@Test public void testLength() { IntBP las = hitsfile.getLASBuffer(); for (int i = 0; i < hits.size(); i++) { assertEquals(!hitsfile.isLeft() ? hits.get(i).rightLength : hits.get(i).leftLength, Hits.getLengthOne(las.get(i))); assertEquals(hitsfile.isLeft() ? hits.get(i).rightLength : hits.get(i).leftLength, Hits.getLengthTwo(las.get(i))); } }
public boolean isLeft () {return isLeft;}
PairedHits extends Hits { public boolean isLeft () {return isLeft;} }
PairedHits extends Hits { public boolean isLeft () {return isLeft;} PairedHits(String prefix, int chrom, boolean isLeft); }
PairedHits extends Hits { public boolean isLeft () {return isLeft;} PairedHits(String prefix, int chrom, boolean isLeft); boolean isLeft(); IntBP getChromsBuffer(); IntBP getOtherPosBuffer(); IntBP getOtherChromsBetween(int firstindex,
                                       int lastindex,
                                       int start,
                                       int stop,
                                       Float minweight,
                                       Boolean isPlus); IntBP getOtherPositionsBetween(int firstindex,
                                          int lastindex,
                                          int start,
                                          int stop,
                                          Float minweight,
                                          Boolean isPlus); static void writePairedHits(List<PairedHit> hits,
                                       String prefix, 
                                       int chrom,
                                       boolean isLeft); void appendPairedHits(List<PairedHit> hits,
                                 String prefix, 
                                 int chrom,
                                 boolean isLeft); }
PairedHits extends Hits { public boolean isLeft () {return isLeft;} PairedHits(String prefix, int chrom, boolean isLeft); boolean isLeft(); IntBP getChromsBuffer(); IntBP getOtherPosBuffer(); IntBP getOtherChromsBetween(int firstindex,
                                       int lastindex,
                                       int start,
                                       int stop,
                                       Float minweight,
                                       Boolean isPlus); IntBP getOtherPositionsBetween(int firstindex,
                                          int lastindex,
                                          int start,
                                          int stop,
                                          Float minweight,
                                          Boolean isPlus); static void writePairedHits(List<PairedHit> hits,
                                       String prefix, 
                                       int chrom,
                                       boolean isLeft); void appendPairedHits(List<PairedHit> hits,
                                 String prefix, 
                                 int chrom,
                                 boolean isLeft);  }