Package bgu.bio.adt.graphs

Examples of bgu.bio.adt.graphs.Tree

17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
import bgu.bio.algorithms.graphs.hsa.matchers.UnorderedMatcherFactory;

public class TestHSAOnInteger {

  private static void run(String file1, String file2) throws IOException {
    Tree t = buildTree(file1);
    Tree s = buildTree(file2);
    t.toDotFile("/home/milon/1.dot", true);
    s.toDotFile("/home/milon/2.dot", true);

    CostFunction w = new CostFunction() {

      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
        if (l1.equals(l2)) {
          return -2;
        }

        return Double.POSITIVE_INFINITY;
      }
    };

    TIntArrayList[] alignment = new TIntArrayList[3];

    UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory,false);

    System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }

    System.out.println();
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.println("(" + t.getLabel(alignment[0].get(i)) + ","
          + s.getLabel(alignment[1].get(i)) + ") ");
    }
  }
View Full Code Here
108
109
110
111
112
113
114
115
    for (int i = 0; i < tEdges.length; i++) {
      tLabels[i] = new NodeLabel(id2Label.get(i));
    }

    Tree t = new Tree(tEdges, tWeights, tSmoothing, tLabels);
    return t;
  }
View Full Code Here
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
    NodeLabel[] tLabels = { new NodeLabel("0"), new NodeLabel("1"),
        new NodeLabel("2"), new NodeLabel("3"), new NodeLabel("4"),
        new NodeLabel("5"), new NodeLabel("6"), new NodeLabel("7"),
        new NodeLabel("8"), new NodeLabel("9"), };

    Tree t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    // TODO Auto-generated method stub
    int[][] sEdges = { { 1, 2, 3, 4, 5 }, { 0 }, { 0 }, { 0 }, { 0 },
        { 0 }, };

    double[][] sWeights = { { 10, 20, 30, 40, 50 }, { 10 }, { 20 }, { 30 },
        { 40 }, { 50 }, };

    double[] sSmooth = { 2, 2, 2, 2, 2, 2 };
    NodeLabel[] sLabels = { new NodeLabel("0"), new NodeLabel("1"),
        new NodeLabel("2"), new NodeLabel("3"), new NodeLabel("4"),
        new NodeLabel("5"), };

    Tree s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    CostFunction w = new CostFunction() {

      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
View Full Code Here
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
    NodeLabel[] tLabels = { new NodeLabel("h"), new NodeLabel("d"),
        new NodeLabel("c"), new NodeLabel("g"), new NodeLabel("b"),
        new NodeLabel("a"), new NodeLabel("e"), new NodeLabel("f"),
        new NodeLabel("i"), };

    Tree t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    int[][] sEdges = { { 3 }, { 2, 8 }, { 3, 1 }, { 0, 4, 2 },
        { 3, 6, 5, 7 }, { 4 }, { 4 }, { 4 }, { 1 } };

    double[][] sWeights = { { 30 }, { 20, 1 }, { 30, 10 }, { 10, 40, 20 },
        { 30, 60, 1, 70 }, { 40 }, { 40 }, { 40 }, { 10 } };

    double[] sSmooth = { 2, 2, 1.2, 2, 2, 2, 2, 2, 2 };
    NodeLabel[] sLabels = { new NodeLabel("a"), new NodeLabel("c"),
        new NodeLabel("j"), new NodeLabel("b"), new NodeLabel("d"),
        new NodeLabel("i"), new NodeLabel("e"), new NodeLabel("f"),
        new NodeLabel("k"), };

    CostFunction w = new CostFunction() {

      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
        if (Arrays.equals(l1.getLabelValue().toArray(), l2
            .getLabelValue().toArray()))
          return -3;
        else
          return 5;
      }
    };

    Tree s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    checkTrees(t, w, s);

    // checking for rooting problems:

    final double INF = MathOperations.INFINITY;

    w = new CostFunction() {
      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
        if (Arrays.equals(l1.getLabelValue().toArray(), l2
            .getLabelValue().toArray()))
          return -3;
        else if (l1.getLabelValue().get(0) == 'b'
            || l2.getLabelValue().get(0) == 'b') {
          return INF;
        } else
          return 5;
      }
    };

    tWeights = new double[][] { { INF, 10, 1 }, { INF, 70, 60 }, { INF },
        { INF }, { 50, 1, 10, 20 }, { INF }, { INF }, { INF }, { INF } };

    t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    sWeights = new double[][] { { INF }, { INF, 1 }, { INF, 10 },
        { 10, 40, 20 }, { INF, 60, 1, 70 }, { INF }, { INF }, { INF },
        { INF } };

    s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    checkTrees(t, w, s);

  }
View Full Code Here
602
603
604
605
606
607
608
  public static void testTree() {
    int[][] neighbors = { { 4 }, { 6 }, { 4 }, { 5 }, { 2, 6, 7, 0 },
        { 6, 3, 9, 8 }, { 1, 4, 5 }, { 4 }, { 5 }, { 5 }, };

    Tree tree = new Tree(neighbors, null, null, null);
  }
View Full Code Here
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
    NodeLabel[] tLabels = { new NodeLabel("0"), new NodeLabel("1"),
        new NodeLabel("2"), new NodeLabel("3"), new NodeLabel("4"),
        new NodeLabel("5"), new NodeLabel("6"), new NodeLabel("7"),
        new NodeLabel("8"), new NodeLabel("9"), };

    Tree t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    int[][] sEdges = { { 1, 2, 3, 4, 5 }, { 0 }, { 0 }, { 0 }, { 0 },
        { 0 }, };

    double[][] sWeights = { { 10, 20, 30, 40, 50 }, { 10 }, { 20 }, { 30 },
        { 40 }, { 50 }, };

    double[] sSmooth = { 2, 2, 2, 2, 2, 2 };
    NodeLabel[] sLabels = { new NodeLabel("0"), new NodeLabel("1"),
        new NodeLabel("2"), new NodeLabel("3"), new NodeLabel("4"),
        new NodeLabel("5"), };

    Tree s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    CostFunction w = new CostFunction() {

      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
View Full Code Here
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
    NodeLabel[] tLabels = { new NodeLabel("h"), new NodeLabel("d"),
        new NodeLabel("c"), new NodeLabel("g"), new NodeLabel("b"),
        new NodeLabel("a"), new NodeLabel("e"), new NodeLabel("f"),
        new NodeLabel("i"), };

    Tree t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    int[][] sEdges = { { 3 }, { 2, 8 }, { 3, 1 }, { 0, 4, 2 },
        { 3, 6, 5, 7 }, { 4 }, { 4 }, { 4 }, { 1 } };

    double[][] sWeights = { { 30 }, { 20, 1 }, { 30, 10 }, { 10, 40, 20 },
        { 30, 60, 1, 70 }, { 40 }, { 40 }, { 40 }, { 10 } };

    double[] sSmooth = { 2, 2, 1.2, 2, 2, 2, 2, 2, 2 };
    NodeLabel[] sLabels = { new NodeLabel("a"), new NodeLabel("c"),
        new NodeLabel("j"), new NodeLabel("b"), new NodeLabel("d"),
        new NodeLabel("i"), new NodeLabel("e"), new NodeLabel("f"),
        new NodeLabel("k"), };

    CostFunction w = new CostFunction() {

      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
        if (Arrays.equals(l1.getLabelValue().toArray(), l2
            .getLabelValue().toArray()))
          return -3;
        else
          return 5;
      }
    };

    Tree s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    checkTrees(t, w, s);

    // checking for rooting problems:

    final double INF = MathOperations.INFINITY;

    w = new CostFunction() {
      @Override
      public double cost(NodeLabel l1, NodeLabel l2) {
        if (Arrays.equals(l1.getLabelValue().toArray(), l2
            .getLabelValue().toArray()))
          return -3;
        else if (l1.getLabelValue().get(0) == 'b'
            || l2.getLabelValue().get(0) == 'b') {
          return INF;
        } else
          return 5;
      }
    };

    tWeights = new double[][] { { INF, 10, 1 }, { INF, 70, 60 }, { INF },
        { INF }, { 50, 1, 10, 20 }, { INF }, { INF }, { INF }, { INF } };

    t = new Tree(tEdges, tWeights, tSmooth, tLabels);

    sWeights = new double[][] { { INF }, { INF, 1 }, { INF, 10 },
        { 10, 40, 20 }, { INF, 60, 1, 70 }, { INF }, { INF }, { INF },
        { INF } };

    s = new Tree(sEdges, sWeights, sSmooth, sLabels);

    checkTrees(t, w, s);

  }
View Full Code Here
725
726
727
728
729
730
731
  public static void testTree() {
    int[][] neighbors = { { 4 }, { 6 }, { 4 }, { 5 }, { 2, 6, 7, 0 },
        { 6, 3, 9, 8 }, { 1, 4, 5 }, { 4 }, { 5 }, { 5 }, };

    Tree tree = new Tree(neighbors, null, null, null);
  }
View Full Code Here
TOP

Related Classes of bgu.bio.adt.graphs.Tree

  • bgu.bio.algorithms.graphs.Test
  • bgu.bio.algorithms.graphs.TestHSA
  • bgu.bio.algorithms.graphs.TestHSAOnInteger
  • java.io.FileWriter
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.