Method for total gapped positions and coverage in aligned sequences

lafita · lafita · commit 8a9927c95be2 · 2016-06-24T16:21:14.000+02:00
biojava#491
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleSequencePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleSequencePair.java
@@ -171,4 +171,10 @@ public AlignedSequence<S, C> getTarget() {
 		return getAlignedSequence(2);
 	}
 
+	@Override
+	public double getPercentageOfIdentity() {
+		double seqid = getNumIdenticals();
+		return seqid / getLength();
+	}
+
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
@@ -96,6 +96,14 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 * @return the number of identical indices
 	 */
 	int getNumIdenticals();
+	
+	/**
+	 * Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
+	 * This is equivalent to {@link #getNumIdenticals()} / {@link #getLength()}.
+	 *
+	 * @return the percentage of sequence identity as a fraction in [0,1]
+	 */
+	double getPercentageOfIdentity();
 
 	/**
 	 * Returns the number of indices for which both the query and target sequences have a similar {@link Compound}.

Original file line number	Diff line number	Diff line change
`@@ -171,4 +171,10 @@ public AlignedSequence<S, C> getTarget() {`
`171`	`171`	`return getAlignedSequence(2);`
`172`	`172`	`}`
`173`	`173`
	`174`	`+ @Override`
	`175`	`+ public double getPercentageOfIdentity() {`
	`176`	`+ double seqid = getNumIdenticals();`
	`177`	`+ return seqid / getLength();`
	`178`	`+ }`
	`179`	`+`
`174`	`180`	`}`