From: jprocter <Jim Procter>
Date: Tue, 19 Aug 2008 09:38:38 +0000 (+0000)
Subject: better check for molecule type when identifying internal sequence cross-references
X-Git-Tag: Release_2_4~17
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5ab495cf0873d14455eaab904823838563620064

better check for molecule type when identifying internal sequence cross-references
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index d063eed..159d96a 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -445,6 +445,7 @@ public class CrossRef
           boolean direct, boolean dna)
   {
     boolean found = false;
+    SequenceI[] typer=new SequenceI[1];
     if (dataset == null)
       return false;
     if (dataset.getSequences() == null)
@@ -465,6 +466,17 @@ public class CrossRef
         }
         if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
         {
+          // check if this is the correct sequence type
+          {
+            typer[0] = nxt;
+            boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+            if ((direct && isDna == dna) || (!direct && isDna!=dna))
+            {
+              // skip this sequence because it is same molecule type
+              continue;
+            }
+          }
+
           // look for direct or indirect references in common
           DBRefEntry[] poss = null, cands = null;
           if (direct)