X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=2da87738f8c9350a6dae9ea7235b621880e76256;hb=49685e6426d5ac136dce4907196751680c667670;hp=f355d1f09c6d139e8c82344e91e46c97de635cd7;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index f355d1f..2da8773 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
@@ -158,7 +176,8 @@ public class CrossRef
       {
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
         {
-          // retrieve CDS dataset sequences
+          System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");
+          // TODO: retrieve CDS dataset sequences
           // need global dataset sequence retriever/resolver to reuse refs
           // and construct Mapping entry.
           // insert gaps in CDS according to peptide gaps.
@@ -444,6 +463,7 @@ public class CrossRef
           boolean direct, boolean dna)
   {
     boolean found = false;
+    SequenceI[] typer=new SequenceI[1];
     if (dataset == null)
       return false;
     if (dataset.getSequences() == null)
@@ -464,6 +484,17 @@ 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)
@@ -549,4 +580,4 @@ public class CrossRef
    * System.out.println("Prod "+p+": "+prod[p].getDisplayId(true)); } }
    *  } }
    */
-}
\ No newline at end of file
+}