Package bgu.bio.adt.tuples

Examples of bgu.bio.adt.tuples.IntPair

216
217
218
219
220
221
222
223
224
225
226
        } else if (secondary.charAt(i) == closeBracket) {
          if (stack.size() == 0) {
            return false;
          }
          final int start = stack.pop();
          ans.add(new IntPair(start, i));
        }
      }
      if (stack.size() != 0) {
        return false;
      }
View Full Code Here
246
247
248
249
250
251
252
253
254
255
256
      for (int i = 0; i < secondary.length(); i++) {
        if (secondary.charAt(i) == openBracket) {
          stack.push(i);
        } else if (secondary.charAt(i) == closeBracket) {
          final int start = stack.pop();
          ans.add(new IntPair(start, i));
        }
      }
    }
    return ans;
  }
View Full Code Here
261
262
263
264
265
266
267
268
269
270
271
    Collections.sort(pairs, new IntPairComparator());

    ArrayList<ArrayList<IntPair>> stackings = new ArrayList<ArrayList<IntPair>>();

    for (int p = 0; p < pairs.size(); p++) {
      IntPair current = pairs.get(p);
      // check all stackings in data
      boolean found = false;
      for (int s = stackings.size() - 1; s >= 0 && !found; s--) {
        ArrayList<IntPair> currentStacking = stackings.get(s);
        if (isExtends(currentStacking, current, maxGapSize)) {
View Full Code Here
297
298
299
300
301
302
303
304
305
306
307
308
309
310
        structure.append('.');
      }
      String sequence = this.primary.substring(current.get(0).getFirst(),
          current.get(0).getSecond() + 1);
      for (int i = 0; i < current.size(); i++) {
        IntPair pair = current.get(i);
        structure.setCharAt(
            pair.getFirst() - current.get(0).getFirst(), '(');
        structure.setCharAt(pair.getSecond()
            - current.get(0).getFirst(), ')');
      }
      String newHeader = this.header;
      try {
        JSONObject json = new JSONObject();
View Full Code Here
322
323
324
325
326
327
328
329
330
331
332
333
  }

  private boolean isExtends(ArrayList<IntPair> currentStacking,
      IntPair current, int maxGapSize) {

    final IntPair edgeOfStack = currentStacking
        .get(currentStacking.size() - 1);
    return (current.getFirst() - edgeOfStack.getFirst() - 1 <= maxGapSize
        && current.getFirst() - edgeOfStack.getFirst() > 0
        && edgeOfStack.getSecond() - current.getSecond() - 1 <= maxGapSize && edgeOfStack
        .getSecond() - current.getSecond() > 0);
  }
View Full Code Here
595
596
597
598
599
600
601
602
603
604
605
      sumOfChararcters += danglingRight.size();

      // move the information to a list and sort by size
      counters = new ArrayList<IntPair>();
      for (int i = 0; i < loopCounters.size(); i++) {
        counters.add(new IntPair(i, loopCounters.get(i)));
      }
      Collections.sort(counters, new Comparator<IntPair>() {

        @Override
        public int compare(IntPair o1, IntPair o2) {
View Full Code Here
11
12
13
14
15
16
17
18
19
20
21
  @Test
  public void testExtractSimple1() {
    RNA rna = new RNA(1, "test", "AAACCCUUU", "(((...)))");
    ArrayList<IntPair> expList = new ArrayList<IntPair>();
    expList.add(new IntPair(0, 8));
    expList.add(new IntPair(1, 7));
    expList.add(new IntPair(2, 6));

    checkLists(expList, rna.extractPairs());
  }
View Full Code Here
22
23
24
25
26
27
28
29
30
31
32
33
34
  @Test
  public void testExtractPK1() {
    RNA rna = new RNA(1, "test", "AAACCCUUUAAGGGCCC", "((([[[)))..]]]...");
    ArrayList<IntPair> expList = new ArrayList<IntPair>();
    expList.add(new IntPair(0, 8));
    expList.add(new IntPair(1, 7));
    expList.add(new IntPair(2, 6));
    expList.add(new IntPair(3, 13));
    expList.add(new IntPair(4, 12));
    expList.add(new IntPair(5, 11));
    checkLists(expList, rna.extractPairs());
  }
View Full Code Here
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
    IntPairComparator comp = new IntPairComparator();

    ArrayList<IntPair> ans = new ArrayList<IntPair>();
    ArrayList<IntPair> exp = new ArrayList<IntPair>();

    ans.add(new IntPair(6, 3));
    ans.add(new IntPair(5, 2));
    ans.add(new IntPair(4, 1));
    for (int i = 0; i < matching[0].size(); ++i) {
      exp.add(new IntPair(matching[0].get(i), matching[1].get(i)));
    }

    Collections.sort(ans, comp);
    Collections.sort(exp, comp);

    isSame(ans, exp);

    Assert.assertEquals("Minimum matching answer is wrong", 7,
        matcher.minCostMatching(), 0.001);

    ans = new ArrayList<IntPair>();
    exp = new ArrayList<IntPair>();

    matching = matcher.getCurrMatching();

    ans.add(new IntPair(3, 5));
    ans.add(new IntPair(0, 4));
    ans.add(new IntPair(6, 3));
    ans.add(new IntPair(5, 2));
    ans.add(new IntPair(4, 1));

    for (int i = 0; i < matching[0].size(); ++i) {
      exp.add(new IntPair(matching[0].get(i), matching[1].get(i)));
    }

    Collections.sort(ans, comp);
    Collections.sort(exp, comp);
View Full Code Here
TOP

Related Classes of bgu.bio.adt.tuples.IntPair

  • bgu.bio.algorithms.graphs.TestHSA
  • bgu.bio.ds.rna.RNA
  • bgu.bio.ds.rna.StemStructure$StemStructureShuffleData
  • bgu.bio.ds.rna.TestRNA
    • 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.