Examples with SourceHSPs edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.costmatrixcreation.dataTypes.SourceHSPs used on opensource projects

Example 1 with SourceHSPs

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.costmatrixcreation.dataTypes.SourceHSPs in project clusterMaker2 by RBVI.

the class Creator method createHSPCluster.

@SuppressWarnings("unchecked")
private void createHSPCluster(BlastFile bf, HashMap<Integer, String> proteins2integers, HashMap<String, Integer> integers2proteins, int[] proteinLengths) {
    HashMap<String, Integer> integers2proteinsClone = (HashMap<String, Integer>) integers2proteins.clone();
    HashMap<Integer, String> proteins2integersClone = (HashMap<Integer, String>) proteins2integers.clone();
    // integers2proteins.clear();
    // proteins2integers.clear();
    HashMap<String, SourceHSPs> sourceHSPs = new HashMap<String, SourceHSPs>();
    for (Iterator<String> iterator = integers2proteinsClone.keySet().iterator(); iterator.hasNext(); ) {
        String id = iterator.next();
        int idInt = integers2proteinsClone.get(id);
        SourceHSPs sHSP = new SourceHSPs(new ArrayList<boolean[]>(), proteinLengths[idInt], new ArrayList<Integer>(), id);
        sourceHSPs.put(id, sHSP);
    }
    for (int i = 0; i < bf.size; i++) {
        if (bf.getSource(i) == bf.getTarget(i))
            continue;
        SourceHSPs sourceHSP = sourceHSPs.get(proteins2integersClone.get(bf.getSource(i)));
        SourceHSPs targetHSP = sourceHSPs.get(proteins2integersClone.get(bf.getTarget(i)));
        boolean[] sourceCoverage = new boolean[proteinLengths[bf.getSource(i)]];
        boolean[] targetCoverage = new boolean[proteinLengths[bf.getTarget(i)]];
        Arrays.fill(sourceCoverage, bf.getStartQuery(i), bf.getEndQuery(i), true);
        Arrays.fill(targetCoverage, bf.getStartSubject(i), bf.getEndSubject(i), true);
        ArrayList<boolean[]> coveragesSource = sourceHSP.getCoverages();
        sourceHSP.addLine(i);
        if (coveragesSource.isEmpty()) {
            coveragesSource.add(sourceCoverage);
            sourceHSP.addCluster(0);
            sourceHSP.addClusterLine(0);
        } else {
            boolean match = false;
            for (int j = 0; j < coveragesSource.size(); j++) {
                boolean[] coverage = coveragesSource.get(j);
                float sim = calculateSimilarity(coverage, sourceCoverage);
                if (sim > 0.8) {
                    match = true;
                    sourceHSP.addCluster(j);
                    break;
                }
            }
            if (!match) {
                coveragesSource.add(sourceCoverage);
                sourceHSP.setClusternr(sourceHSP.getClusternr() + 1);
                sourceHSP.addClusterLine(i);
                sourceHSP.addCluster(sourceHSP.getClusternr());
            }
        }
        ArrayList<boolean[]> coveragesTarget = targetHSP.getCoverages();
        targetHSP.addLine(i);
        if (coveragesTarget.isEmpty()) {
            coveragesTarget.add(targetCoverage);
            targetHSP.addCluster(0);
            targetHSP.addClusterLine(0);
        } else {
            boolean match = false;
            for (int j = 0; j < coveragesTarget.size(); j++) {
                boolean[] coverage = coveragesTarget.get(j);
                float sim = calculateSimilarity(coverage, targetCoverage);
                if (sim > 0.8) {
                    match = true;
                    targetHSP.addCluster(j);
                    break;
                }
            }
            if (!match) {
                coveragesTarget.add(targetCoverage);
                targetHSP.setClusternr(targetHSP.getClusternr() + 1);
                targetHSP.addClusterLine(i);
                targetHSP.addCluster(targetHSP.getClusternr());
            }
        }
    }
    for (Iterator iterator = sourceHSPs.keySet().iterator(); iterator.hasNext(); ) {
        String key = (String) iterator.next();
        SourceHSPs s = sourceHSPs.get(key);
    }
    try {
        BufferedReader br = new BufferedReader(new FileReader(Config.blastFile));
        BufferedWriter bw = new BufferedWriter(new FileWriter(Config.blastFile + "HSP"));
        String line;
        int k = 0;
        while ((line = br.readLine()) != null) {
            if (line.trim().equals(""))
                continue;
            String[] tabs = line.split("\t");
            if (tabs[0].equals(tabs[1])) {
                k++;
                continue;
            }
            SourceHSPs source = sourceHSPs.get(tabs[0]);
            SourceHSPs target = sourceHSPs.get(tabs[1]);
            int sourceIndex = source.getLines().indexOf(k);
            int targetIndex = target.getLines().indexOf(k);
            bw.write(tabs[0] + "_HSP" + source.getCluster(sourceIndex) + "\t" + tabs[1] + "_HSP" + target.getCluster(targetIndex) + "\t");
            for (int j = 2; j < tabs.length; j++) {
                bw.write(tabs[j]);
                if (j < tabs.length - 1) {
                    bw.write("\t");
                } else {
                    bw.newLine();
                }
            }
            k++;
        }
        br.close();
        bw.flush();
        bw.close();
        br = new BufferedReader(new FileReader(Config.fastaFile));
        bw = new BufferedWriter(new FileWriter(Config.fastaFile + "HSP"));
        String sequence = "";
        String id = "";
        while ((line = br.readLine()) != null) {
            if (line.trim().equals(""))
                continue;
            if (line.startsWith(">")) {
                if (!sequence.equals("")) {
                    SourceHSPs source = sourceHSPs.get(id);
                    for (int j = 0; j <= source.getClusternr(); j++) {
                        bw.write(">" + id + "_HSP" + j);
                        bw.newLine();
                        bw.write(sequence);
                        bw.newLine();
                    }
                    sequence = "";
                }
                id = line.substring(1);
            } else {
                sequence += line;
            }
        }
        SourceHSPs source = sourceHSPs.get(id);
        for (int j = 0; j <= source.getClusternr(); j++) {
            bw.write(">" + id + "_HSP" + j);
            bw.newLine();
            bw.write(sequence);
            bw.newLine();
        }
        br.close();
        bw.flush();
        bw.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }
}