From f59f68c0a389bef51cfc9397dc0c4b645be51c05 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 13 Jan 2005 12:05:10 +0000
Subject: [PATCH] GetResidueBoxColour altered for faster rendering

---
 src/jalview/gui/SequenceRenderer.java |   71 +++++++++++++++++----------------
 1 file changed, 36 insertions(+), 35 deletions(-)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5022050..6483e8b 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -11,7 +11,8 @@ public class SequenceRenderer implements RendererI
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  Color color;
+  Color resBoxColour = Color.white;
+  Graphics graphics;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -26,72 +27,72 @@ public class SequenceRenderer implements RendererI
 
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-   Color c = Color.white;
-try{
-     if (cs != null)
-       c = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
-   }catch(Exception ex){}
+    getBoxColour(cs, seq, i);
+    return resBoxColour;
+  }
+
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
 
-    return c;
+   if (cs != null)
+       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
+   else
+       resBoxColour = Color.white;
   }
 
   public void drawSequence(Graphics g,SequenceI seq,SequenceGroup sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
   {
     currentSequenceGroup = sg;
 
-    drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);
+    graphics = g;
+
+    drawBoxes(seq, start, end, x1, y1, (int) width, height, pid);
 
     fm = g.getFontMetrics();
-    drawText(g,seq,start,end,x1,y1,(int)width,height);
+    drawText(seq,start,end,x1,y1,(int)width,height);
 
   }
 
-  public void drawBoxes(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
+  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
     int i      = start;
     int length = seq.getLength();
 
-    Color currentColor = Color.WHITE;
-
     int curStart = x1;
     int curWidth = width;
 
+    Color tempColour = Color.red;
     while (i <= end && i < length)
     {
-      color = color.white;
-
       if(inCurrentSequenceGroup(i))
       {
         if( currentSequenceGroup.getDisplayBoxes())
-             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
+             getBoxColour(currentSequenceGroup.cs, seq, i);
       }
       else if(av.getShowBoxes())
-           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
-
+           getBoxColour(av.getGlobalColourScheme(), seq, i);
 
-      if (color != currentColor || color != null)
+      if (resBoxColour != tempColour)
       {
-        g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-
-        currentColor = color;
-        g.setColor(color);
+        graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        graphics.setColor(resBoxColour);
 
         curStart = i;
         curWidth = width;
+        tempColour = resBoxColour;
+
       }
       else
         curWidth += width;
 
       i++;
     }
-    g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+    graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
   }
 
-  public void drawText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
   {
     int pady = height/5;
     int charOffset=0;
-    g.setColor(Color.black);
-
     char s;
     // Need to find the sequence position here.
     for (int i = start; i <= end; i++)
@@ -104,7 +105,7 @@ try{
         if(!renderGaps && jalview.util.Comparison.isGap(s))
           continue;
 
-        g.setColor(Color.black);
+        graphics.setColor(Color.black);
 
         if (inCurrentSequenceGroup(i))
         {
@@ -112,7 +113,7 @@ try{
             continue;
 
           if(currentSequenceGroup.getColourText())
-            g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());
+            graphics.setColor(resBoxColour.darker());
         }
         else
         {
@@ -120,11 +121,11 @@ try{
             continue;
 
           if(av.getColourText())
-            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());
+            graphics.setColor(resBoxColour.darker());
         }
 
       charOffset =  (width - fm.charWidth(s))/2;
-      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
+      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
     }
 
 
@@ -138,13 +139,13 @@ try{
     return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;
   }
 
-  public void drawHighlightedText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
   {
     int pady = height/5;
     int charOffset=0;
-    g.setColor(Color.BLACK);
-    g.fillRect(x1,y1,width*(end-start+1),height);
-    g.setColor(Color.white);
+    graphics.setColor(Color.BLACK);
+    graphics.fillRect(x1,y1,width*(end-start+1),height);
+    graphics.setColor(Color.white);
 
     char s='~';
     // Need to find the sequence position here.
@@ -154,7 +155,7 @@ try{
           s = seq.getSequence().charAt(i);
 
       charOffset =  (width - fm.charWidth(s))/2;
-      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
+      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
     }
   }
 
-- 
1.7.10.2