From 4aa5be109de9af01dc494c31c0189377f8874f4e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Jul 2007 17:17:56 +0000
Subject: [PATCH] fix crossRef retrieval so either protein OR nucleotide

---
 src/jalview/analysis/CrossRef.java |   16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 9e69ca4..9e99c7c 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -196,7 +196,7 @@ public class CrossRef
   {
     Vector rseqs = new Vector();
     Alignment ral = null;
-    AlignedCodonFrame cf=new AlignedCodonFrame(dataset.getWidth()); // nominal width
+    AlignedCodonFrame cf=new AlignedCodonFrame(0); // nominal width
     for (int s = 0; s < seqs.length; s++)
     {
       SequenceI dss = seqs[s];
@@ -210,6 +210,7 @@ public class CrossRef
       {
         System.out.println("Attempting to find ds Xrefs refs.");
         DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less ambiguous would be a 'find primary dbRefEntry' method.
+        // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset, rseqs, cf);
       }
       for (int r = 0; xrfs!=null && r < xrfs.length; r++)
@@ -244,6 +245,8 @@ public class CrossRef
           if (dataset != null)
           {
             found = searchDataset(dss, xrfs[r], dataset, rseqs, cf);
+            if (found)
+              xrfs[r] = null; // we've recovered seqs for this one.
           }
         }
       }
@@ -262,8 +265,8 @@ public class CrossRef
           for (int r = 0; r < xrfs.length; r++)
           {
             // filter out any irrelevant or irretrievable references
-            if ((source != null && !source.equals(xrfs[r].getSource()))
-                    || !sftch.isFetchable(xrfs[r].getSource()))
+            if (xrfs[r]==null || ((source != null && !source.equals(xrfs[r].getSource()))
+                    || !sftch.isFetchable(xrfs[r].getSource())))
             {
               l--;
               xrfs[r] = null;
@@ -347,10 +350,9 @@ public class CrossRef
    * 
    * @param sequenceI
    * @param xrf
-   * @param dna
    * @param dataset
    * @param rseqs
-   * @param cf 
+   * @param cf
    * @return true if sequences were found and added
    */
   public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
@@ -422,10 +424,10 @@ public class CrossRef
                 }
               }
             }
+            // TODO: add mapping between sequences if necessary
+            found = true;
           }
           
-          // TODO: add mapping between sequences if necessary
-          found = true;
         }
       }
     }
-- 
1.7.10.2