From 23444dd246b45e21346f6cc85564cf3f876320fd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:31:09 +0000
Subject: [PATCH] search ids added

---
 src/jalview/gui/IdCanvas.java |   26 ++++++++++++++++++++++----
 src/jalview/gui/IdPanel.java  |   14 ++++++++++++++
 2 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 6c50f31..d7a034c 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -19,6 +19,8 @@ public class IdCanvas extends JPanel
   int imgHeight=0;
   boolean fastPaint = false;
 
+  java.util.ArrayList searchResults;
+
   public IdCanvas(AlignViewport av)
   {
     setLayout(new BorderLayout());
@@ -29,8 +31,13 @@ public class IdCanvas extends JPanel
   public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
       int charHeight = av.getCharHeight();
 
-
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {
+      if(searchResults!=null && searchResults.contains(s))
+      {
+        gg.setColor(Color.black);
+        gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
+        gg.setColor(Color.white);
+      }
+      else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {
 	  gg.setColor(Color.lightGray);
 	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
 	  gg.setColor(Color.white);
@@ -145,10 +152,15 @@ public class IdCanvas extends JPanel
       {
         // Selected sequence colours
 
-        if (av.getSelectionGroup()!= null
+        if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))
+        {
+          gg.setColor(Color.black);
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+      }
+      else if (av.getSelectionGroup()!= null
             && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))
         {
-       //   if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
@@ -180,4 +192,10 @@ public class IdCanvas extends JPanel
     }
 
   }
+
+  public void setHighlighted(java.util.ArrayList found)
+  {
+    searchResults = found;
+    repaint();
+  }
 }
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 3444881..fcf8e92 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -176,6 +176,20 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     PaintRefresher.Refresh(this);
   }
 
+  public void highlightSearchResults( java.util.ArrayList found )
+  {
+    idCanvas.setHighlighted( found );
+
+    if(found == null)
+      return;
+
+    int index = av.alignment.findIndex( (SequenceI)found.get(0));
+
+    // do we need to scroll the panel?
+    if(av.getStartSeq()>index || av.getEndSeq()<index)
+        alignPanel.setScrollValues( av.getStartRes(), index);
+  }
+
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread
       extends Thread
-- 
1.7.10.2