Examples with BidiMap org.apache.commons.collections4.BidiMap used on opensource projects

Example 6 with BidiMap

use of org.apache.commons.collections4.BidiMap in project fmv by f-agu.

the class FontUtils method loadAllSystemFonts.

// ***************************************
/**
 */
private static void loadAllSystemFonts() {
    if (fontMap != null) {
        return;
    }
    BidiMap<String, Font> tmpFontBidiMap = new DualHashBidiMap<>();
    Map<Font, File> fileMap = new HashMap<>();
    File folder = new File(getSystemFontPath());
    for (File file : folder.listFiles((FileFilter) new SuffixFileFilter(".ttf", IOCase.INSENSITIVE))) {
        try {
            Font font = Font.createFont(Font.TRUETYPE_FONT, file);
            tmpFontBidiMap.put(font.getName().toLowerCase(), font);
            fileMap.put(font, file);
        } catch (FontFormatException | IOException e) {
        // e.printStackTrace();
        }
    }
    fontMap = tmpFontBidiMap;
    fontFileMap = fileMap;
}

Example 7 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class NNsuperscaffold method nj.

public void nj(double max_r) {
    // TODO Auto-generated method stub
    final BidiMap<String, Integer> scaffs = new DualHashBidiMap<>();
    final BidiMap<Cluster, Integer> clusts = new DualHashBidiMap<>();
    final TreeMap<Double, Set<ClustPair>> minRfs = new TreeMap<>();
    try {
        BufferedReader br1 = Utils.getBufferedReader(rf_file);
        int c = 0;
        String line, scaff;
        String[] s;
        double minf;
        double[] allf;
        Cluster c1, c2;
        int i1, i2;
        ClustPair pair;
        long line_count = 0;
        while ((line = br1.readLine()) != null) {
            if (line.startsWith("#")) {
                scaff = line.trim().replaceAll("^##", "");
                scaffs.put(scaff, c);
                c1 = new Cluster(c);
                clusts.put(c1, c);
                ++c;
            } else {
                ++line_count;
                if (line_count % 1000000 == 0)
                    myLogger.info("#lines loaded: " + line_count);
                s = line.trim().split("\\s+");
                minf = Double.parseDouble(s[0]);
                i1 = scaffs.get(s[5]);
                i2 = scaffs.get(s[6]);
                c1 = clusts.getKey(i1);
                c2 = clusts.getKey(i2);
                // recomb freqs arranged in i1<i2 order
                allf = new double[4];
                allf[0] = Double.parseDouble(s[1]);
                allf[3] = Double.parseDouble(s[4]);
                if (i1 < i2) {
                    allf[1] = Double.parseDouble(s[2]);
                    allf[2] = Double.parseDouble(s[3]);
                } else {
                    allf[1] = Double.parseDouble(s[3]);
                    allf[2] = Double.parseDouble(s[2]);
                }
                c1.minf.put(c2, minf);
                c1.allf.put(c2, allf);
                c2.minf.put(c1, minf);
                c2.allf.put(c1, allf);
                // cluster pair arranged in i1<i2 order
                pair = i1 < i2 ? new ClustPair(c1, c2) : new ClustPair(c2, c1);
                minRfs.putIfAbsent(minf, new HashSet<>());
                minRfs.get(minf).add(pair);
            }
        }
        myLogger.info("####total lines loaded: " + line_count);
        br1.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    int nclust = clusts.size();
    Map.Entry<Double, Set<ClustPair>> entry;
    double f, extf;
    Set<ClustPair> pairs;
    ClustPair pair;
    Cluster c1, c2, c, cc;
    boolean j1, j2;
    Map<Cluster, Double> minf;
    Map<Cluster, double[]> allf;
    int i1, i2;
    double[] fs, fs1, fs2;
    Set<Double> fs2cl = new HashSet<>();
    while (!minRfs.isEmpty()) {
        entry = minRfs.firstEntry();
        f = entry.getKey();
        pairs = entry.getValue();
        if (f > max_r)
            break;
        myLogger.info("####" + nclust + " " + f + " " + clusts.size());
        // all pairs have same recombination frequencies
        // need to decide which pair to join
        // before that need to decide the orientation of join
        pair = null;
        extf = Double.MAX_VALUE;
        for (ClustPair p : pairs) {
            p.join();
            if (p.extf < extf)
                pair = p;
        }
        if (pair == null)
            pair = pairs.iterator().next();
        // now join the pair
        c1 = pair.c1;
        c2 = pair.c2;
        j1 = pair.j1;
        j2 = pair.j2;
        i1 = c1.clust;
        i2 = c2.clust;
        c = new Cluster(nclust, c1, c2, j1, j2, f);
        allf = c.allf;
        minf = c.minf;
        // now update clusts
        clusts.remove(c1);
        clusts.remove(c2);
        // now update allf and minf
        for (int i : clusts.values()) {
            cc = clusts.getKey(i);
            fs = new double[4];
            // ** for c1
            fs1 = c1.allf.get(cc);
            if (i < i1) {
                if (j1) {
                    fs[0] = fs1[1];
                    fs[2] = fs1[3];
                } else {
                    fs[0] = fs1[0];
                    fs[2] = fs1[2];
                }
            } else {
                if (j1) {
                    fs[0] = fs1[2];
                    fs[2] = fs1[3];
                } else {
                    fs[0] = fs1[0];
                    fs[2] = fs1[1];
                }
            }
            // ** for c2
            fs2 = c2.allf.get(cc);
            if (i < i2) {
                if (j2) {
                    fs[1] = fs2[0];
                    fs[3] = fs2[2];
                } else {
                    fs[1] = fs2[1];
                    fs[3] = fs2[3];
                }
            } else {
                if (j2) {
                    fs[1] = fs2[0];
                    fs[3] = fs2[1];
                } else {
                    fs[1] = fs2[2];
                    fs[3] = fs2[3];
                }
            }
            f = StatUtils.min(fs);
            allf.put(cc, fs);
            minf.put(cc, f);
            cc.allf.put(c, fs);
            cc.minf.put(c, f);
        }
        // now update minf
        for (Map.Entry<Cluster, double[]> ent : allf.entrySet()) minf.put(ent.getKey(), StatUtils.min(ent.getValue()));
        // now update minRfs
        pairs.remove(pair);
        // remove pairs with c1 c2
        for (Map.Entry<Cluster, Integer> ent : clusts.entrySet()) {
            cc = ent.getKey();
            int i = cc.clust;
            if (i1 < i) {
                minRfs.get(c1.minf.get(cc)).remove(new ClustPair(c1, cc));
            } else {
                minRfs.get(cc.minf.get(c1)).remove(new ClustPair(cc, c1));
            }
            if (i2 < i) {
                minRfs.get(c2.minf.get(cc)).remove(new ClustPair(c2, cc));
            } else {
                minRfs.get(cc.minf.get(c2)).remove(new ClustPair(cc, c2));
            }
        }
        // add pairs with c
        for (Map.Entry<Cluster, Double> ent : minf.entrySet()) {
            f = ent.getValue();
            minRfs.putIfAbsent(f, new HashSet<>());
            minRfs.get(f).add(new ClustPair(ent.getKey(), c));
        }
        // clear empty entries in minRfs
        fs2cl.clear();
        for (Map.Entry<Double, Set<ClustPair>> ent : minRfs.entrySet()) if (ent.getValue().isEmpty())
            fs2cl.add(ent.getKey());
        for (double f2cl : fs2cl) minRfs.remove(f2cl);
        // clear c1 c2 from minf and allf
        for (Cluster c0 : clusts.keySet()) {
            c0.minf.remove(c1);
            c0.minf.remove(c2);
            c0.allf.remove(c1);
            c0.allf.remove(c2);
        }
        // add new cluster c and update nclust
        clusts.put(c, nclust);
        ++nclust;
    }
    myLogger.info("####clusters: " + clusts.size());
    StringBuilder out = new StringBuilder();
    List<Integer> ids;
    List<Double> dists;
    List<Boolean> joins;
    try {
        BufferedWriter bw = Utils.getBufferedWriter(this.out_prefix + ".nns");
        for (Map.Entry<Cluster, Integer> ent : clusts.entrySet()) {
            c = ent.getKey();
            out.setLength(0);
            ids = c.ids;
            dists = c.dists;
            joins = c.joins;
            out.append("-c ");
            out.append(scaffs.getKey(ids.get(0)));
            for (int i = 1; i < ids.size(); i++) {
                out.append(":");
                out.append(scaffs.getKey(ids.get(i)));
            }
            if (dists.size() > 0) {
                out.append(" -s ");
                out.append(dists.get(0));
                for (int i = 1; i < dists.size(); i++) {
                    out.append(":");
                    out.append(dists.get(i));
                }
            }
            if (joins.size() > 1) {
                out.append(" -r ");
                out.append(joins.get(0));
                for (int i = 1; i < joins.size(); i++) {
                    out.append(":");
                    out.append(joins.get(i));
                }
            }
            myLogger.info("#" + ent.getValue() + "\t" + out.toString());
            for (int i = 0; i < ids.size() - 1; i++) myLogger.info(scaffs.getKey(ids.get(i)) + "\t" + dists.get(i) + "\t" + joins.get(i));
            myLogger.info(scaffs.getKey(ids.get(ids.size() - 1)) + "\t\t\t\t" + joins.get(joins.size() - 1));
            out.append("\n");
            bw.write(out.toString());
        }
        bw.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 8 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class RFUtils method makeRMatrix.

/**
 * make RData object from Renjin
 * renjin-script-engine-*-with dependencies.jar required
 * https://nexus.bedatadriven.com/content/groups/public/org/renjin/renjin-script-engine/
 */
protected static void makeRMatrix(String in_rf, String out_Rmat) {
    // TODO Auto-generated method stub
    ScriptEngineManager manager = new ScriptEngineManager();
    ScriptEngine engine = manager.getEngineByName("Renjin");
    if (engine == null) {
        throw new RuntimeException("Renjin not found!!!");
    }
    try {
        BufferedReader br = Utils.getBufferedReader(in_rf);
        final BidiMap<Integer, String> scaffs = new TreeBidiMap<Integer, String>();
        String line;
        String[] s;
        int w = 0;
        double d, l;
        while ((line = br.readLine()) != null && line.startsWith("##")) {
            scaffs.put(w++, line.replaceAll("^##", ""));
        }
        int n = scaffs.size();
        int A = w * (w - 1) / 2;
        DoubleMatrixBuilder dMat = new DoubleMatrixBuilder(n, n);
        DoubleMatrixBuilder lMat = new DoubleMatrixBuilder(n, n);
        DoubleMatrixBuilder iMat = new DoubleMatrixBuilder(n, n);
        DoubleMatrixBuilder dAllMat = new DoubleMatrixBuilder(A * 2, 4);
        DoubleMatrixBuilder lAllMat = new DoubleMatrixBuilder(A * 2, 4);
        w = 0;
        while (line != null) {
            s = line.split("\\s+");
            int i = scaffs.getKey(s[5]), j = scaffs.getKey(s[6]), hs = Integer.parseInt(s[7]);
            d = Math.min(RF_MAX, Double.parseDouble(s[0]));
            l = calcLODFromRf(d, hs);
            dMat.set(i, j, d);
            dMat.set(j, i, d);
            lMat.set(i, j, l);
            lMat.set(j, i, l);
            iMat.set(i, j, w + 1);
            iMat.set(j, i, w + 1 + A);
            for (int k = 0; k < 4; k++) {
                d = Math.min(RF_MAX, Double.parseDouble(s[k + 1]));
                l = calcLODFromRf(d, hs);
                dAllMat.set(w, k, d);
                dAllMat.set(w + A, (k == 0 || k == 3) ? k : (3 - k), d);
                lAllMat.set(w, k, l);
                lAllMat.set(w + A, (k == 0 || k == 3) ? k : (3 - k), l);
            }
            w++;
            line = br.readLine();
        }
        br.close();
        StringVector scf = new StringArrayVector(scaffs.values());
        dMat.setRowNames(scf);
        dMat.setColNames(scf);
        lMat.setRowNames(scf);
        lMat.setColNames(scf);
        iMat.setRowNames(scf);
        iMat.setColNames(scf);
        Context context = Context.newTopLevelContext();
        FileOutputStream fos = new FileOutputStream(out_Rmat);
        GZIPOutputStream zos = new GZIPOutputStream(fos);
        RDataWriter writer = new RDataWriter(context, zos);
        ListVector.NamedBuilder Rdat = new ListVector.NamedBuilder();
        Rdat.add("scaffs", scf);
        Rdat.add("n", n);
        Rdat.add("A", A);
        Rdat.add("distanceMat", dMat.build());
        Rdat.add("distanceAll", dAllMat.build());
        Rdat.add("lodMat", lMat.build());
        Rdat.add("lodAll", lAllMat.build());
        Rdat.add("indexMat", iMat.build());
        writer.save(Rdat.build());
        writer.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}