@Test public void testGetLocationInAlignment() { assertEquals(global.getLocationInAlignment(), new SimpleLocation(2, 6, Strand.UNDEFINED, new SimpleLocation(2, 3, Strand.UNDEFINED), new SimpleLocation(5, 6, Strand.UNDEFINED))); assertEquals(local.getLocationInAlignment(), new SimpleLocation(1, 8, Strand.UNDEFINED, new SimpleLocation(1, 2, Strand.UNDEFINED), new SimpleLocation(5, 5, Strand.UNDEFINED), new SimpleLocation(7, 8, Strand.UNDEFINED))); assertEquals(local2.getLocationInAlignment(), new SimpleLocation(1, 3, Strand.UNDEFINED)); }
@Override public Location getLocationInAlignment() { return location; }
SimpleAlignedSequence implements AlignedSequence<S, C> { @Override public Location getLocationInAlignment() { return location; } }
SimpleAlignedSequence implements AlignedSequence<S, C> { @Override public Location getLocationInAlignment() { return location; } SimpleAlignedSequence(S original, List<Step> steps);  SimpleAlignedSequence(S original, List<Step> steps, int numBefore, int numAfter);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps, int numBefore, int numAfter); }
SimpleAlignedSequence implements AlignedSequence<S, C> { @Override public Location getLocationInAlignment() { return location; } SimpleAlignedSequence(S original, List<Step> steps);  SimpleAlignedSequence(S original, List<Step> steps, int numBefore, int numAfter);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps, int numBefore, int numAfter); @Override void clearCache(); @Override int getAlignmentIndexAt(int sequenceIndex); @Override Point getEnd(); @Override Location getLocationInAlignment(); @Override int getNumGaps(); @Override S getOriginalSequence(); @Override int getOverlapCount(); @Override int getSequenceIndexAt(int alignmentIndex); @Override Point getStart(); @Override boolean isCircular(); @Override boolean isGap(int alignmentIndex); @Override int countCompounds(C... compounds); @Override AccessionID getAccession(); @Override List<C> getAsList(); @Override C getCompoundAt(int alignmentIndex); @Override CompoundSet<C> getCompoundSet(); @Override int getIndexOf(C compound); @Override int getLastIndexOf(C compound); @Override int getLength(); @Override String getSequenceAsString(); @Override SequenceView<C> getSubSequence(Integer start, Integer end); @Override Iterator<C> iterator(); @Override String toString(); @Override //TODO Needs to implements SequenceView<C> getInverse(); }
SimpleAlignedSequence implements AlignedSequence<S, C> { @Override public Location getLocationInAlignment() { return location; } SimpleAlignedSequence(S original, List<Step> steps);  SimpleAlignedSequence(S original, List<Step> steps, int numBefore, int numAfter);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps);  SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps, int numBefore, int numAfter); @Override void clearCache(); @Override int getAlignmentIndexAt(int sequenceIndex); @Override Point getEnd(); @Override Location getLocationInAlignment(); @Override int getNumGaps(); @Override S getOriginalSequence(); @Override int getOverlapCount(); @Override int getSequenceIndexAt(int alignmentIndex); @Override Point getStart(); @Override boolean isCircular(); @Override boolean isGap(int alignmentIndex); @Override int countCompounds(C... compounds); @Override AccessionID getAccession(); @Override List<C> getAsList(); @Override C getCompoundAt(int alignmentIndex); @Override CompoundSet<C> getCompoundSet(); @Override int getIndexOf(C compound); @Override int getLastIndexOf(C compound); @Override int getLength(); @Override String getSequenceAsString(); @Override SequenceView<C> getSubSequence(Integer start, Integer end); @Override Iterator<C> iterator(); @Override String toString(); @Override //TODO Needs to implements SequenceView<C> getInverse();  }