t\t//\t\t\t\t\tcontinue;\r\n\t\t//\t\t\t\t}\r\n\t\t//\t\t\t\tString relationname = l[2];\r\n\t\t//\t\t\t\tif (!relationname2id.containsKey(relationname)) {\r\n\t\t//\t\t\t\t\trelationname2id.put(relationname, relationname2id.size());\r\n\t\t//\t\t\t\t}\r\n\t\t//\t\t\t\tint relid = relationname2id.get(relationname);\r\n\t\t//\t\t\t\tdw.write(l[1], gid, relid, l[3]);\r\n\t\t//\t\t\t}\r\n\t\t//\t\t\tdr.close();\r\n\t\t//\t\t}\r\n\t\t//\t\t{\r\n\t\t//\t\t\tDelimitedReader dr = new DelimitedReader(Main.file_visible_str);\r\n\t\t//\t\t\tString[] l;\r\n\t\t//\t\t\twhile ((l = dr.read()) != null) {\r\n\t\t//\t\t\t\tString mid1 = l[0];\r\n\t\t//\t\t\t\tString mid2 = l[3];\r\n\t\t//\t\t\t\tInteger gid1 = namedmid2name.get(mid1);\r\n\t\t//\t\t\t\tInteger gid2 = namedmid2name.get(mid2);\r\n\t\t//\t\t\t\tif (gid1 == null || gid2 == null) {\r\n\t\t//\t\t\t\t\tdw_debug.write(l);\r\n\t\t//\t\t\t\t\tcontinue;\r\n\t\t//\t\t\t\t}\r\n\t\t//\t\t\t\tString relationname = l[2];\r\n\t\t//\t\t\t\tif (!relationname2id.containsKey(relationname)) {\r\n\t\t//\t\t\t\t\trelationname2id.put(relationname, relationname2id.size());\r\n\t\t//\t\t\t\t}\r\n\t\t//\t\t\t\tint relid = relationname2id.get(relationname);\r\n\t\t//\t\t\t\tdw.write(l[1], gid1, relid, gid2, l[3]);\r\n\t\t//\t\t\t}\r\n\t\t//\t\t\tdr.close();\r\n\t\t//\t\t}\r\n\t\t//\t\tdw.close();\r\n\t\t//\t\t{\r\n\t\t//\t\t\tDelimitedWriter dwrel = new DelimitedWriter(Main.dir + \"/visible_relations.temp\");\r\n\t\t//\t\t\tfor (Entry e : relationname2id.entrySet()) {\r\n\t\t//\t\t\t\tdwrel.write(e.getValue(), e.getKey());\r\n\t\t//\t\t\t}\r\n\t\t//\t\t\tdwrel.close();\r\n\t\t//\t\t\tSort.sort(Main.dir + \"/visible_relations.temp\", Main.dir + \"/visible_relations\", Main.dir,\r\n\t\t//\t\t\t\t\tnew Comparator() {\r\n\t\t//\t\t\t\t\t\t@Override\r\n\t\t//\t\t\t\t\t\tpublic int compare(String[] o1, String[] o2) {\r\n\t\t//\t\t\t\t\t\t\t// TODO Auto-generated method stub\r\n\t\t//\t\t\t\t\t\t\treturn Integer.parseInt(o1[0]) - Integer.parseInt(o2[0]);\r\n\t\t//\t\t\t\t\t\t}\r\n\t\t//\r\n\t\t//\t\t\t\t\t});\r\n\t\t//\t\t}\r\n\t\t//\t\t{\r\n\t\t//\t\t\tDelimitedWriter dwmid = new DelimitedWriter(Main.dir + \"/visible_mid2gid.temp\");\r\n\t\t//\t\t\tfor (Entry e : namedmid2name.entrySet()) {\r\n\t\t//\t\t\t\tdwmid.write(e.getValue(), e.getKey());\r\n\t\t//\t\t\t}\r\n\t\t//\t\t\tdwmid.close();\r\n\t\t//\t\t\tSort.sort(Main.dir + \"/visible_mid2gid.temp\", Main.dir + \"/visible_mid2gid\", Main.dir,\r\n\t\t//\t\t\t\t\tnew Comparator() {\r\n\t\t//\t\t\t\t\t\t@Override\r\n\t\t//\t\t\t\t\t\tpublic int compare(String[] o1, String[] o2) {\r\n\t\t//\t\t\t\t\t\t\t// TODO Auto-generated method stub\r\n\t\t//\t\t\t\t\t\t\treturn Integer.parseInt(o1[0]) - Integer.parseInt(o2[0]);\r\n\t\t//\t\t\t\t\t\t}\r\n\t\t//\r\n\t\t//\t\t\t\t\t});\r\n\t\t//\t\t}\r\n\t}","public void map()\n\t{\n\t // key is the documentId\n\t\t// value is the url\n\t\t//fetch the document using the documentId\n\t\t\n\t}","private void saveMap() {\r\n new Thread(() -> {\r\n try {\r\n FileOutputStream f = new FileOutputStream(this.save_file);\r\n ObjectOutputStream S = new ObjectOutputStream(f);\r\n S.writeObject(this.music_map);\r\n S.close();\r\n f.close();\r\n if (!this.save_file.setLastModified(this.music_root.lastModified())) {\r\n throw new IllegalStateException(\"Impossibile aggiornare il file dizionario\");\r\n }\r\n } catch (IOException e) {\r\n e.printStackTrace();\r\n }\r\n }).start();\r\n }","private static void collectVariables(Document document){\n //collecting all the nodes inside a list\n nodeList = document.selectNodes(NOTES);\n\n //initialising the lists\n entriesList = new ArrayList<>();\n locationsList = new ArrayList<>();\n attachmentList = new ArrayList<>();\n tagsForEntryList = new ArrayList<>();\n\n //hashSet for handling the duplicate fileNames\n fileNameSet = new LinkedHashSet<>();\n\n //linkedHashMap for storing the uid for each tag\n uidForEachTag = new LinkedHashMap<>();\n uidForEachLocation = new LinkedHashMap<>();\n\n //id set for storing unique location id\n locationsIdSet = new LinkedHashSet<>();\n\n Tags tags;\n Location location;\n Entry entry;\n Attachment attachment;\n\n byte[] decoded = null;\n\n //looping through the list\n for(Node node : nodeList){\n\n String title = \"\";\n String parsedHtml = \"\";\n String formattedDate = \"\";\n String location_uid = \"\";\n String mime = \"\";\n String fileName = \"\";\n String attachment_uid = null;\n String entry_uid = \"\";\n String type = \"photo\";\n String baseEncoding;\n String tag_uid = \"\";\n\n //get all tags including duplicates\n if( node.selectSingleNode(TAG) !=null) {\n List evernote_tags = node.selectNodes(TAG);\n for (Node evenote_tag : evernote_tags) {\n //generate unique id for the tag and map it.\n //if the name id pair does not exist\n if(!uidForEachTag.containsKey(evenote_tag.getText())) {\n uidForEachTag.put(evenote_tag.getText(), Entry.generateRandomUid());\n }\n //create new diaro.Tags Object\n tags = new Tags(uidForEachTag.get(evenote_tag.getText()),evenote_tag.getText());\n tagsForEntryList.add(tags);\n }\n }\n\n //get all Locations\n // using diaro.Entry.concatLatLng to add title as { attachmentsForEachEntry = node.selectNodes(RESOURCE);\n //loop through all the attachments for a single note/entry\n for (Node attachmentForeach : attachmentsForEachEntry) {\n try {\n mime = attachmentForeach.selectSingleNode(MIME).getText();\n\n }catch( NullPointerException e){\n e.printStackTrace();\n }\n // check for a valid attachment\n if(checkForImageMime(mime)) {\n try {\n fileName = attachmentForeach.selectSingleNode(RESOURCE_ATTRIBUTE_FILENAME).getText();\n attachment_uid = Entry.generateRandomUid();\n entry_uid = entry.uid;\n baseEncoding = attachmentForeach.selectSingleNode(DATA).getText();\n //----- please do a check for valid Base64--\n decoded = Base64.getMimeDecoder().decode(baseEncoding);\n // assign primary_photo uid to entry\n entry.primary_photo_uid = attachment_uid;\n }catch(IllegalArgumentException | NullPointerException e){\n e.printStackTrace();\n }\n // check if the fileName already exists\n // if true generate a new fileName to prevent duplicates\n if(fileNameSet.add(fileName)){\n fileNameSet.add(fileName);\n attachment = new Attachment(attachment_uid, entry_uid, type,fileName,decoded);\n }else{\n String newFileName = ImportUtils.generateNewFileName(fileName);\n fileNameSet.add(newFileName);\n attachment = new Attachment(attachment_uid, entry_uid, type,newFileName,decoded);\n }\n attachmentList.add(attachment);\n }\n }\n }\n }\n\n }","private HashMap> convertIndexToMap(IndexReader reader) throws IOException{\n\t\t HashMap> hmap = new HashMap>();\n\t\t HashSet docIdSet;\n\t\t \n\t\t for(int i=0; i();\n\t \t\t docIdSet.add(doc.get(\"url\"));\n\t \t\t hmap.put(strTerm, docIdSet);\n\t \t }\n\t }\n\t }\n\t\t }\n\t\t \n\t\t return hmap;\n\t}","public void IndexADocument(String docno, String content) throws IOException {\n\t\tthis.idWriter.write(docID+\":\"+docno);\n\t\tthis.idWriter.newLine();\n\t\tthis.idWriter.flush();\n\t\tString[] words = content.split(\" \");\n\t\tHashMap count = new HashMap<>();\n\t\tfor(String s:words){\n\t\t\tcount.put(s,count.getOrDefault(s,0)+1);\n\t\t}\n\t\tfor(String key: count.keySet()){\n\t\t\tif(this.map.containsKey(key)){\n\t\t\t\tthis.map.get(key).append(docID).append(\":\").append(count.get(key)).append(\",\");\n\t\t\t}else {\n\t\t\t\tStringBuilder sb = new StringBuilder();\n\t\t\t\tthis.map.put(key, sb.append(docID).append(\":\").append(count.get(key)).append(\",\"));\n\t\t\t}\n\t\t}\n\t\tdocID++;\n\t}","public void writeDocumentForA(String filename, String path) throws Exception\r\n\t{\n\t\tFile folder = new File(path);\r\n\t\tFile[] listOfFiles = folder.listFiles();\r\n\t \r\n\t \r\n\t \tFileWriter fwText;\r\n\t\tBufferedWriter bwText;\r\n\t\t\r\n\t\tfwText = new FileWriter(\"C:/Users/jipeng/Desktop/Qiang/updateSum/TAC2008/Parag/\"+ filename+\"/\" +\"A.txt\");\r\n\t\tbwText = new BufferedWriter(fwText);\r\n\t\t\r\n\t \tfor ( int i=0; i> sentences = MaxentTagger.tokenizeText(new BufferedReader(new FileReader(\"C:/pun.txt\")));\r\n\t\t\t\r\n\t\t\t//System.out.println(text);\r\n\t\t\tArrayList textList = new ArrayList();\r\n\t\t\t\r\n\t\t\tfor (List sentence : sentences)\r\n\t\t\t {\r\n\t\t\t ArrayList tSentence = tagger.tagSentence(sentence);\r\n\t\t\t \r\n\t\t\t for(int j=0; j2 )\r\n\t\t\t\t \t{\r\n\t\t\t \t\t\t if (!m_EnStopwords.isStopword(token)) \r\n\t\t\t \t\t\t {\r\n\t\t\t \t\t\t\t\r\n\t\t\t\t\t\t\t\t if (word2IdHash.get(token)==null)\r\n\t\t\t\t\t\t\t\t {\r\n\t\t\t\t\t\t\t\t\t textList.add(id);\r\n\t\t\t\t\t\t\t\t\t // bwText.write(String.valueOf(id)+ \" \");\r\n\t\t\t\t\t\t\t\t\t\r\n\t\t\t\t\t\t\t\t\t word2IdHash.put(token, id);\r\n\t\t\t\t\t\t\t\t\t \r\n\t\t\t\t\t\t\t\t\t allWordsArr.add(token);\r\n\t\t\t\t\t\t\t\t\t \r\n\t\t\t\t\t\t\t\t\t id++;\r\n\t\t\t\t\t\t\t\t } else\r\n\t\t\t\t\t\t\t\t {\r\n\t\t\t\t\t\t\t\t \tint wid=(Integer)word2IdHash.get(token);\r\n\t\t\t\t\t\t\t\t \tif(!textList.contains(wid))\r\n\t\t\t\t\t\t\t\t \t\ttextList.add(wid);\r\n\t\t\t\t\t\t\t\t \t//bwText.write(String.valueOf(wid)+ \" \");\r\n\t\t\t\t\t\t\t\t }\r\n\t\t\t\t\t\t\t\t \t\r\n\t\t\t\t\t\t\t\t }\r\n\t\t\t\t\t\t\t\t \r\n\t\t\t\t\t \t}\r\n\t\t\t \t }\r\n\t\t\t }\r\n\t\t\tCollections.sort(textList);\r\n\t\t \r\n\t\t\tString text2 = valueFromList(textList);\r\n\t\t bwText.write(text2);\r\n\t\t //System.out.println(text2);\r\n\t\t bwText.newLine();\r\n\t\t textList.clear();\r\n\t\t \r\n\t \t}\r\n\t \tbwText.close();\r\n\t fwText.close();\r\n\t}","public static void pageRankmain() {\n\t\t\t\n\t\t\tstopWordStore();\n\t\t\t//File[] file_read= dir.listFiles();\n\t\t\t//textProcessor(file_read);// Will be called from LinkCrawler\n\t\t\t//queryProcess();\n\t\t\t//System.out.println(\"docsave \"+ docsave);\n\t\t\t/*for ( Map.Entry> entry : docsave.entrySet()) {\n\t\t\t String key = entry.getKey();\n\t\t\t List values = entry.getValue();\n\t\t\t System.out.print(\"Key = \" + key);\n\t\t\t System.out.println(\" , Values = \"+ values);\n\t\t\t}*/\n\t\t\t//########## RESPOINSIBLE FOR CREATING INVERTED INDEX OF TERMS ##########\n\t\t\tfor(int i=0;i nestMap = new HashMap();\n\t\t\t\tfor ( Map.Entry> entry : docsave.entrySet()) {\n\t\t\t\t String keyMain = entry.getKey();\n\t\t\t\t List values = entry.getValue();\n\t\t\t\t if(values.contains(vocabulary.get(i)))\n\t\t\t\t \t{\n\t\t\t\t \tentryDf.put(vocabulary.get(i), count);//entryDf stores documents frequency of vocabulary word \\\\it increase the count value for specific key\n\t\t\t\t \tcount++;\n\t\t\t\t \t}\n\t\t\t\t \n\t\t\t\t nestMap.put(keyMain, Collections.frequency(values,vocabulary.get(i)));\n\t\t\t \t\n\t\t\t \t//System.out.println(\"VOC \"+ vocabulary.get(i)+ \" KeyMain \" +keyMain+ \" \"+ Collections.frequency(values,vocabulary.get(i)));\n\t\t\t\t\t}\n\t\t\t\t\ttfList.put(vocabulary.get(i), nestMap);\n\t\t\t}\n\t\t\t//########## RESPOINSIBLE FOR CREATING A MAP \"storeIdf\" TO STORE IDF VALUES OF TERMS ##########\n\t\t\tfor ( Map.Entry endf : entryDf.entrySet()) {\n\t\t\t\tString keydf = endf.getKey();\n\t\t\t\tint valdf = endf.getValue();\n\t\t\t\t//System.out.print(\"Key = \" + \"'\"+keydf+ \"'\");\n\t\t\t //System.out.print(\" , Values = \"+ valdf);\n\t\t\t double Hudai = (double) (docsave.size())/valdf;\n\t\t\t //System.out.println(\"docsave size \"+docsave.size()+ \" valdf \"+ valdf + \" Hudai \"+ Hudai+ \" log Value1 \"+ Math.log(Hudai)+ \" log Value2 \"+ Math.log(2));\n\t\t\t double idf= Math.log(Hudai)/Math.log(2);\n\t\t\t storeIdf.put(keydf, idf);\n\t\t\t //System.out.print(\" idf-> \"+ idf);\n\t\t\t //System.out.println();\n\t\t\t} \n\t\t\t\n\t\t\t//############ Just for Printing ##########NO WORK HERE########\n\t\t\tfor (Map.Entry> tokTf : tfList.entrySet()) {\n\t\t\t\tString keyTf = tokTf.getKey();\n\t\t\t\tMap valTF = tokTf.getValue();\n\t\t\t\tSystem.out.println(\"Inverted Indexing by Key Word = \" + \"'\"+keyTf+ \"'\");\n\t\t\t\tfor (Map.Entry nesTf : valTF.entrySet()) {\n\t\t\t\t\tString keyTF = nesTf.getKey();\n\t\t\t\t\tInteger valTf = nesTf.getValue();\n\t\t\t\t\tSystem.out.print(\" Document Consists This Key Word = \" + \"'\"+ keyTF+ \"'\");\n\t\t\t\t\tSystem.out.println(\" , Term Frequencies in This Doc = \"+ valTf);\n\t\t\t\t} \n\t\t\t}\n\t\t\t//########### FOR CALCULATING DOCUMENT LENTH #############//\n\t\t\tfor ( Map.Entry> entry_new : docsave.entrySet()) // Iterating Number of Documents\n\t\t\t{\n\t\t\t\tString keyMain_new = entry_new.getKey();\n\t\t\t\t//int countStop=0;\n\t\t\t\tdouble sum=0;\n\t\t\t\t for(Map.Entry> tokTf_new : tfList.entrySet()) // Iterating through the vocabulary\n\t\t\t\t { \n\t\t\t\t\t Map valTF_new = tokTf_new.getValue();\n\t\t\t\t\t for (Map.Entry nesTf_new : valTF_new.entrySet()) // Iterating Through the Documents\n\t\t\t\t\t {\n\t\t\t\t\t\t if(keyMain_new.equals(nesTf_new.getKey())) // Only doc name EQUAL with docsave name can enter here\n\t\t\t\t\t\t {\n\t\t\t\t\t\t\t double val = nesTf_new.getValue()* (Double) storeIdf.get(tokTf_new.getKey());\n\t\t\t\t\t\t\t sum = sum+ Math.pow(val, 2);\n\t\t\t\t\t\t }\n\t\t\t\t\t }\n\t\t\t\t\t \n\t\t\t\t\t //countStop++;\n\t\t\t\t }\n\t\t\t\t docLength.put(keyMain_new, Math.sqrt(sum));\n\t\t\t\t sum=0;\n\t\t\t}\n\t\t\t\n\t\t\t\n\t\t\tSystem.out.println(\"Document Length \"+ docLength);\n\t\t\t//System.out.println(\"tfList \"+tfList);\n\t\t\t\n\t\t\t //########### FOR CALCULATING QUERY LENTH #############///\n\t\t\t\tdouble qrySum=0;\n\t\t\t\t for(String qryTerm: queryList) // Iterating through the vocabulary\n\t\t\t\t {\n\t\t\t\t\t//entryQf.put(qryTerm, Collections.frequency(queryList,qryTerm));// VUl ase\n\t\t\t\t\t \n\t\t\t\t\t\t if(storeIdf.get(qryTerm) != null) \n\t\t\t\t\t\t {\n\t\t\t\t\t\t\t entryQf.put(qryTerm, Collections.frequency(queryList,qryTerm));\n\t\t\t\t\t\t\t double val = entryQf.get(qryTerm)* (Double) storeIdf.get(qryTerm);\n\t\t\t\t\t\t\t qrySum = qrySum+ Math.pow(val, 2);\n\t\t\t\t\t\t }\n\t\t\t\t\t System.out.println(qryTerm+\" \"+entryQf.get(qryTerm)+ \" \"+ (Double) storeIdf.get(qryTerm));\n\t\t\t\t }\n\t\t\t\t qrySum=Math.sqrt(qrySum);\n\t\t\t\t System.out.println(\"qrySum \" + qrySum);\n\t\t\t\t \n\t\t\t\t//########### FOR CALCULATING COSINE SIMILARITY #############///\n\t\t\t\t for ( Map.Entry> entry_dotP : docsave.entrySet()) // Iterating Number of Documents\n\t\t\t\t\t{\n\t\t\t\t\t\tdouble sumProduct=0;\n\t\t\t\t\t\tdouble productTfIdf=0;\n\t\t\t\t\t\tString keyMain_new = entry_dotP.getKey(); //Geting Doc Name\n\t\t\t\t\t\t for(Map.Entry qryTermItr : entryQf.entrySet()) // Iterating through the vocabulary\n\t\t\t\t\t\t {\n\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t Map matchTerm = tfList.get(qryTermItr.getKey()); // Getting a map of doc Names by a Query Term as value of tfList\n\n\t\t\t\t\t\t\t\t if(matchTerm.containsKey(keyMain_new)) // Only doc name EQUAL with docsave name can enter here\n\t\t\t\t\t\t\t\t {\n\t\t\t\t\t\t\t\t\t //System.out.println(\"Test \"+ matchTerm.get(keyMain_new) +\" keyMain_new \" + keyMain_new);\n\t\t\t\t\t\t\t\t\t double docTfIdf= matchTerm.get(keyMain_new) * storeIdf.get(qryTermItr.getKey());\n\t\t\t\t\t\t\t\t\t double qryTfIdf= qryTermItr.getValue() * storeIdf.get(qryTermItr.getKey());\n\t\t\t\t\t\t\t\t\t productTfIdf = docTfIdf * qryTfIdf;\n\t\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t \n\t\t\t\t\t\t\t sumProduct= sumProduct+productTfIdf;\n\t\t\t\t\t\t\t //System.out.println(\"productTfIdf \"+productTfIdf+\" sumProduct \"+ sumProduct);\n\t\t\t\t\t\t\t productTfIdf=0;\n\t\t\t\t\t\t }\n\t\t\t\t\t\t cosineProd.put(entry_dotP.getKey(), sumProduct/(docLength.get(entry_dotP.getKey())*qrySum));\n\t\t\t\t\t\t sumProduct=0;\n\t\t\t\t\t\t //System.out.println(entry_dotP.getKey()+ \" \" + docLength.get(entry_dotP.getKey()));\n\t\t\t\t\t}\n\t\t\t\t System.out.println(\"cosineProd \"+ cosineProd);\n\t\t\t\t \n\t\t\t\t System.out.println(\"Number of Top Pages you want to see\");\n\t\t\t\t int topRank = Integer.parseInt(scan.nextLine());\n\t\t\t\t Map result = cosineProd.entrySet().stream()\n\t\t\t .sorted(Map.Entry.comparingByValue(Comparator.reverseOrder())).limit(topRank)\n\t\t\t .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue,\n\t\t\t (oldValue, newValue) -> oldValue, LinkedHashMap::new));\n\n\t\t\t\t scan.close();\n\t\t\t //Alternative way\n\t\t\t //Map result2 = new LinkedHashMap<>();\n\t\t\t //cosineProd.entrySet().stream().sorted(Map.Entry.comparingByValue().reversed()).limit(2).forEachOrdered(x -> result2.put(x.getKey(), x.getValue()));\n\n\t\t\t System.out.println(\"Sorted...\");\n\t\t\t System.out.println(result);\n\t\t\t //System.out.println(result2);\n\t}","private ArrayList loadIds() {\n\n\t\tArrayList idArray = new ArrayList();\n\t\ttry {\n\t\t\tFileInputStream fileInputStream = context.openFileInput(SAVE_FILE);\n\t\t\tInputStreamReader inputStreamReader = new InputStreamReader(\n\t\t\t\t\tfileInputStream);\n\t\t\tType listType = new TypeToken>() {\n\t\t\t}.getType();\n\t\t\tGsonBuilder builder = new GsonBuilder();\n\t\t\tGson gson = builder.create();\n\t\t\tArrayList list = gson.fromJson(inputStreamReader, listType);\n\t\t\tidArray = list;\n\t\t} catch (IOException e) {\n\t\t\te.printStackTrace();\n\t\t}\n\t\treturn idArray;\n\t}","public List getSavedIds() {\n if (dbObjects.length > 0 && dbObjects[0] instanceof JacksonDBObject) {\n throw new UnsupportedOperationException(\n \"Generated _id retrieval not supported when using stream serialization\");\n }\n\n List ids = new ArrayList();\n for (DBObject dbObject : dbObjects) {\n ids.add(jacksonDBCollection.convertFromDbId(dbObject.get(\"_id\")));\n }\n\n return ids;\n }","private synchronized void saveInternal() {\n if (relatedDocumentsCounter == 0) {\r\n return;\r\n }\r\n\r\n final TrigramIndexJsonModel model = new TrigramIndexJsonModel( relatedDocuments, indexGeneration, trigram );\r\n final TrigramDocumentCountJsonModel count = new TrigramDocumentCountJsonModel( trigram, globalRelatedDocumentsCounter );\r\n\r\n indexGeneration++;\r\n relatedDocuments = new TreeSet<>();\r\n relatedDocumentsCounter = 0;\r\n\r\n // put that save action and all unnecessary path calculations into a thread pool, \r\n // no need that other word can't be indexed, because of someone's save action... \r\n\r\n Runnable runnable = new Runnable() {\r\n @Override\r\n public void run() {\r\n Path trigramsPath = TrigramSubPathCalculator.getPathForTrigram( trigramsBasePath, trigram,\r\n \".\" + model.getIndexGeneration() + TRIGRAM_REFERENCE_SUFFIX );\r\n createTargetDirectoryIfNotExist( trigramsPath.getParent() );\r\n\r\n // write content of one part of the index\r\n try (BufferedWriter writer = Files.newBufferedWriter( trigramsPath, StandardCharsets.UTF_8 )) {\r\n Gson gson = new Gson();\r\n writer.write( gson.toJson( model ) );\r\n }\r\n catch (IOException e) {\r\n System.out.println( String.format( \"saving file: '%s' caused this error...\", trigramsPath ) );\r\n e.printStackTrace();\r\n }\r\n\r\n // write+overwrite the global documents counter as well\r\n Path trigramCountPath = TrigramSubPathCalculator.getPathForTrigram( trigramsBasePath, trigram, TRIGRAM_COUNT_SUFFIX );\r\n\r\n try (BufferedWriter writer = Files.newBufferedWriter( trigramCountPath, StandardCharsets.UTF_8 )) {\r\n Gson gson = new Gson();\r\n writer.write( gson.toJson( count ) );\r\n }\r\n catch (IOException e) {\r\n System.out.println( String.format( \"saving file: '%s' caused this error...\", trigramCountPath ) );\r\n e.printStackTrace();\r\n }\r\n\r\n }\r\n };\r\n\r\n // TODO: put into task thread-pool (deque) for really saving indexing time.\r\n runnable.run();\r\n }","private void saveGenres(){\n\t\tFile genreList = new File(Paths.get(\"genres.txt\").toString());\n\t\ttry{\n\t\t\tBufferedWriter writer = new BufferedWriter(new FileWriter(genreList));\n\t\t\tfor (String s : genres){\n\t\t\t\twriter.write(s);\n\t\t\t\twriter.newLine();\n\t\t\t}\n\t\t\twriter.close();\n\t\t} catch(IOException ex){\n\t\t\t\n\t\t}\n\t}","public static Map indexEmails(String fileName)\n\t{\n\t\tMap authBank= new HashMap();\t\t \n\t\tAuthorMod curAuth;\n\t\t//vars for for loop - one loop per email\n\t\tString curTok;\n\t\tString lastTok;\n\t\t\n\t\ttry \n\t\t{\n\t\t\tScanner scanner = new Scanner(new FileInputStream(fileName));\n\t\t try \n\t\t {\n\t\t while (scanner.hasNextLine())\n\t\t {\n\t\t \n\t\t \t String[] emailToks= SimpleTokenizer.INSTANCE.tokenize(scanner.nextLine());\n\t\t \t\n\t\t \t lastTok = \"\";\n\t\t \t curTok = emailToks[3]; //maybe 2, check output\n\t\t \t Pair firstBg = new Pair(lastTok, curTok);\t\t \t \n\t\t \t //author check, possible set\n\t\t \t String authID = emailToks[0] + emailToks[1] + emailToks[2]; //check output from the tokenizer\t \t\n\t\t \t if (authBank.containsKey(authID)){\n\t\t \t\t curAuth = authBank.get(authID);\n\t\t \t\t curAuth.trainSize = curAuth.trainSize + (emailToks.length-2);\n\t\t \t\t curAuth.ug.updateSeen(lastTok);\n\t\t \t } else {\n\t\t \t\t curAuth = new AuthorMod();\n\t\t \t\t curAuth.id = authID;\n\t\t \t\t curAuth.trainSize = emailToks.length - 2;\n\t\t\t \t curAuth.ug.addNew(lastTok);\n\t\t \t }\n\t\t \t \n\t\t \t //initalize loop\n\t\t \t if(curAuth.ug.contains(curTok)) {\n\t\t \t\t curAuth.ug.updateSeen(curTok);\n\t\t \t } \n\t\t \t else {\t\t \n\t\t \t\t curAuth.ug.addNew(curTok);\n\t\t \t }\n\n\t\t \t if(curAuth.bg.containsBg(firstBg)) {\n\t\t \t\t curAuth.bg.updateSeen(firstBg);\n\t\t \t } else {\n\t\t \t\t curAuth.bg.addNew(firstBg);\n\t\t \t }\n\t\t \t \t \n\t\t \t //index for that author, code very similar to bigram/unigram\n\t\t \t for(int i = 4; i < emailToks.length; i++)\t\t \n\t\t \t\t {\n\t\t \t\t\t curTok= emailToks[i];\n\t\t \t\t\t Pair loopBg = new Pair(lastTok, curTok);\n\t\t \t\t\t \n\t\t \t\t\t //three cases. \n\t\t \t\t\t //1) bigram has been seen\n\t\t \t\t\t if (curAuth.bg.containsBg(loopBg))\n\t\t \t\t\t {\n\t\t \t\t\t\t curAuth.bg.updateSeen(loopBg);\n\t\t \t\t\t\t curAuth.ug.updateSeen(curTok);\n\t\t \t\t\t } \n\t\t \t\t\t //2) word seen, but not bigram\n\t\t \t\t\t else\n\t\t \t\t\t { \n\t\t \t\t\t\t if (curAuth.ug.contains(curTok))\n\t\t \t\t\t \t\t{\n\t\t \t\t\t\t\t curAuth.bg.addNew(loopBg);\n\t\t \t\t\t\t\t curAuth.ug.updateSeen(curTok);\n\t\t \t\t\t\t\t} \n\t\t \t\t\t\t //3) new word entirely\n\t\t \t\t\t\t else\n\t\t \t\t\t\t {\n\t\t \t\t\t\t\t curAuth.ug.addNew(curTok);\n\t\t \t\t\t\t\t curAuth.bg.addNew(loopBg); \n\t\t \t\t\t\t } \n\t\t \t\t\t }\t \n\t\t \t\t\t lastTok = curTok;\n\t\t \t\t\t} //end inner loop\n\t\t \tauthBank.put(curAuth.id, curAuth); \n\t\t \t\t} //end outer loop \n\t\t }\t\n\t\t finally\n\t\t {\n\t\t scanner.close();\n\t\t }\n\t\t}\n\t\tcatch(Exception e)\n\t\t{\n\t\t\tSystem.err.println(\"Error: \" + e.getMessage());\n\t\t}\n\t\treturn authBank;\n\t}","Map getTokens();","private Map>> buildDictionary(Document doc){\n\t\t\n\t\tElement root = doc.getDocumentElement();\n\t\t\n\t\t\n\t\tMap>> dictionary = new HashMap>>();\n\t\tthis.termSet = new TreeSet();\n\t\t\n\t\tNodeList termList = doc.getElementsByTagName(\"term\");\n\t\tfor(int i = 0; i < termList.getLength(); i++){\n\t\t\tElement termElement = (Element) termList.item(i);\n\t\t\tElement nameElement = (Element) termElement.getElementsByTagName(\"name\").item(0);\n\t\t\tString name = nameElement.getTextContent();\n\t\t\tthis.termSet.add(name);\n\n\t\t\tMap> synonymGroup = new HashMap>();\n\t\t\tsynonymGroup.put(\"exact\", new ArrayList());\n\t\t\tsynonymGroup.put(\"related\", new ArrayList());\n\t\t\tsynonymGroup.put(\"broad\", new ArrayList());\n\t\t\tsynonymGroup.put(\"narrow\", new ArrayList());\n\t\t\t\n\t\t\tNodeList synonyms = termElement.getElementsByTagName(\"synonym\");\n\t\t\tfor(int j=0; j synonymList = (List) synonymGroup.get(scope);\n\t\t\t\t\n\t\t\t\t//System.out.println(synonym);\n\t\t\t\t\n\t\t\t\tsynonymList.add(synonym);\n\t\t\t}\n\t\t\t\n\t\t\tdictionary.put(name,synonymGroup);\t\t\n\t\t\t\n\t\t}\n\t\t\n\t\treturn dictionary;\n\t}","public synchronized List getDocIdsTodosDocumentos() throws Exception{\r\n\t\tList lista = new ArrayList();\r\n\t\t\r\n\t\tMTDIterator iterator = iterator();\r\n\t\twhile(iterator.hasNext()){\r\n\t\t\tMTDDocument doc = iterator.next();\r\n\t\t\tlista.add(doc.getDocId());\r\n\t\t}\r\n\t\titerator.close();\r\n\t\t\r\n\t\treturn lista;\r\n\t}","private static Map>>[] splitYagoDataIntoDocumentSets(File yagoInputFile) {\r\n\t\tMap>> trainData = new HashMap>>();\r\n\t\tMap>> testaData = new HashMap>>();\r\n\t\tMap>> testbData = new HashMap>>();\r\n\t\t\r\n\t\tBufferedReader reader = FileUtil.getFileReader(yagoInputFile.getAbsolutePath());\r\n\t\ttry {\r\n\t\t\tString documentName = null;\r\n\t\t\tString documentSet = null;\r\n\t\t\tList> documentLines = null;\r\n\t\t\tList sentenceLines = null;\r\n\t\t\tString line = null;\r\n\t\t\twhile ((line = reader.readLine()) != null) {\r\n\t\t\t\tif (line.startsWith(\"-DOCSTART-\")) {\r\n\t\t\t\t\tif (documentSet != null) {\r\n\t\t\t\t\t\tif (documentSet.equals(\"train\"))\r\n\t\t\t\t\t\t\ttrainData.put(documentName, documentLines);\r\n\t\t\t\t\t\telse if (documentSet.equals(\"testa\"))\r\n\t\t\t\t\t\t\ttestaData.put(documentName, documentLines);\r\n\t\t\t\t\t\telse if (documentSet.equals(\"testb\"))\r\n\t\t\t\t\t\t\ttestbData.put(documentName, documentLines);\r\n\t\t\t\t\t}\r\n\t\t\t\t\t\r\n\t\t\t\t\tString docId = line.substring(\"-DOCSTART- (\".length(), line.length() - 1);\r\n\t\t\t\t\tString[] docIdParts = docId.split(\" \");\r\n\t\t\t\t\tdocumentName = docIdParts[0] + \"_\" + docIdParts[1];\r\n\t\t\t\t\t\r\n\t\t\t\t\tif (docIdParts[0].endsWith(\"testa\"))\r\n\t\t\t\t\t\tdocumentSet = \"testa\";\r\n\t\t\t\t\telse if (docIdParts[0].endsWith(\"testb\"))\r\n\t\t\t\t\t\tdocumentSet = \"testb\";\r\n\t\t\t\t\telse\r\n\t\t\t\t\t\tdocumentSet = \"train\";\r\n\t\t\t\t\t\r\n\t\t\t\t\tdocumentLines = new ArrayList>();\r\n\t\t\t\t\tsentenceLines = new ArrayList();\r\n\t\t\t\t} else if (line.trim().length() == 0) {\r\n\t\t\t\t\tdocumentLines.add(sentenceLines);\r\n\t\t\t\t\tsentenceLines = new ArrayList();\r\n\t\t\t\t} else {\r\n\t\t\t\t\tsentenceLines.add(line);\r\n\t\t\t\t}\r\n\t\t\t}\r\n\t\t\t\r\n\t\t\tif (documentSet.equals(\"train\"))\r\n\t\t\t\ttrainData.put(documentName, documentLines);\r\n\t\t\telse if (documentSet.equals(\"testa\"))\r\n\t\t\t\ttestaData.put(documentName, documentLines);\r\n\t\t\telse if (documentSet.equals(\"testb\"))\r\n\t\t\t\ttestbData.put(documentName, documentLines);\r\n\t\t} catch (IOException e) {\r\n\t\t\treturn null;\r\n\t\t}\r\n\r\n\t\t@SuppressWarnings(\"unchecked\")\r\n\t\tMap>>[] returnData = new HashMap[3];\r\n\t\treturnData[0] = trainData;\r\n\t\treturnData[1] = testaData;\r\n\t\treturnData[2] = testbData;\r\n\t\t\r\n\t\treturn returnData;\r\n\t}","private static void writeToCoordinateFile(String idNames, String[] id_to_coord_list, String outputFileName){\n String[] stringToWrite = getStringBasedOnCoordinate( idNames, id_to_coord_list); //list of id we found, ignore the first 0th index\n writeToFile(stringToWrite, outputFileName);\n }","public void allartongs() throws IOException{\r\n writefiles data=new writefiles(\"d:\\\\documents\\\\textfiles\\\\AllArtSongs.txt\",true);\r\n Map ArrangerNamesLineMap=new HashMap<>();\r\n for(int songid:ArrangerLinesMap.keySet()){\r\n int arrangerid=ArrangerLinesMap.get(songid);\r\n ArrangersMap.get((songid));\r\n ArrangerNamesLineMap.put(test.getsongName(songid), ArrangersMap.get(arrangerid));\r\n }\r\n for(String songname:ArrangerNamesLineMap.keySet()){\r\n System.out.println(\"The artist is:\"+ArrangerNamesLineMap.get(songname)+\" The song is:\"+songname);\r\n data.writeToFile(\"The artist is:\"+ArrangerNamesLineMap.get(songname)+\" The song is:\"+songname);\r\n }\r\n System.out.println(ArrangerNamesLineMap.size());\r\n }","public synchronized List getDocumentos(Collection ids){\r\n\t\tArrayList listaRetorno = new ArrayList();\r\n\t\tDirectoryReader reader;\r\n\t\ttry {\r\n\t\t\treader = DirectoryReader.open(getCopiaDiretorioMemoria());\r\n\t\tIndexSearcher searcher = new IndexSearcher(reader);\t\t\r\n\t for(Integer docId: ids){\r\n \t\tDocument documento = searcher.doc(docId.intValue());\r\n \t\tif(documento != null){\r\n \t\tMTDDocument doc = new MTDDocumentBuilder().buildDocument(documento).build();\r\n \t\tdoc.setDocId(docId.intValue());\r\n \t\tlistaRetorno.add(doc);\r\n \t\t}else\r\n \t\t{System.out.println(\"Document with docId \"+docId.intValue()+\" not found.\");}\r\n\t }\r\n\t\t} catch (IOException e) {\r\n\t\t\t// TODO Auto-generated catch block\r\n\t\t\te.printStackTrace();\r\n\t\t}\r\n\t\treturn listaRetorno;\r\n\t}","private static void writeMappingsToFile(String releaseNumber, List> stableIdsToOldIdsMappings, Set currentStableIdentifiers) throws IOException {\n\t\tPath oldStableIdsMappingFilePath = Paths.get(releaseNumber, \"reactome_stable_ids.txt\");\n\t\tString header = \"# Reactome stable IDs for release \" + releaseNumber + \"\\n\" + \"Stable_ID\\told_identifier(s)\\n\";\n\t\tFiles.write(oldStableIdsMappingFilePath, header.getBytes(), StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING);\n\t\tfor (List