From b0e7370d001804e563320570d2a11453954c393e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 16:57:56 +0000
Subject: [PATCH] New function to highlight text search results

---
 src/jalview/gui/SequenceRenderer.java |   34 ++++++++++++++++++++++++++++++---
 1 file changed, 31 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0c1bfdc..192e252 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -9,6 +9,12 @@ import java.util.*;
 public class SequenceRenderer implements RendererI
 {
   FontMetrics fm;
+  boolean renderGaps = true;
+
+  public void renderGaps(boolean b)
+  {
+    renderGaps = b;
+  }
 
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -104,13 +110,14 @@ public class SequenceRenderer implements RendererI
     // Need to find the sequence position here.
     for (int i = start; i <= end; i++)
     {
-        if (i < end && i < seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else if(i<seq.getLength())
+        if(i<seq.getLength())
           s = seq.getSequence().charAt(i);
         else
           s = ' ';
 
+        if(!renderGaps && (s=='-' || s=='.' || s==' '))
+          continue;
+
         if (colText)
         {
             Color c = getResidueBoxColour(cs, seq, i);
@@ -124,4 +131,25 @@ public class SequenceRenderer implements RendererI
     }
   }
 
+  public void drawHighlightedText(Graphics g, 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);
+
+    char s='~';
+    // Need to find the sequence position here.
+    for (int i = start; i <= end; i++)
+    {
+       if(i<seq.getLength())
+          s = seq.getSequence().charAt(i);
+
+      charOffset =  (width - fm.charWidth(s))/2;
+      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
+    }
+  }
+
+
 }
-- 
1.7.10.2