New function to highlight text search results

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0c1bfdc..192e252 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -9,6 +9,12 @@ import java.util.*;
 public class SequenceRenderer implements RendererI\r
 {\r
   FontMetrics fm;\r
+  boolean renderGaps = true;\r
+\r
+  public void renderGaps(boolean b)\r
+  {\r
+    renderGaps = b;\r
+  }\r
 \r
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r
@@ -104,13 +110,14 @@ public class SequenceRenderer implements RendererI
     // Need to find the sequence position here.\r
     for (int i = start; i <= end; i++)\r
     {\r
-        if (i < end && i < seq.getLength())\r
-          s = seq.getSequence().charAt(i);\r
-        else if(i<seq.getLength())\r
+        if(i<seq.getLength())\r
           s = seq.getSequence().charAt(i);\r
         else\r
           s = ' ';\r
 \r
+        if(!renderGaps && (s=='-' || s=='.' || s==' '))\r
+          continue;\r
+\r
         if (colText)\r
         {\r
             Color c = getResidueBoxColour(cs, seq, i);\r
@@ -124,4 +131,25 @@ public class SequenceRenderer implements RendererI
     }\r
   }\r
 \r
+  public void drawHighlightedText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+  {\r
+    int pady = height/5;\r
+    int charOffset=0;\r
+    g.setColor(Color.BLACK);\r
+    g.fillRect(x1,y1,width*(end-start+1),height);\r
+    g.setColor(Color.white);\r
+\r
+    char s='~';\r
+    // Need to find the sequence position here.\r
+    for (int i = start; i <= end; i++)\r
+    {\r
+       if(i<seq.getLength())\r
+          s = seq.getSequence().charAt(i);\r
+\r
+      charOffset =  (width - fm.charWidth(s))/2;\r
+      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+    }\r
+  }\r
+\r
+\r
 }\r