X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=107d98d39bc5e0164b8aae03c1f043ead8c0053d;hb=a4d934a390625eaa414656a6dc356acd7236e7b0;hp=d91d43ef33487e6eb23c7e9e36d14f02c90004dd;hpb=dfb45c8f874124d3ff3caac2902ed0c4a0e87cf5;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index d91d43e..107d98d 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -77,6 +77,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     Bond highlightBond1, highlightBond2;
     boolean errorLoading = false;
     boolean seqColoursReady = false;
+    jalview.appletgui.FeatureRenderer fr;
 
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
     {
@@ -118,7 +119,7 @@ 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);
@@ -479,6 +480,18 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     // Applet and Application specific sequence renderers to be used
     void colourBySequence(PDBChain chain)
     {
+      boolean showFeatures = false;
+
+      if(seqcanvas.getViewport().getShowSequenceFeatures())
+        {
+          if(fr==null)
+          {
+            fr = new jalview.appletgui.FeatureRenderer(seqcanvas.getViewport());
+          }
+          fr.transferSettings( seqcanvas.getFeatureRenderer());
+          showFeatures = true;
+        }
+
       for (int i = 0; i < chain.bonds.size(); i++)
       {
         Bond tmp = (Bond) chain.bonds.elementAt(i);
@@ -498,8 +511,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
               tmp.startCol = seqcanvas.getSequenceRenderer().
                   getResidueBoxColour( sequence, index);
 
-          //    tmp.startCol = seqcanvas.getFeatureRenderer().
-         //         findFeatureColour(tmp.startCol, sequence, index);
+              if(showFeatures)
+              tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
             }
         }
 
@@ -509,18 +522,23 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         {
           tmp.endCol = seqcanvas.getSequenceRenderer().
               getResidueBoxColour( sequence, index);
-        //  tmp.endCol = seqcanvas.getFeatureRenderer().
-        //      findFeatureColour(tmp.endCol, sequence, index);
+
+          if(showFeatures)
+          tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
         }
       }
     }
 
 
+    Zsort zsort;
     public void drawScene(Graphics g)
     {
+        if (zbuffer)
+        {
+          if(zsort ==null)
+            zsort = new Zsort();
 
-        if (zbuffer) {
-            Zsort.Zsort(visiblebonds);
+          zsort.Zsort(visiblebonds);
         }
 
 
@@ -716,35 +734,24 @@ 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);
     }