X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=10b0659573efeace10c7ac52e77c29c8120e4c53;hb=ab0f35021e8e5dbbe1da52ad0e1991099525d269;hp=17db1a0b26059f5fce1386a0c44c5609f84ba94b;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 17db1a0..10b0659 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -72,6 +72,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     PDBChain mainchain;
     Vector highlightRes;
     boolean pdbAction = false;
+    boolean seqColoursReady = false;
+    jalview.gui.FeatureRenderer fr;
+    Color backgroundColour = Color.black;
 
     public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
     {
@@ -198,6 +201,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     Vector visiblebonds;
     void setupBonds()
     {
+      seqColoursReady = false;
       // Sort the bonds by z coord
       visiblebonds = new Vector();
 
@@ -215,6 +219,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
 
       updateSeqColours();
+      seqColoursReady = true;
       redrawneeded = true;
       repaint();
     }
@@ -369,7 +374,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     {
       super.paintComponent(g);
 
-      if(visiblebonds==null)
+      if(!seqColoursReady)
       {
         g.setColor(Color.black);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
@@ -413,7 +418,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void drawAll(Graphics g, int width, int height)
     {
-      g.setColor(Color.black);
+      g.setColor(backgroundColour);
       g.fillRect(0, 0, width, height);
       drawScene(g);
       drawLabels(g);
@@ -474,11 +479,20 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     void colourBySequence(PDBChain chain)
     {
      // System.out.println("colour by seq");
+     boolean showFeatures = false;
+     if(seqcanvas.getViewport().getShowSequenceFeatures())
+     {
+       showFeatures = true;
+       if (fr == null)
+         fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
+
+       fr.transferSettings( seqcanvas.getFeatureRenderer() );
+     }
+
+      Bond tmp;
       for (int i = 0; i < chain.bonds.size(); i++)
       {
-        Bond tmp = (Bond) chain.bonds.elementAt(i);
-        tmp.startCol = Color.lightGray;
-        tmp.endCol = Color.lightGray;
+        tmp = (Bond) chain.bonds.elementAt(i);
 
         if(chain!=mainchain)
           continue;
@@ -492,11 +506,12 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             {
               tmp.startCol = seqcanvas.getSequenceRenderer().
                   getResidueBoxColour( sequence, index);
+
+              if(showFeatures)
+                tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+
               if(tmp.startCol==null)
                 tmp.startCol = Color.white;
-
-              tmp.startCol = seqcanvas.getFeatureRenderer().
-                  findFeatureColour(tmp.startCol, sequence, index);
             }
         }
 
@@ -510,95 +525,118 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             {
               tmp.endCol = seqcanvas.getSequenceRenderer().
                   getResidueBoxColour( sequence, index);
+
+              if(showFeatures)
+                tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
+
               if(tmp.endCol==null)
                 tmp.endCol = Color.white;
-              tmp.endCol = seqcanvas.getFeatureRenderer().
-                  findFeatureColour(tmp.endCol, sequence, index);
             }
         }
       }
     }
 
 
+    Zsort zsort;
     public void drawScene(Graphics g)
     {
-        if (zbuffer)
-        {
-            Zsort.Zsort(visiblebonds);
-        }
+      if (zbuffer)
+      {
+        if (zsort == null)
+          zsort = new Zsort();
 
-        Bond tmpBond=null;
-        for (int i = 0; i < visiblebonds.size(); i++)
-        {
-            tmpBond = (Bond) visiblebonds.elementAt(i);
+        zsort.Zsort(visiblebonds);
+      }
 
-            xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
-                (getWidth() / 2));
-            ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
-                (getHeight() / 2));
+      Bond tmpBond = null;
+      for (int i = 0; i < visiblebonds.size(); i++)
+      {
+        tmpBond = (Bond) visiblebonds.elementAt(i);
 
-            xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
-                (getWidth() / 2));
-            yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
-                (getHeight() / 2));
+        xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
+                        (getWidth() / 2));
+        ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+                        (getHeight() / 2));
 
-            xmid = (xend + xstart) / 2;
-            ymid = (yend + ystart) / 2;
+        xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
+                      (getWidth() / 2));
+        yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+                      (getHeight() / 2));
 
-            if (depthcue && !bymolecule)
-            {
-                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
-                    g.setColor(tmpBond.startCol.darker().darker());
-                    drawLine(g, xstart, ystart, xmid, ymid);
-                    g.setColor(tmpBond.endCol.darker().darker());
-                    drawLine(g, xmid, ymid, xend, yend);
-                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
-                    g.setColor(tmpBond.startCol.darker());
-                    drawLine(g, xstart, ystart, xmid, ymid);
-
-                    g.setColor(tmpBond.endCol.darker());
-                    drawLine(g, xmid, ymid, xend, yend);
-                } else {
-                    g.setColor(tmpBond.startCol);
-                    drawLine(g, xstart, ystart, xmid, ymid);
+        xmid = (xend + xstart) / 2;
+        ymid = (yend + ystart) / 2;
+        if (depthcue && !bymolecule)
+        {
+          if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
+          {
 
-                    g.setColor(tmpBond.endCol);
-                    drawLine(g, xmid, ymid, xend, yend);
-                }
-            } else if (depthcue && bymolecule) {
-                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
-                    g.setColor(Color.green.darker().darker());
-                    drawLine(g, xstart, ystart, xend, yend);
-                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
-                    g.setColor(Color.green.darker());
-                    drawLine(g, xstart, ystart, xend, yend);
-                } else {
-                    g.setColor(Color.green);
-                    drawLine(g, xstart, ystart, xend, yend);
-                }
-            } else if (!depthcue && !bymolecule) {
-                g.setColor(tmpBond.startCol);
-                drawLine(g, xstart, ystart, xmid, ymid);
-                g.setColor(tmpBond.endCol);
-                drawLine(g, xmid, ymid, xend, yend);
-            } else {
-                drawLine(g, xstart, ystart, xend, yend);
-            }
+            g.setColor(tmpBond.startCol.darker().darker());
+            drawLine(g, xstart, ystart, xmid, ymid);
+            g.setColor(tmpBond.endCol.darker().darker());
+            drawLine(g, xmid, ymid, xend, yend);
 
-            if(highlightBond1!=null && highlightBond1==tmpBond)
-            {
-              g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());
-              drawLine(g, xmid, ymid, xend, yend);
-            }
+          }
+          else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
+          {
+            g.setColor(tmpBond.startCol.darker());
+            drawLine(g, xstart, ystart, xmid, ymid);
 
-            if(highlightBond2!=null && highlightBond2==tmpBond)
-            {
-              g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());
-              drawLine(g, xstart, ystart, xmid, ymid);
-            }
+            g.setColor(tmpBond.endCol.darker());
+            drawLine(g, xmid, ymid, xend, yend);
+          }
+          else
+          {
+            g.setColor(tmpBond.startCol);
+            drawLine(g, xstart, ystart, xmid, ymid);
 
+            g.setColor(tmpBond.endCol);
+            drawLine(g, xmid, ymid, xend, yend);
+          }
+        }
+        else if (depthcue && bymolecule)
+        {
+          if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
+          {
+            g.setColor(Color.green.darker().darker());
+            drawLine(g, xstart, ystart, xend, yend);
+          }
+          else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
+          {
+            g.setColor(Color.green.darker());
+            drawLine(g, xstart, ystart, xend, yend);
+          }
+          else
+          {
+            g.setColor(Color.green);
+            drawLine(g, xstart, ystart, xend, yend);
+          }
+        }
+        else if (!depthcue && !bymolecule)
+        {
+          g.setColor(tmpBond.startCol);
+          drawLine(g, xstart, ystart, xmid, ymid);
+          g.setColor(tmpBond.endCol);
+          drawLine(g, xmid, ymid, xend, yend);
+        }
+        else
+        {
+          drawLine(g, xstart, ystart, xend, yend);
+        }
+
+        if (highlightBond1 != null && highlightBond1 == tmpBond)
+        {
+          g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());
+          drawLine(g, xmid, ymid, xend, yend);
         }
 
+        if (highlightBond2 != null && highlightBond2 == tmpBond)
+        {
+          g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());
+          drawLine(g, xstart, ystart, xmid, ymid);
+        }
+
+      }
+
 
     }
 
@@ -663,7 +701,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 if (highlightRes == null)
                   highlightRes = new Vector();
 
-                if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
+                if (highlightRes.contains(fatom.alignmentMapping+""))
                   highlightRes.remove(fatom.alignmentMapping + "");
                 else
                   highlightRes.add(fatom.alignmentMapping + "");
@@ -715,35 +753,24 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     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);
     }
 
 
@@ -929,6 +956,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
    Bond highlightBond1, highlightBond2;
    public void highlightRes(int ii)
   {
+    if( !seqColoursReady )
+      return;
 
     if (highlightRes != null
         && highlightRes.contains((ii-1) + ""))