Merge branch 'master' of github.com:biojava/biojava

andreasprlic · andreasprlic · commit b3d749fad3bf · 2013-04-24T23:22:10.000-07:00
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/model/AFPChain.java
@@ -285,6 +285,7 @@ public String toDBSearchResult(){
 	}
 
 	protected void calcSimilarity() {
+		System.out.println("calcSimilarity");
 		Map<String,Double> idMap = AFPAlignmentDisplay.calcIdSimilarity(alnseq1,alnseq2,alnLength);
 
 		//probability = idMap.get("probability");
@@ -1224,8 +1225,10 @@ public void setProbability(double probability)
  * @return a value between 0 and 1
  */
 	public double getIdentity() {
-		if ( identity <= 0)
+		if ( identity <= 0) {
+			System.out.println("recaclulating ID and SIM (" + identity +")");
 			calcSimilarity();
+		}
 		return identity;
 	}
 
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AFPAlignmentDisplay.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AFPAlignmentDisplay.java
@@ -346,6 +346,7 @@ public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int
 		double similarity = 0.0;
 		
 		if ( seq1 == null || seq2 == null){
+			System.err.println("AFPAlignmentDisplay can't calc ID if alignment strings are null! ");
 			Map<String, Double> m = new HashMap<String, Double>();
 			m.put("similarity", similarity);
 			m.put("identity", identity);
