X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=107d98d39bc5e0164b8aae03c1f043ead8c0053d;hb=05cc1e453976137138e0d24ba0264b8e5f35b628;hp=346ae1e2fa1ba6cab0e4edab42ea40e308b750fb;hpb=b76229ec7f87020dfb2c26b11d910899f8b2c97d;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 346ae1e..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);
@@ -363,7 +364,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         g.drawString("Error loading PDB data!!", 50, getSize().height/2);
         return;
       }
-      else if( !seqColoursReady )
+
+      if( !seqColoursReady )
       {
         g.setColor(Color.black);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
@@ -417,7 +419,13 @@ 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)
@@ -472,6 +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);
@@ -491,8 +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);
             }
         }
 
@@ -502,18 +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);
         }
 
 
@@ -709,35 +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);
     }
 
 
@@ -928,6 +942,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     public void highlightRes(int ii)
    {
+     if(!seqColoursReady)
+       return;
 
      if (highlightRes != null
          && highlightRes.contains((ii-1) + ""))