From e141c1213b46aa8d98e525f0332a25515161892b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 1 Mar 2006 14:03:52 +0000
Subject: [PATCH] propagate SearchResult object use to MCView's highlighted
 residue renderer.

---
 src/MCview/AppletPDBCanvas.java |   31 ++++++++++---------------------
 src/MCview/PDBCanvas.java       |   25 +++++++------------------
 2 files changed, 17 insertions(+), 39 deletions(-)

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index b2b2c61..dc4cf0b 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -498,8 +498,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
               tmp.startCol = seqcanvas.getSequenceRenderer().
                   getResidueBoxColour( sequence, index);
 
-          //    tmp.startCol = seqcanvas.getFeatureRenderer().
-         //         findFeatureColour(tmp.startCol, sequence, index);
+              tmp.startCol = seqcanvas.getFeatureRenderer().
+                  findFeatureColour(tmp.startCol, sequence, index);
             }
         }
 
@@ -509,8 +509,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         {
           tmp.endCol = seqcanvas.getSequenceRenderer().
               getResidueBoxColour( sequence, index);
-        //  tmp.endCol = seqcanvas.getFeatureRenderer().
-        //      findFeatureColour(tmp.endCol, sequence, index);
+          tmp.endCol = seqcanvas.getFeatureRenderer().
+              findFeatureColour(tmp.endCol, sequence, index);
         }
       }
     }
@@ -716,35 +716,24 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     void highlightSeqcanvas(int pos)
     {
-      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
-
-      int size = pos==-1?0:3;
-
-      if(highlightRes!=null)
-        size += highlightRes.size()*3;
-
-      int [] array = new int[size];
-      int i=0;
+      SearchResults searchResults = new SearchResults();
       if(highlightRes!=null)
       {
-        for (i = 0; i < highlightRes.size(); i++)
+        for (int i = 0; i < highlightRes.size(); i++)
         {
           int a = Integer.parseInt(highlightRes.elementAt(
               i).toString())+1;
-          array[i * 3] = index;
-          array[ (i * 3) + 1] = a;
-          array[ (i * 3) + 2] = a;
+
+          searchResults.addResult(sequence, a, a);
         }
       }
 
       if(pos!=-1)
       {
-        array[i * 3] = index;
-        array[i * 3 + 1] = pos+1;
-        array[i * 3 + 2] = pos+1;
+        searchResults.addResult(sequence, pos+1, pos+1);
       }
 
-      seqcanvas.highlightSearchResults(array);
+      seqcanvas.highlightSearchResults(searchResults);
     }
 
 
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 6014455..80b65ae 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -666,7 +666,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 if (highlightRes == null)
                   highlightRes = new Vector();
 
-                if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
+                if (highlightRes.contains(fatom.alignmentMapping+""))
                   highlightRes.remove(fatom.alignmentMapping + "");
                 else
                   highlightRes.add(fatom.alignmentMapping + "");
@@ -718,35 +718,24 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     void highlightSeqcanvas(int pos)
     {
-      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
-
-      int size = pos==-1?0:3;
-
-      if(highlightRes!=null)
-        size += highlightRes.size()*3;
-
-      int [] array = new int[size];
-      int i=0;
+      SearchResults searchResults = new SearchResults();
       if(highlightRes!=null)
       {
-        for (i = 0; i < highlightRes.size(); i++)
+        for (int i = 0; i < highlightRes.size(); i++)
         {
           int a = Integer.parseInt(highlightRes.elementAt(
               i).toString())+1;
-          array[i * 3] = index;
-          array[ (i * 3) + 1] = a;
-          array[ (i * 3) + 2] = a;
+
+          searchResults.addResult(sequence, a, a);
         }
       }
 
       if(pos!=-1)
       {
-        array[i * 3] = index;
-        array[i * 3 + 1] = pos+1;
-        array[i * 3 + 2] = pos+1;
+        searchResults.addResult(sequence, pos+1, pos+1);
       }
 
-      seqcanvas.highlightSearchResults(array);
+      seqcanvas.highlightSearchResults(searchResults);
     }
 
 
-- 
1.7.10.2