@Test public void testGetNumIdenticals() { assertEquals(global.getNumIdenticals(), 2); assertEquals(local.getNumIdenticals(), 2); }
@Override public int getNumIdenticals() { if (identicals == -1) { identicals = 0; for (int i = 1; i <= getLength(); i++) { if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) { identicals++; } } getQuery().clearCache(); getTarget().clearCache(); } return identicals; }
SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getNumIdenticals() { if (identicals == -1) { identicals = 0; for (int i = 1; i <= getLength(); i++) { if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) { identicals++; } } getQuery().clearCache(); getTarget().clearCache(); } return identicals; } }
SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getNumIdenticals() { if (identicals == -1) { identicals = 0; for (int i = 1; i <= getLength(); i++) { if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) { identicals++; } } getQuery().clearCache(); getTarget().clearCache(); } return identicals; } SimpleSequencePair(AlignedSequence<S, C> query, AlignedSequence<S, C> target);  SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy);  SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya); }
SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getNumIdenticals() { if (identicals == -1) { identicals = 0; for (int i = 1; i <= getLength(); i++) { if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) { identicals++; } } getQuery().clearCache(); getTarget().clearCache(); } return identicals; } SimpleSequencePair(AlignedSequence<S, C> query, AlignedSequence<S, C> target);  SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy);  SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya); @Override C getCompoundInQueryAt(int alignmentIndex); @Override C getCompoundInTargetAt(int alignmentIndex); @Override int getIndexInQueryAt(int alignmentIndex); @Override int getIndexInQueryForTargetAt(int targetIndex); @Override int getIndexInTargetAt(int alignmentIndex); @Override int getIndexInTargetForQueryAt(int queryIndex); @Override int getNumIdenticals(); @Override int getNumSimilars(); @Override AlignedSequence<S, C> getQuery(); @Override AlignedSequence<S, C> getTarget(); }
SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getNumIdenticals() { if (identicals == -1) { identicals = 0; for (int i = 1; i <= getLength(); i++) { if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) { identicals++; } } getQuery().clearCache(); getTarget().clearCache(); } return identicals; } SimpleSequencePair(AlignedSequence<S, C> query, AlignedSequence<S, C> target);  SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy);  SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya); @Override C getCompoundInQueryAt(int alignmentIndex); @Override C getCompoundInTargetAt(int alignmentIndex); @Override int getIndexInQueryAt(int alignmentIndex); @Override int getIndexInQueryForTargetAt(int targetIndex); @Override int getIndexInTargetAt(int alignmentIndex); @Override int getIndexInTargetForQueryAt(int queryIndex); @Override int getNumIdenticals(); @Override int getNumSimilars(); @Override AlignedSequence<S, C> getQuery(); @Override AlignedSequence<S, C> getTarget();  }