From 4741fc6fc72b7c5ffd75af5b1bc17070fef448f9 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 7 May 2007 13:57:03 +0000
Subject: [PATCH] Dont use gold colouring for highlight

---
 src/MCview/AppletPDBCanvas.java       |    9 +++------
 src/jalview/appletgui/AppletJmol.java |   11 ++++++-----
 2 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index bfcd67a..e11e558 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -118,7 +118,6 @@ public class AppletPDBCanvas
     int pdbend = 0;
     int seqstart = 0;
     int seqend = 0;
-    AlignSeq maxAlignseq = null;
 
     //JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
@@ -165,8 +164,7 @@ public class AppletPDBCanvas
         pdbend = as.seq2end;
         seqstart = as.seq1start + sequence.getStart() - 1;
         seqend = as.seq1end + sequence.getEnd() - 1;
-        maxAlignseq = as;
-      }
+       }
 
       mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
       mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
@@ -498,7 +496,7 @@ public class AppletPDBCanvas
   // Applet and Application specific sequence renderers to be used
   void colourBySequence()
   {
-    SequenceRenderer sr = ap.getSequenceRenderer();
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
 
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
@@ -1078,7 +1076,7 @@ public class AppletPDBCanvas
   ///StructureListener
   public String getPdbFile()
   {
-    return "???";
+    return pdbentry.getFile();
   }
 
 
@@ -1159,7 +1157,6 @@ public class AppletPDBCanvas
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
     colourBySequence();
     redrawneeded = true;
     repaint();
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index f873230..14e6704 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -441,14 +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());
 
-- 
1.7.10.2