From: jprocter <Jim Procter>
Date: Fri, 11 Jun 2010 09:41:29 +0000 (+0000)
Subject: patch for JAL-556 - more robust mapping of sequence to structure sequence with correc... 
X-Git-Tag: Release_2_5_1~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5f4142b92b29077571a78d891c0483a30579812e;p=jalview.git

patch for JAL-556 - more robust mapping of sequence to structure sequence with correct substitution matrix
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 6be8dd5..cdad671 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -176,8 +176,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
+      // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
-              .elementAt(i)).sequence, "pep");
+              .elementAt(i)).sequence, ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 478706a..483f1a4 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -133,8 +133,10 @@ public class StructureSelectionManager
 
       for (int i = 0; i < pdb.chains.size(); i++)
       {
+        
+        // TODO: correctly determine sequence type for mixed na/peptide structures
         AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, AlignSeq.PEP);
+                .elementAt(i)).sequence, ((PDBChain)pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));