From 1dbe649695c2c5d4475dcf61e51ed24cddf16594 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 5 May 2005 13:25:49 +0000
Subject: [PATCH] pdb end seq and startseq determined here

---
 src/MCview/rotCanvas.java |   53 ++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 50 insertions(+), 3 deletions(-)

diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java
index 5df8d9f..9b822f3 100755
--- a/src/MCview/rotCanvas.java
+++ b/src/MCview/rotCanvas.java
@@ -5,6 +5,8 @@ import java.awt.event.*;
 import java.util.*;
 import java.io.*;
 import javax.swing.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.*;
 
 public class rotCanvas extends JPanel implements KeyListener,
                                                  MouseListener,
@@ -53,7 +55,53 @@ public class rotCanvas extends JPanel implements KeyListener,
 
   Font font = new Font("Helvetica",Font.PLAIN,10);
 
-  public rotCanvas(PDBfile pdb) throws IOException {
+  public rotCanvas(PDBfile pdb, Sequence sequence, jalview.gui.AlignViewport av) throws IOException {
+
+    int max = -10;
+    int maxchain = -1;
+    int pdbstart=0, pdbend=0,  seqstart =0,  seqend=0;
+
+
+    for (int i=0; i < pdb.chains.size(); i++) {
+      // Now lets compare the sequences to get
+      // the start and end points.
+
+    java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), ".");
+    String newString = "";
+
+    while (str.hasMoreTokens()) {
+        newString += str.nextToken();
+    }
+      // Align the sequence to the pdb
+      AlignSeq as = new AlignSeq(sequence,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
+      as.calcScoreMatrix();
+      as.traceAlignment();
+      as.printAlignment();
+
+      if (as.maxscore > max) {
+        max = as.maxscore;
+        maxchain = i;
+
+        pdbstart = as.seq2start;
+        pdbend = as.seq2end;
+        seqstart = as.seq1start  - 1 ;
+        seqend = as.seq1end  -1;
+      }
+
+      System.out.println("PDB start/end " + pdbstart + " " + pdbend);
+      System.out.println("SEQ start/end " + seqstart + " " + seqend);
+    }
+
+
+    ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
+    ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbend = pdbend;
+    ( (PDBChain)pdb.chains.elementAt(maxchain)).seqstart = seqstart;
+     ( (PDBChain)pdb.chains.elementAt(maxchain)).seqend = seqend;
+     ( (PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
+     ( (PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
+     ( (PDBChain)pdb.chains.elementAt(maxchain)).colourBySequence(av, sequence);
+
+
 
     this.pdb      = pdb;
     this.prefsize = new Dimension( getWidth(), getHeight());
@@ -231,7 +279,7 @@ public class rotCanvas extends JPanel implements KeyListener,
     centre[2] = ztot / (2 * (float)bsize);
   }
 
-  public void paintComponent(Graphics g) {
+  public void paint(Graphics g) {
     //Only create the image at the beginning -
     //this saves much memory usage
     if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {
@@ -473,7 +521,6 @@ public class rotCanvas extends JPanel implements KeyListener,
     if(fatom!=null)
      {
        this.setToolTipText(fatom.resName);
-       System.out.println(fatom.resName);
      }
      else
         this.setToolTipText(null);
-- 
1.7.10.2