From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 11:00:35 +0000 (+0000)
Subject: Colour PDB by sequence
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e12d7b37af23fcf0d84b6b970c2b3c651601a02d;p=jalview.git

Colour PDB by sequence
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 192156e..86755dd 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -230,22 +230,29 @@ public class PDBChain {
         }
     }
 
-    public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
-        jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
+    public void colourBySequence(jalview.gui.SequenceRenderer sr,
+                                 jalview.gui.FeatureRenderer fr)
+    {
 
-        for (int i = 0; i < bonds.size(); i++) {
+        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))) {
+                        (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 {
+
+                    int index = sequence.findIndex(pos);
+
+                    tmp.startCol = sr.findSequenceColour(Color.gray, sequence,  index);
+
+                    tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+
+                } else
+                {
                     tmp.startCol = Color.gray;
                 }
 
@@ -253,17 +260,15 @@ public class PDBChain {
                         (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
                     int pos = seqstart +
                         (tmp.at2.resNumber - pdbstart - offset);
-                    int index = seq.findIndex(pos);
+                    int index = sequence.findIndex(pos);
 
-                    tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
-                            seq, index);
-                } else {
+                   tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);
+                   tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);
+                }
+                else
+                {
                     tmp.endCol = Color.gray;
                 }
-            } catch (Exception e) {
-                tmp.startCol = Color.lightGray;
-                tmp.endCol = Color.lightGray;
-            }
         }
     }
 
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f97216b..ae1e4ec 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -97,11 +97,6 @@ public class PDBfile extends jalview.io.FileParse {
 
         makeResidueList();
         makeCaBondList();
-
-        //    for (int i=0; i < chains.size() ; i++) {
-        //  String pog = ((PDBChain)chains.elementAt(i)).print();
-        //  System.out.println(pog);
-        // }
     }
 
     public void makeResidueList() {
@@ -139,12 +134,11 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void colourBySequence(Sequence seq) {
-        //SMJS TODO
-        //    int max = seq.maxchain;
-        //    if (seq.maxchain != -1) {
-        //      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-        //    }
+    public void colourBySequence(jalview.gui.SequenceRenderer sr,
+                                 jalview.gui.FeatureRenderer fr) {
+            for (int i = 0; i < chains.size(); i++) {
+              ((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
+            }
     }
 
     public void setChainColours() {