List of usage examples for java.util Collections EMPTY_MAP
Map EMPTY_MAP
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From source file:Main.java
public static void main(String args[]) { List list = Collections.EMPTY_LIST; Set set = Collections.EMPTY_SET; Map map = Collections.EMPTY_MAP; List<String> s = Collections.emptyList(); Set<Long> l = Collections.emptySet(); Map<Date, String> d = Collections.emptyMap(); }
From source file:biomine.nodeimportancecompression.ImportanceCompressionReport.java
public static void main(String[] args) throws IOException, java.text.ParseException { opts.addOption("algorithm", true, "Used algorithm for compression. Possible values are 'brute-force', " + "'brute-force-edges','brute-force-merges','randomized','randomized-merges'," + "'randomized-edges'," + "'fast-brute-force'," + "'fast-brute-force-merges','fast-brute-force-merge-edges'. Default is 'brute-force'."); opts.addOption("query", true, "Query nodes ids, separated by comma."); opts.addOption("queryfile", true, "Read query nodes from file."); opts.addOption("ratio", true, "Goal ratio"); opts.addOption("importancefile", true, "Read importances straight from file"); opts.addOption("keepedges", false, "Don't remove edges during merges"); opts.addOption("connectivity", false, "Compute and output connectivities in edge oriented case"); opts.addOption("paths", false, "Do path oriented compression"); opts.addOption("edges", false, "Do edge oriented compression"); // opts.addOption( "a", double sigma = 1.0; CommandLineParser parser = new PosixParser(); CommandLine cmd = null;//from w w w. ja v a 2 s. co m try { cmd = parser.parse(opts, args); } catch (ParseException e) { e.printStackTrace(); System.exit(0); } String queryStr = cmd.getOptionValue("query"); String[] queryNodeIDs = {}; double[] queryNodeIMP = {}; if (queryStr != null) { queryNodeIDs = queryStr.split(","); queryNodeIMP = new double[queryNodeIDs.length]; for (int i = 0; i < queryNodeIDs.length; i++) { String s = queryNodeIDs[i]; String[] es = s.split("="); queryNodeIMP[i] = 1; if (es.length == 2) { queryNodeIDs[i] = es[0]; queryNodeIMP[i] = Double.parseDouble(es[1]); } else if (es.length > 2) { System.out.println("Too many '=' in querynode specification: " + s); } } } String queryFile = cmd.getOptionValue("queryfile"); Map<String, Double> queryNodes = Collections.EMPTY_MAP; if (queryFile != null) { File in = new File(queryFile); BufferedReader read = new BufferedReader(new FileReader(in)); queryNodes = readMap(read); read.close(); } String impfile = cmd.getOptionValue("importancefile"); Map<String, Double> importances = null; if (impfile != null) { File in = new File(impfile); BufferedReader read = new BufferedReader(new FileReader(in)); importances = readMap(read); read.close(); } String algoStr = cmd.getOptionValue("algorithm"); CompressionAlgorithm algo = null; if (algoStr == null || algoStr.equals("brute-force")) { algo = new BruteForceCompression(); } else if (algoStr.equals("brute-force-edges")) { algo = new BruteForceCompressionOnlyEdges(); } else if (algoStr.equals("brute-force-merges")) { algo = new BruteForceCompressionOnlyMerges(); } else if (algoStr.equals("fast-brute-force-merges")) { //algo = new FastBruteForceCompressionOnlyMerges(); algo = new FastBruteForceCompression(true, false); } else if (algoStr.equals("fast-brute-force-edges")) { algo = new FastBruteForceCompression(false, true); //algo = new FastBruteForceCompressionOnlyEdges(); } else if (algoStr.equals("fast-brute-force")) { algo = new FastBruteForceCompression(true, true); } else if (algoStr.equals("randomized-edges")) { algo = new RandomizedCompressionOnlyEdges(); //modified } else if (algoStr.equals("randomized")) { algo = new RandomizedCompression(); } else if (algoStr.equals("randomized-merges")) { algo = new RandomizedCompressionOnlyMerges(); } else { System.out.println("Unsupported algorithm: " + algoStr); printHelp(); } String ratioStr = cmd.getOptionValue("ratio"); double ratio = 0; if (ratioStr != null) { ratio = Double.parseDouble(ratioStr); } else { System.out.println("Goal ratio not specified"); printHelp(); } String infile = null; if (cmd.getArgs().length != 0) { infile = cmd.getArgs()[0]; } else { printHelp(); } BMGraph bmg = BMGraphUtils.readBMGraph(new File(infile)); HashMap<BMNode, Double> queryBMNodes = new HashMap<BMNode, Double>(); for (String id : queryNodes.keySet()) { queryBMNodes.put(bmg.getNode(id), queryNodes.get(id)); } long startMillis = System.currentTimeMillis(); ImportanceGraphWrapper wrap = QueryImportance.queryImportanceGraph(bmg, queryBMNodes); if (importances != null) { for (String id : importances.keySet()) { wrap.setImportance(bmg.getNode(id), importances.get(id)); } } ImportanceMerger merger = null; if (cmd.hasOption("edges")) { merger = new ImportanceMergerEdges(wrap.getImportanceGraph()); } else if (cmd.hasOption("paths")) { merger = new ImportanceMergerPaths(wrap.getImportanceGraph()); } else { System.out.println("Specify either 'paths' or 'edges'."); System.exit(1); } if (cmd.hasOption("keepedges")) { merger.setKeepEdges(true); } algo.compress(merger, ratio); long endMillis = System.currentTimeMillis(); // write importance { BufferedWriter wr = new BufferedWriter(new FileWriter("importance.txt", false)); for (BMNode nod : bmg.getNodes()) { wr.write(nod + " " + wrap.getImportance(nod) + "\n"); } wr.close(); } // write sum of all pairs of node importance added by Fang /* { BufferedWriter wr = new BufferedWriter(new FileWriter("sum_of_all_pairs_importance.txt", true)); ImportanceGraph orig = wrap.getImportanceGraph(); double sum = 0; for (int i = 0; i <= orig.getMaxNodeId(); i++) { for (int j = i+1; j <= orig.getMaxNodeId(); j++) { sum = sum+ wrap.getImportance(i)* wrap.getImportance(j); } } wr.write(""+sum); wr.write("\n"); wr.close(); } */ // write uncompressed edges { BufferedWriter wr = new BufferedWriter(new FileWriter("edges.txt", false)); ImportanceGraph orig = wrap.getImportanceGraph(); ImportanceGraph ucom = merger.getUncompressedGraph(); for (int i = 0; i <= orig.getMaxNodeId(); i++) { String iname = wrap.intToNode(i).toString(); HashSet<Integer> ne = new HashSet<Integer>(); ne.addAll(orig.getNeighbors(i)); ne.addAll(ucom.getNeighbors(i)); for (int j : ne) { if (i < j) continue; String jname = wrap.intToNode(j).toString(); double a = orig.getEdgeWeight(i, j); double b = ucom.getEdgeWeight(i, j); wr.write(iname + " " + jname + " " + a + " " + b + " " + Math.abs(a - b)); wr.write("\n"); } } wr.close(); } // write distance { // BufferedWriter wr = new BufferedWriter(new // FileWriter("distance.txt",false)); BufferedWriter wr = new BufferedWriter(new FileWriter("distance.txt", true)); //modified by Fang ImportanceGraph orig = wrap.getImportanceGraph(); ImportanceGraph ucom = merger.getUncompressedGraph(); double error = 0; for (int i = 0; i <= orig.getMaxNodeId(); i++) { HashSet<Integer> ne = new HashSet<Integer>(); ne.addAll(orig.getNeighbors(i)); ne.addAll(ucom.getNeighbors(i)); for (int j : ne) { if (i <= j) continue; double a = orig.getEdgeWeight(i, j); double b = ucom.getEdgeWeight(i, j); error += (a - b) * (a - b) * wrap.getImportance(i) * wrap.getImportance(j); // modify by Fang: multiply imp(u)imp(v) } } error = Math.sqrt(error); //////////error = Math.sqrt(error / 2); // modified by Fang: the error of each // edge is counted twice wr.write("" + error); wr.write("\n"); wr.close(); } // write sizes { ImportanceGraph orig = wrap.getImportanceGraph(); ImportanceGraph comp = merger.getCurrentGraph(); // BufferedWriter wr = new BufferedWriter(new // FileWriter("sizes.txt",false)); BufferedWriter wr = new BufferedWriter(new FileWriter("sizes.txt", true)); //modified by Fang wr.write(orig.getNodeCount() + " " + orig.getEdgeCount() + " " + comp.getNodeCount() + " " + comp.getEdgeCount()); wr.write("\n"); wr.close(); } //write time { System.out.println("writing time"); BufferedWriter wr = new BufferedWriter(new FileWriter("time.txt", true)); //modified by Fang double secs = (endMillis - startMillis) * 0.001; wr.write("" + secs + "\n"); wr.close(); } //write change of connectivity for edge-oriented case // added by Fang { if (cmd.hasOption("connectivity")) { BufferedWriter wr = new BufferedWriter(new FileWriter("connectivity.txt", true)); ImportanceGraph orig = wrap.getImportanceGraph(); ImportanceGraph ucom = merger.getUncompressedGraph(); double diff = 0; for (int i = 0; i <= orig.getMaxNodeId(); i++) { ProbDijkstra pdori = new ProbDijkstra(orig, i); ProbDijkstra pducom = new ProbDijkstra(ucom, i); for (int j = i + 1; j <= orig.getMaxNodeId(); j++) { double oriconn = pdori.getProbTo(j); double ucomconn = pducom.getProbTo(j); diff = diff + (oriconn - ucomconn) * (oriconn - ucomconn) * wrap.getImportance(i) * wrap.getImportance(j); } } diff = Math.sqrt(diff); wr.write("" + diff); wr.write("\n"); wr.close(); } } //write output graph { BMGraph output = bmg;//new BMGraph(bmg); int no = 0; BMNode[] nodes = new BMNode[merger.getGroups().size()]; for (ArrayList<Integer> gr : merger.getGroups()) { BMNode bmgroup = new BMNode("Group", "" + (no + 1)); bmgroup.setAttributes(new HashMap<String, String>()); bmgroup.put("autoedges", "0"); nodes[no] = bmgroup; no++; if (gr.size() == 0) continue; for (int x : gr) { BMNode nod = output.getNode(wrap.intToNode(x).toString()); BMEdge belongs = new BMEdge(nod, bmgroup, "belongs_to"); output.ensureHasEdge(belongs); } output.ensureHasNode(bmgroup); } for (int i = 0; i < nodes.length; i++) { for (int x : merger.getCurrentGraph().getNeighbors(i)) { if (x == i) { nodes[x].put("selfedge", "" + merger.getCurrentGraph().getEdgeWeight(i, x)); //ge.put("goodness", ""+merger.getCurrentGraph().getEdgeWeight(i, x)); continue; } BMEdge ge = new BMEdge(nodes[x], nodes[i], "groupedge"); ge.setAttributes(new HashMap<String, String>()); ge.put("goodness", "" + merger.getCurrentGraph().getEdgeWeight(i, x)); output.ensureHasEdge(ge); } } System.out.println(output.getGroupNodes()); BMGraphUtils.writeBMGraph(output, "output.bmg"); } }
From source file:diffhunter.DiffHunter.java
/** * @param args the command line arguments * @throws org.apache.commons.cli.ParseException * @throws java.io.IOException/*from w w w.jav a 2s .c o m*/ */ public static void main(String[] args) throws ParseException, IOException { //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString(); // TODO code application logic here /*args = new String[] { "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData" };*/ /*args = new String[] { "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData" };*/ Options options = new Options(); // add t option options.addOption("i", "index", false, "Indexing BED files."); options.addOption("b", "bed", true, "bed file to be indexed"); options.addOption("o", "output", true, "Folder that the index/comparison file will be created."); options.addOption("r", "reference", true, "Reference annotation file to be used for indexing"); options.addOption("c", "compare", false, "Finding differences between two conditions"); options.addOption("1", "first", true, "First sample index location"); options.addOption("2", "second", true, "Second sample index location"); options.addOption("w", "window", true, "Length of window for identifying differences"); options.addOption("s", "sliding", true, "Length of sliding"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); boolean indexing = false; boolean comparing = false; //Indexing! if (cmd.hasOption("i")) { //if(cmd.hasOption("1")) //System.err.println("sasan"); //System.out.println("sasa"); indexing = true; } else if (cmd.hasOption("c")) { //System.err.println(""); comparing = true; } else { //System.err.println("Option is not deteced."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } //Indexing is selected // if (indexing == true) { //Since indexing is true. //User have to provide file for indexing. if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String bedfile_ = cmd.getOptionValue("b"); String reference_file = cmd.getOptionValue("r"); String folder_loc = cmd.getOptionValue("o"); String sample_name = FilenameUtils.getBaseName(bedfile_); try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB( Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) { Indexer indexing_ = new Indexer(reference_file); indexing_.Make_Index(B2, bedfile_, Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString()); B2.close(); } } else if (comparing == true) { if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1") || cmd.hasOption("2"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String folder_loc = cmd.getOptionValue("o"); int window_ = Integer.parseInt(cmd.getOptionValue("w")); //int window_=600; int slide_ = Integer.parseInt(cmd.getOptionValue("s")); String first = cmd.getOptionValue("1").replace("_BDB", ""); String second = cmd.getOptionValue("2").replace("_BDB", ""); String reference_file = cmd.getOptionValue("r"); //String folder_loc=cmd.getOptionValue("o"); String sample_name_first = FilenameUtils.getBaseName(first); String sample_name_second = FilenameUtils.getBaseName(second); Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first); Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second); List<String> first_condition_genes = Files .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath()) .collect(Collectors.toList()); List<String> second_condition_genes = Files .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath()) .collect(Collectors.toList()); System.out.println("First and second condition are loaded!!! "); List<String> intersection_ = new ArrayList<>(first_condition_genes); intersection_.retainAll(second_condition_genes); BufferedWriter output = new BufferedWriter( new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt") .toAbsolutePath().toString(), false)); List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>()); Worker_New worker_class = new Worker_New(); worker_class.Read_Reference(reference_file); while (!intersection_.isEmpty()) { List<String> selected_genes = new ArrayList<>(); //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));} //else selected_genes.addAll(intersection_.subList(0, 10000)); if (intersection_.size() <= intersection_.size()) { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } else { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } intersection_.removeAll(selected_genes); //System.out.println("Intersection count is:"+intersection_.size()); //final List<Result_Window> resultssss_=new ArrayList<>(); IntStream.range(0, selected_genes.size()).parallel().forEach(i -> { System.out.println(selected_genes.get(i) + "\tprocessing......"); String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2"; int start = worker_class.dic_genes.get(gene_of_interest).start_loc; int end = worker_class.dic_genes.get(gene_of_interest).end_loc; Map<Integer, Integer> first_ = Collections.EMPTY_MAP; try { first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } Map<Integer, Integer> second_ = Collections.EMPTY_MAP; try { second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_); List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_); //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i)); // System.out.println("top_window_first_Count\t"+top_windows_first.size()); // System.out.println("top_window_second_Count\t"+top_windows_second.size()); if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) { return; } List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, sample_name_first, sample_name_second, 0.01); if (!res_temp.isEmpty()) { final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01)); } //System.out.println(selected_genes.get(i)+"\tprocessed."); }); /*selected_genes.parallelStream().forEach(i -> { });*/ List<Double> pvals = new ArrayList<>(); for (int i = 0; i < final_results.size(); i++) { pvals.add(final_results.get(i).p_value); } List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals); System.out.println("Writing to file..."); output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR"); output.newLine(); for (int i = 0; i < final_results.size(); i++) { Result_Window item = final_results.get(i); output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } /* for (Result_Window item : final_results) { output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } */ final_results.clear(); } output.close(); } System.out.println("Done."); }
From source file:Main.java
public static Map getMy() { String nullFlag = null;/*from w w w .j av a2s . c om*/ if (nullFlag == null) { return Collections.EMPTY_MAP; } return null; }
From source file:Main.java
public static <M extends Map> M wrapNullToImmutableEmptyMap(M map) { if (map != null) { return map; }//from ww w . j av a 2 s . co m return (M) Collections.EMPTY_MAP; }
From source file:Main.java
static Map<String, Component> getComponents(Container container) { Map<String, Component> listComponent = Collections.EMPTY_MAP; if (container.getComponentCount() > 0) { listComponent = new HashMap<>(); for (Component component : container.getComponents()) { if (component.getName() != null) { if (component instanceof JScrollPane) { listComponent.putAll(getComponents(((JScrollPane) component).getViewport())); } else { listComponent.put(component.getName(), component); }//from w w w . j av a 2 s . c o m } } } return listComponent; }
From source file:com.ctrip.infosec.rule.resource.QiAn.java
/** * ip??//from ww w . java 2 s. com * * @param ip * @param mobile * @return * {"msg":null,"success":1,"mobile":{"score":null,"is_notreal":null},"ip":{"is_proxy":0,"score":50.0,"ip":"218.17.231.209"}} */ public static Map<String, Object> queryRegEvent(String ip, String mobile) { if (StringUtils.isBlank(ip) && StringUtils.isBlank(mobile)) { return Collections.EMPTY_MAP; } Map<String, Object> params = new HashMap<>(); params.put("mobile", mobile); params.put("ip", ip); return DataProxy.queryForMap(serviceName, operationName, params); }
From source file:Main.java
@SuppressWarnings("unchecked") public static <T, U> Map<T, U> emptyMap(Class<T> keyType, Class<U> valueType) { return Collections.EMPTY_MAP; }
From source file:com.ctrip.infosec.rule.resource.TongDun.java
/** * ?ip??/*from ww w. j a v a 2s. c o m*/ * * @param ip * @param mobile * @return * {"reason_code":null,"final_decision":"Accept","seq_id":"1442309654522-72705995","final_score":0,"success":true} */ public static Map<String, Object> queryRegEvent(String ip, String mobile) { if (StringUtils.isBlank(ip) && StringUtils.isBlank(mobile)) { return Collections.EMPTY_MAP; } Map<String, Object> params = new HashMap<>(); params.put("account_mobile", mobile); params.put("ip_address", ip); return DataProxy.queryForMap(serviceName, operationName_reg, params); }
From source file:org.blocks4j.reconf.client.validation.ConfigurationRepositoryElementValidator.java
public static Map<String, String> validate(ConfigurationRepositoryElement arg) { if (arg == null) { return Collections.EMPTY_MAP; }/*from www .j a v a2 s . co m*/ Map<String, String> errors = new LinkedHashMap<String, String>(); checkConnectionSettings(arg, errors); checkComponent(arg, errors); checkProduct(arg, errors); checkUpdateFrequency(arg, errors); checkInterfaceClass(arg, errors); checkConfigurationItemElements(arg, errors); return errors; }