X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=14e67048a86bd6cd460c0b0fabda3bbd9b8e008b;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=3f3c3ddc30365beb9393db45d922468d475ff70a;hpb=bdb9169fe2d203d921a111dc683d7daf7b887c25;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f3c3dd..14e6704 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -67,6 +67,7 @@ public class AppletJmol extends Frame
   TextField inputLine;
   TextArea history;
   SequenceI[] sequence;
+  String [] chains;
   StructureSelectionManager ssm;
   RenderPanel renderPanel;
   AlignmentPanel ap;
@@ -78,11 +79,13 @@ public class AppletJmol extends Frame
 
   public AppletJmol(PDBEntry pdbentry,
                     SequenceI[] seq,
+                    String[] chains,
                     AlignmentPanel ap,
                     String protocol)
   {
     this.ap = ap;
     this.sequence = seq;
+    this.chains = chains;
     this.pdbentry = pdbentry;
 
    String alreadyMapped = StructureSelectionManager
@@ -92,7 +95,7 @@ public class AppletJmol extends Frame
     if (alreadyMapped != null)
     {
        StructureSelectionManager.getStructureSelectionManager()
-            .setMapping(seq, pdbentry.getFile(), protocol);
+            .setMapping(seq, chains, pdbentry.getFile(), protocol);
        //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
        //FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
@@ -166,9 +169,7 @@ public class AppletJmol extends Frame
           viewer.openFile(pdbentry.getFile());
     }
 
-    this.setBounds(400, 400, 400, 400);
-
-    this.setVisible(true);
+    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
   }
 
   public void loadInline(String string)
@@ -440,14 +441,15 @@ public class AppletJmol extends Frame
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";color gold;wireframe 100");
+    eval.append(";wireframe 100");//;color gold
 
     Color col = new Color(viewer.getAtomArgb(atomIndex));
 
-    resetLastRes.append(";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];wireframe 0");
+    resetLastRes.append(";wireframe 0;"//color["
+                       // + col.getRed() + ","
+                       // + col.getGreen() + ","
+                       // + col.getBlue() + "]"
+                       );
 
     viewer.evalStringQuiet(eval.toString());
 
@@ -470,6 +472,7 @@ public class AppletJmol extends Frame
   }
 
   FeatureRenderer fr;
+  String lastCommand;
   public void colourBySequence(AlignmentPanel ap)
   {
     if(!colourBySequence)
@@ -481,7 +484,7 @@ public class AppletJmol extends Frame
     if (mapping.length < 1)
       return;
 
-    SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
 
     boolean showFeatures = false;
     if (ap.av.showSequenceFeatures)
@@ -502,7 +505,8 @@ public class AppletJmol extends Frame
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        if (mapping[m].getSequence() == sequence[s])
+        if (mapping[m].getSequence() == sequence[s]
+            && ap.av.alignment.findIndex(sequence[s])>-1)
         {
           for (int r = 0; r < sequence[s].getLength(); r++)
           {
@@ -547,7 +551,10 @@ public class AppletJmol extends Frame
       }
     }
 
-    viewer.evalStringQuiet(command.toString());
+    if (lastCommand == null || !lastCommand.equals(command.toString()))
+      viewer.evalStringQuiet(command.toString());
+
+    lastCommand = command.toString();
   }
 
   StringBuffer condenseCommand(String command, int pos)
@@ -615,14 +622,14 @@ public class AppletJmol extends Frame
       MCview.PDBfile pdb;
       if (loadedInline)
       {
-        pdb = ssm.setMapping(sequence,
+        pdb = ssm.setMapping(sequence,chains,
                                 pdbentry.getFile(),
                                 AppletFormatAdapter.PASTE);
         pdbentry.setFile("INLINE"+pdb.id);
       }
       else
       {
-         pdb = ssm.setMapping(sequence,
+         pdb = ssm.setMapping(sequence,chains,
                               pdbentry.getFile(),
                               AppletFormatAdapter.URL);
       }