X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=69db54d3b00590f249de23480df4944af244a9ab;hb=8220e64aa2718d0f81f39a93df46c3f2265a9fa4;hp=e8cf340051d669e508f8888ac3080a9dc1c15b55;hpb=10c6c64a1ad5f2f4ebd75dc0a4eb3c0dbc9798d5;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e8cf340..69db54d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -11,7 +11,9 @@ public class SequenceRenderer implements RendererI
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  Color color;
+  SequenceGroup [] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -26,101 +28,74 @@ public class SequenceRenderer implements RendererI
 
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-   Color c = Color.white;
-
-     if (cs != null)
-       c = cs.findColour(seq, seq.getSequence(i, i + 1), i, av.getConsensus(false));
+    getBoxColour(cs, seq, i);
+    return resBoxColour;
+  }
 
-    return c;
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+   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)
+  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;
+    allGroups = sg;
+
+    graphics = g;
 
-    drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);
+    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;
 
-  //  int threshold = 80;
-
+    Color tempColour = null;
     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);
+      else
+        resBoxColour = Color.white;
 
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
-    //  String    s     = (String)hash.get("maxResidue");
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();
-  //    int       max   = ((Integer)hash.get("size")).intValue();
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));
 
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||
-	  s.equals("-") ||
-	  s.equals(".") ||
-	  s.equals(" "))
-      {
-	c = Color.white;
-      } else {
-	if (frac > 0.9) {
-	  c = Color.red;
-	} else if (frac > 0.8) {
-	  c = Color.orange;
-	} else if (frac > 0.7) {
-	  c = Color.pink;
-	} else if (frac > 0.5) {
-	  c = Color.yellow;
-	} else if (frac> 0.3) {
-	    c = Color.lightGray;
-	}
-      }*/
-
-      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++)
@@ -130,18 +105,21 @@ public class SequenceRenderer implements RendererI
         else
           s = ' ';
 
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))
+        if(!renderGaps && jalview.util.Comparison.isGap(s))
           continue;
 
-        g.setColor(Color.black);
+        graphics.setColor(Color.black);
 
         if (inCurrentSequenceGroup(i))
         {
           if(!currentSequenceGroup.getDisplayText())
             continue;
 
-          if(currentSequenceGroup.getColourText())
-            g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());
+            if (currentSequenceGroup.getColourText())
+            {
+              getBoxColour(currentSequenceGroup.cs, seq, i);
+              graphics.setColor(resBoxColour.darker());
+            }
         }
         else
         {
@@ -149,11 +127,14 @@ public class SequenceRenderer implements RendererI
             continue;
 
           if(av.getColourText())
-            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());
+           {
+             getBoxColour(av.getGlobalColourScheme(), seq, i);
+             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);
     }
 
 
@@ -161,19 +142,26 @@ public class SequenceRenderer implements RendererI
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(currentSequenceGroup==null)
+    if(allGroups ==null)
       return false;
 
-    return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;
+    for(int i=0; i<allGroups.length; i++)
+      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+      {
+         currentSequenceGroup = allGroups[i];
+         return true;
+      }
+
+    return 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.
@@ -183,7 +171,7 @@ public class SequenceRenderer implements RendererI
           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);
     }
   }