From 92fba5062ad24d8bb5a8167b775d44e67f375012 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 17:06:42 +0000
Subject: [PATCH] Find routine added

---
 src/jalview/gui/SeqCanvas.java |   75 +++++++++++++++++++++++++++-------------
 1 file changed, 51 insertions(+), 24 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4e287b1..8785454 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -21,19 +21,16 @@ public class SeqCanvas extends JPanel
     int oldstarty;
     int oldendx;
     int oldendy;
-
     public boolean paintFlag = false;
+
     boolean showScores = false;
+    boolean displaySearch = false;
+    int [] searchResults = null;
 
     int chunkHeight;
     int chunkWidth;
 
-    Graphics debugG;
-   // FeatureRenderer fr = new FeatureRenderer();
-  //  BlockRenderer   br = new BlockRenderer();
-  //  CpGRenderer     cgr = new CpGRenderer();
-
-    ColourSchemeI    cs = new ZappoColourScheme();
+    ColourSchemeI   cs = new ZappoColourScheme();
 
     public SeqCanvas(AlignViewport av)
     {
@@ -65,14 +62,14 @@ public class SeqCanvas extends JPanel
  */
 
   public void paintComponent(Graphics g) {
-    debugG = g;
 
     AlignmentI da = av.getAlignment();
 
     if (img == null ||
         imgWidth  !=  getWidth()  ||
-        imgHeight !=  getHeight() ||
-        paintFlag == true) {
+        imgHeight !=  getHeight()
+        || paintFlag)
+    {
 
       imgWidth  = (getWidth() > 0 ? getWidth() : 1);
       imgHeight = (getHeight() > 0 ? getHeight() : 1);
@@ -80,18 +77,13 @@ public class SeqCanvas extends JPanel
       img = createImage(imgWidth,imgHeight);
       gg  = img.getGraphics();
 
-     // SMJS I added this in to update the AV when the size changes
-      //      until I figure out how this should be done
-      setFont(av.getFont());
-
       gg.setFont(av.getFont());
 
-      paintFlag = false;
-
       oldstartx = -1;
       oldendx   = -1;
       oldstarty = -1;
       oldendy   = -1;
+      paintFlag = false;
     }
 
     int startx = av.getStartRes();
@@ -267,9 +259,9 @@ public class SeqCanvas extends JPanel
     }
 
 
-    gg.setColor(Color.red);
-    gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY );
-    gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 );
+  //  gg.setColor(Color.red);
+  //  gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY );
+   // gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 );
 
 
     g.drawImage(img,0,0,this);
@@ -327,7 +319,6 @@ public class SeqCanvas extends JPanel
     SequenceGroup group;
     for (int i = y1 ; i < y2 ;i++)
     {
-      RendererI r = sr;
     /*  if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
           r = fr;
           System.out.println("use feature renderer");
@@ -342,7 +333,7 @@ public class SeqCanvas extends JPanel
      group = av.alignment.findGroup( nextSeq );
      if( group!=null )
      {
-       r.drawSequence(g, group.cs, nextSeq,
+       sr.drawSequence(g, group.cs, nextSeq,
                       x1,
                       x2,
                       (int) ( (x1 - startx) * charWidth),
@@ -353,7 +344,7 @@ public class SeqCanvas extends JPanel
      }
      else
      {
-       r.drawSequence(g, cs, nextSeq,
+       sr.drawSequence(g, cs, nextSeq,
                       x1,
                       x2,
                       (int) ( (x1 - startx) * charWidth),
@@ -367,11 +358,37 @@ public class SeqCanvas extends JPanel
 
     }
 
-  }
 
-  public int groupX, groupY, groupendX, groupendY;
+    if(displaySearch)
+    {
+      for(int r=0; r<searchResults.length; r+=3)
+      {
+        int searchSeq = searchResults[r];
+        int searchStart = searchResults[r+1];
+        int searchEnd = searchResults[r+2];
+
+        if (searchSeq >= y1 && searchSeq <= y2)
+        {
+          SequenceRenderer ssr = (SequenceRenderer) sr;
+          ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),
+                                  searchStart,
+                                  searchEnd,
+                                  (int) ( (searchStart - startx) * charWidth),
+                                  offset +
+                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
+              charHeight),
+                                  (int) charWidth,
+                                  charHeight);
+
+        }
+      }
+    }
 
 
+  }
+
+ // public int groupX, groupY, groupendX, groupendY;
+
   public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
     g.setColor(c);
     g.fillRect(x1,y1,width,height);
@@ -381,4 +398,14 @@ public class SeqCanvas extends JPanel
     return chunkWidth;
   }
 
+  public void highlightSearchResults(int [] results)
+  {
+    // results are in the order sequence, startRes, endRes
+    searchResults = results;
+    displaySearch = true;
+    paintFlag = true;
+    repaint();
+  }
+
+
 }
-- 
1.7.10.2