From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 5 May 2005 13:25:12 +0000 (+0000)
Subject: colour by sequence just about works
X-Git-Tag: Release_2_0~311
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c1f5bec45d222fc1513a5bc8c75376145a93c2c7;p=jalview.git

colour by sequence just about works
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 15de7c3..92627d5 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -34,6 +34,8 @@ public class PDBChain {
   public Sequence sequence;
   public boolean isVisible = false;
 
+  public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
+
   //public DrawableSequence ds;
 
   public PDBChain(String id) {
@@ -209,38 +211,41 @@ public class PDBChain {
   }
 
 
-  public void colourBySequence(Sequence seq) {
-
-//    for (int i = 0; i < bonds.size(); i++) {
-//      Bond tmp = (Bond)bonds.elementAt(i);
-//      try {
-//
-//        if (tmp.at1.resNumber >= (offset + seq.pdbstart - 1) && tmp.at1.resNumber <= (offset + seq.pdbend - 1)) {
-//
-//          int pos   = seq.seqtart() + (tmp.at1.resNumber - seq.pdbstart - offset) ;
-//          int index = seq.findIndex(pos);
-//
-//          tmp.startCol = (Color)seq.getResidueBoxColour(index);
-//
-//        } else {
-//          tmp.startCol = Color.gray;
-//        }
-//
-//        if (tmp.at2.resNumber >= (offset + seq.pdbstart -1) && tmp.at2.resNumber <= (seq.pdbend+offset-1)) {
-//
-//          int pos    = seq.seqstart + (tmp.at2.resNumber - seq.pdbstart-offset);
-//          int index  = seq.findIndex(pos);
-//
-//          tmp.endCol = (Color)seq.getResidueBoxColour(index);
-//
-//        } else {
-//          tmp.endCol = Color.gray;
-//        }
-//      } catch (Exception e) {
-//        tmp.startCol = Color.lightGray;
-//        tmp.endCol = Color.lightGray;
-//      }
-//    }
+  public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
+jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
+
+
+    for (int i = 0; i < bonds.size(); i++) {
+      Bond tmp = (Bond)bonds.elementAt(i);
+      try {
+
+        if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
+
+          int pos   = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
+          int index = seq.findIndex(pos);
+
+
+          tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
+
+        } else {
+          tmp.startCol = Color.gray;
+        }
+
+        if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
+
+          int pos    = seqstart + (tmp.at2.resNumber - pdbstart-offset);
+          int index  = seq.findIndex(pos);
+
+          tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
+
+        } else {
+          tmp.endCol = Color.gray;
+        }
+      } catch (Exception e) {
+        tmp.startCol = Color.lightGray;
+        tmp.endCol = Color.lightGray;
+      }
+    }
   }
 
   public void setChainColours() {