Alignments of zero length return a null Location instead of crashing during alignment

d-cameron · d-cameron · commit a30699156eb9 · 2013-12-11T13:20:44.000+11:00
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java
@@ -359,9 +359,15 @@ private void setLocation(List<Step> steps) {
         }
 
         // combine sublocations into 1 Location
-        location = (sublocations.size() == 1) ? sublocations.get(0) : new SimpleLocation(
-                sublocations.get(0).getStart(), sublocations.get(sublocations.size() - 1).getEnd(), Strand.UNDEFINED,
-                false, sublocations);
+        if (sublocations.size() == 0) {
+        	location = null;
+        } else if (sublocations.size() == 1) {
+        	location = sublocations.get(0);
+        } else {
+        	location = new SimpleLocation(sublocations.get(0).getStart(), sublocations.get(sublocations.size() - 1).getEnd(),
+        			Strand.UNDEFINED,
+                    false, sublocations);
+        }
         // TODO handle circular alignments
 
         // check that alignment has correct number of compounds in it to fit original sequence
diff --git a/biojava3-alignment/src/test/java/org/biojava3/alignment/LocalAlignmentTest.java b/biojava3-alignment/src/test/java/org/biojava3/alignment/LocalAlignmentTest.java
@@ -45,6 +45,6 @@ public void shouldAllowZeroLengthMatches() {
         SimpleGapPenalty gapP = new SimpleGapPenalty((short)5, (short)2);
         PairwiseSequenceAligner<DNASequence, NucleotideCompound> result = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);
         assertEquals(0, result.getScore());
-        assertEquals(0, result.getProfile().getSize());
+        assertEquals(0, result.getProfile().getLength());
 	}
 }

Original file line number	Diff line number	Diff line change
`@@ -45,6 +45,6 @@ public void shouldAllowZeroLengthMatches() {`
`45`	`45`	`SimpleGapPenalty gapP = new SimpleGapPenalty((short)5, (short)2);`
`46`	`46`	`PairwiseSequenceAligner<DNASequence, NucleotideCompound> result = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);`
`47`	`47`	`assertEquals(0, result.getScore());`
`48`		`- assertEquals(0, result.getProfile().getSize());`
	`48`	`+ assertEquals(0, result.getProfile().getLength());`
`49`	`49`	`}`
`50`	`50`	`}`