pdbfile details not essential to sequence

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7a48c2b..8928425 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -8,21 +8,14 @@ import MCview.*;
 \r
 public class Sequence implements SequenceI\r
 {\r
-  protected String   name;\r
-  protected String   sequence;\r
+  protected String name;\r
+  protected String sequence;\r
   protected String description;\r
-  protected int      start;\r
-  protected int      end;\r
-  protected String   displayId;\r
-  protected Color    color = Color.white;\r
+  protected int start;\r
+  protected int end;\r
+  protected String displayId;\r
+  protected Color color = Color.white;\r
   String pdbId;\r
-  PDBfile pdb;\r
-\r
-   public int maxchain = -1;\r
-   public int pdbstart;\r
-   public int pdbend;\r
-   public int seqstart;\r
-   public int seqend;\r
 \r
    public Vector sequenceFeatures = new Vector();\r
    public void setSequenceFeatures(Vector v)\r
@@ -42,47 +35,6 @@ public class Sequence implements SequenceI
      return pdbId;\r
    }\r
 \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