From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 18 Nov 2004 18:37:45 +0000 (+0000)
Subject: updates
X-Git-Tag: Release_2_0~917
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=28c732f6b0a3a43029bcc529fef8ac1174befa69;p=jalview.git

updates
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aad8014..cc5d760 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,7 +1,10 @@
 package jalview.datamodel;
 
-
+import jalview.analysis.*;
 import java.awt.*;
+import java.util.StringTokenizer;
+import MCview.*;
+
 
 public class Sequence implements SequenceI
 {
@@ -13,6 +16,54 @@ public class Sequence implements SequenceI
   protected int      charHeight;
   protected String   displayId;
   protected Color    color = Color.white;
+  PDBfile pdb;
+   public int maxchain = -1;
+
+   public int pdbstart;
+   public int pdbend;
+   public int seqstart;
+   public int seqend;
+   public void setPDBfile(PDBfile pdb)
+   {
+     this.pdb = pdb;
+     int max = -10;
+     maxchain = -1;
+
+     for (int i=0; i < pdb.chains.size(); i++) {
+
+       System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);
+       // Now lets compare the sequences to get
+       // the start and end points.
+
+
+     StringTokenizer str = new StringTokenizer(sequence, ".");
+     String newString = "";
+
+     while (str.hasMoreTokens()) {
+         newString += str.nextToken();
+     }
+       // Align the sequence to the pdb
+       AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
+       as.calcScoreMatrix();
+       as.traceAlignment();
+       as.printAlignment();
+
+       System.out.println("Score = " + as.maxscore);
+       if (as.maxscore > max) {
+         System.out.println("New max score");
+         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);
+     }
+   }
 
   public Sequence(String name, String sequence, int start, int end)
   {