Can specify PDB chain to map sequence to - only used by applet so far

[jalview.git] / src / jalview / gui / AppJMol.java

diff --git a/src/jalview/gui/AppJMol.java b/src/jalview/gui/AppJMol.java
index e3aa9ea..3f2d895 100644 (file)
--- a/src/jalview/gui/AppJMol.java
+++ b/src/jalview/gui/AppJMol.java
@@ -49,6 +49,7 @@ public class AppJMol
   ScriptWindow scriptWindow;
   PDBEntry pdbentry;
   SequenceI[] sequence;
+  String [] chains;
   StructureSelectionManager ssm;
   JSplitPane splitPane;
   RenderPanel renderPanel;
@@ -68,6 +69,7 @@ public class AppJMol
     pdbentry = new PDBEntry();
     pdbentry.setFile(file);
     pdbentry.setId(id);
+    this.chains = chains;
     this.sequence = seq;
     this.ap = ap;
     this.setBounds(bounds);
@@ -104,7 +106,7 @@ public synchronized void addSequence(SequenceI [] seq)
      sequence = tmp;
    }
 
-  public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap)
+  public AppJMol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
   {
     //////////////////////////////////
     //Is the pdb file already loaded?
@@ -123,7 +125,7 @@ public synchronized void addSequence(SequenceI [] seq)
       if (option == JOptionPane.YES_OPTION)
       {
         StructureSelectionManager.getStructureSelectionManager()
-            .setMapping(seq, alreadyMapped, AppletFormatAdapter.FILE);
+            .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
         if (ap.seqPanel.seqCanvas.fr!=null) {
           ap.seqPanel.seqCanvas.fr.featuresAdded();
           ap.paintAlignment(true);
@@ -739,7 +741,7 @@ public synchronized void addSequence(SequenceI [] seq)
 
       //FILE LOADED OK
       ssm = StructureSelectionManager.getStructureSelectionManager();
-      MCview.PDBfile pdbFile = ssm.setMapping(sequence, pdbentry.getFile(), AppletFormatAdapter.FILE);
+      MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
       ssm.addStructureViewerListener(this);
       Vector chains = new Vector();
       for(int i=0; i<pdbFile.chains.size(); i++)