X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=f64014b7fb09d21e5c1a9818219fb9aec03fe669;hb=6173092ff5cb03f039cac674bfc8bc4f969976a5;hp=3f3c3ddc30365beb9393db45d922468d475ff70a;hpb=bdb9169fe2d203d921a111dc683d7daf7b887c25;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f3c3dd..f64014b 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)
@@ -353,6 +354,7 @@ public class AppletJmol extends Frame
   {
     if (evt.getSource() == seqColour)
     {
+      lastCommand = null;
       colourBySequence = seqColour.getState();
       colourBySequence(ap);
     }
@@ -440,14 +442,11 @@ public class AppletJmol extends Frame
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";color gold;wireframe 100");
+    eval.append(";wireframe 100;"+eval.toString()+".CA;");
 
-    Color col = new Color(viewer.getAtomArgb(atomIndex));
+    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 
-    resetLastRes.append(";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];wireframe 0");
+    eval.append("spacefill 200;select none");
 
     viewer.evalStringQuiet(eval.toString());
 
@@ -469,21 +468,24 @@ public class AppletJmol extends Frame
     return new Color(viewer.getAtomArgb(atomIndex));
   }
 
-  FeatureRenderer fr;
-  public void colourBySequence(AlignmentPanel ap)
+  String lastCommand;
+  FeatureRenderer fr=null;
+  public void colourBySequence(AlignmentPanel sourceap)
   {
-    if(!colourBySequence)
-      return;
+    this.ap = sourceap;
 
+    if (!colourBySequence)
+      return;
 
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     if (mapping.length < 1)
       return;
 
-    SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
 
     boolean showFeatures = false;
+
     if (ap.av.showSequenceFeatures)
     {
       showFeatures = true;
@@ -502,14 +504,15 @@ 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++)
           {
             int pos = mapping[m].getPDBResNum(
                 sequence[s].findPosition(r));
 
-            if (pos < 1 || pos==lastPos)
+            if (pos < 1 || pos == lastPos)
               continue;
 
             lastPos = pos;
@@ -519,7 +522,7 @@ public class AppletJmol extends Frame
             if (showFeatures)
               col = fr.findFeatureColour(col, sequence[s], r);
 
-            if (command.toString().endsWith(":" + mapping[m].getChain()+
+            if (command.toString().endsWith(":" + mapping[m].getChain() +
                                             ";color["
                                             + col.getRed() + ","
                                             + col.getGreen() + ","
@@ -537,19 +540,23 @@ public class AppletJmol extends Frame
             }
 
             command.append(";color["
-                             + col.getRed() + ","
-                             + col.getGreen() + ","
-                             + col.getBlue() + "]");
-
+                           + col.getRed() + ","
+                           + col.getGreen() + ","
+                           + col.getBlue() + "]");
           }
           break;
         }
       }
     }
 
-    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);
       }
@@ -721,7 +728,7 @@ public class AppletJmol extends Frame
       picked+=strInfo.substring(strInfo.indexOf(":")+1,
                                strInfo.indexOf("."));
 
-    picked+=".C";
+    picked+=".CA";
 
     if (!atomsPicked.contains(picked))
     {