X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=dc4cf0b6fda07d02f1b6393c721c31ad79d0e07a;hb=9a5435d4f6b25c70aa7c10c66f022ccd86eb4de1;hp=d6247f4ebc2f3d3a6cdb274d688763dbe4ce8b3c;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index d6247f4..dc4cf0b 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -76,6 +76,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     boolean pdbAction = false;
     Bond highlightBond1, highlightBond2;
     boolean errorLoading = false;
+    boolean seqColoursReady = false;
 
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
     {
@@ -117,7 +118,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
                     ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
             as.calcScoreMatrix();
             as.traceAlignment();
-            PrintStream  ps = new PrintStream(System.out)
+            PrintStream ps = new PrintStream(System.out)
            {
               public void print(String x) {
                    mappingDetails.append(x);
@@ -186,6 +187,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     Vector visiblebonds;
     void setupBonds()
     {
+      seqColoursReady = false;
       // Sort the bonds by z coord
       visiblebonds = new Vector();
 
@@ -202,6 +204,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         }
       }
       updateSeqColours();
+      seqColoursReady = true;
       redrawneeded = true;
       repaint();
     }
@@ -360,7 +363,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         g.drawString("Error loading PDB data!!", 50, getSize().height/2);
         return;
       }
-      else if(visiblebonds==null)
+
+      if( !seqColoursReady )
       {
         g.setColor(Color.black);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
@@ -414,7 +418,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       drawLabels(ig);
     }
 
-
+   void setColours(jalview.schemes.ColourSchemeI cs)
+   {
+     bysequence = false;
+     pdb.setColours(cs);
+     redrawneeded = true;
+     repaint();
+   }
     public void updateSeqColours()
     {
       if (pdbAction)
@@ -488,8 +498,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
               tmp.startCol = seqcanvas.getSequenceRenderer().
                   getResidueBoxColour( sequence, index);
 
-          //    tmp.startCol = seqcanvas.getFeatureRenderer().
-         //         findFeatureColour(tmp.startCol, sequence, index);
+              tmp.startCol = seqcanvas.getFeatureRenderer().
+                  findFeatureColour(tmp.startCol, sequence, index);
             }
         }
 
@@ -499,8 +509,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         {
           tmp.endCol = seqcanvas.getSequenceRenderer().
               getResidueBoxColour( sequence, index);
-        //  tmp.endCol = seqcanvas.getFeatureRenderer().
-        //      findFeatureColour(tmp.endCol, sequence, index);
+          tmp.endCol = seqcanvas.getFeatureRenderer().
+              findFeatureColour(tmp.endCol, sequence, index);
         }
       }
     }
@@ -706,35 +716,24 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     void highlightSeqcanvas(int pos)
     {
-      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
-
-      int size = pos==-1?0:3;
-
-      if(highlightRes!=null)
-        size += highlightRes.size()*3;
-
-      int [] array = new int[size];
-      int i=0;
+      SearchResults searchResults = new SearchResults();
       if(highlightRes!=null)
       {
-        for (i = 0; i < highlightRes.size(); i++)
+        for (int i = 0; i < highlightRes.size(); i++)
         {
           int a = Integer.parseInt(highlightRes.elementAt(
               i).toString())+1;
-          array[i * 3] = index;
-          array[ (i * 3) + 1] = a;
-          array[ (i * 3) + 2] = a;
+
+          searchResults.addResult(sequence, a, a);
         }
       }
 
       if(pos!=-1)
       {
-        array[i * 3] = index;
-        array[i * 3 + 1] = pos+1;
-        array[i * 3 + 2] = pos+1;
+        searchResults.addResult(sequence, pos+1, pos+1);
       }
 
-      seqcanvas.highlightSearchResults(array);
+      seqcanvas.highlightSearchResults(searchResults);
     }
 
 
@@ -925,6 +924,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     public void highlightRes(int ii)
    {
+     if(!seqColoursReady)
+       return;
 
      if (highlightRes != null
          && highlightRes.contains((ii-1) + ""))