From cc20fe9a60ad018141ae58142e93cb3c6b83ec3c Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 23 Jun 2011 15:45:07 +0100
Subject: [PATCH] patch for JAL-846 made targetChain mapping constraint
 selective so computed mappings are limited to cases where
 chain codes were explicitly supplied

---
 .../structure/StructureSelectionManager.java       |   23 +++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index d1bccd8..32241a5 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -152,16 +152,32 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    
     String targetChain;
     for (int s = 0; s < sequence.length; s++)
     {
+      boolean infChain = true;
       if (targetChains != null && targetChains[s] != null)
+      {
+        infChain = false;
         targetChain = targetChains[s];
+      }
       else if (sequence[s].getName().indexOf("|") > -1)
       {
         targetChain = sequence[s].getName().substring(
                 sequence[s].getName().lastIndexOf("|") + 1);
+        if (targetChain.length() > 1)
+        {
+          if (targetChain.trim().length() == 0)
+          {
+            targetChain = " ";
+          }
+          else
+          {
+            // not a valid chain identifier
+            targetChain = "";
+          }
+        }
       }
       else
         targetChain = "";
@@ -173,14 +189,11 @@ public class StructureSelectionManager
       boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may
-        // need to be revoked
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
-        if (targetChain.length() > 0 && !targetChain.equals(chain.id))
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
         {
           continue; // don't try to map chains don't match.
         }
-        // end of patch for limiting computed mappings
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         AlignSeq as = new AlignSeq(sequence[s],
-- 
1.7.10.2