updates

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aad8014..cc5d760 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,7 +1,10 @@
 package jalview.datamodel;\r
 \r
-\r
+import jalview.analysis.*;\r
 import java.awt.*;\r
+import java.util.StringTokenizer;\r
+import MCview.*;\r
+\r
 \r
 public class Sequence implements SequenceI\r
 {\r
@@ -13,6 +16,54 @@ public class Sequence implements SequenceI
   protected int      charHeight;\r
   protected String   displayId;\r
   protected Color    color = Color.white;\r
+  PDBfile pdb;\r
+   public int maxchain = -1;\r
+\r
+   public int pdbstart;\r
+   public int pdbend;\r
+   public int seqstart;\r
+   public int seqend;\r
+   public void setPDBfile(PDBfile pdb)\r
+   {\r
+     this.pdb = pdb;\r
+     int max = -10;\r
+     maxchain = -1;\r
+\r
+     for (int i=0; i < pdb.chains.size(); i++) {\r
+\r
+       System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);\r
+       // Now lets compare the sequences to get\r
+       // the start and end points.\r
+\r
+\r
+     StringTokenizer str = new StringTokenizer(sequence, ".");\r
+     String newString = "";\r
+\r
+     while (str.hasMoreTokens()) {\r
+         newString += str.nextToken();\r
+     }\r
+       // Align the sequence to the pdb\r
+       AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
+       as.calcScoreMatrix();\r
+       as.traceAlignment();\r
+       as.printAlignment();\r
+\r
+       System.out.println("Score = " + as.maxscore);\r
+       if (as.maxscore > max) {\r
+         System.out.println("New max score");\r
+         max = as.maxscore;\r
+         maxchain = i;\r
+\r
+         pdbstart = as.seq2start;\r
+         pdbend = as.seq2end;\r
+         seqstart = as.seq1start  - 1 ;\r
+         seqend = as.seq1end  -1;\r
+       }\r
+\r
+       System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
+       System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
+     }\r
+   }\r
 \r
   public Sequence(String name, String sequence, int start, int end)\r
   {\r