X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=8928425f607b54b4cff148bc8d93d3b19ec9e921;hb=e542a2b9968ee6a7def19e79e84c27684ee686e3;hp=99f2de2dc286be0f702046b0e0a972be60127b0d;hpb=1fea111206bcb8b84284805a3b6e233d5879084c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 99f2de2..8928425 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -8,21 +8,14 @@ import MCview.*;
 
 public class Sequence implements SequenceI
 {
-  protected String   name;
-  protected String   sequence;
+  protected String name;
+  protected String sequence;
   protected String description;
-  protected int      start;
-  protected int      end;
-  protected String   displayId;
-  protected Color    color = Color.white;
+  protected int start;
+  protected int end;
+  protected String displayId;
+  protected Color color = Color.white;
   String pdbId;
-  PDBfile pdb;
-
-   public int maxchain = -1;
-   public int pdbstart;
-   public int pdbend;
-   public int seqstart;
-   public int seqend;
 
    public Vector sequenceFeatures = new Vector();
    public void setSequenceFeatures(Vector v)
@@ -42,47 +35,6 @@ public class Sequence implements SequenceI
      return pdbId;
    }
 
-   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)
   {
@@ -194,18 +146,30 @@ public class Sequence implements SequenceI
     }
     return pos;
   }
+
+  public int[] gapMap() {
+    // Returns an int array giving the position of each residue in the sequence in the alignment
+    String seq = jalview.analysis.AlignSeq.extractGaps("-. ",sequence);
+    int[] map = new int[seq.length()];
+    int j=0;
+    int p=0;
+    while (j<sequence.length()) {
+      if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {
+        map[p++]=j;
+      }
+      j++;
+    }
+    return map;
+  }
+
   public void deleteCharAt(int i)
   {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.deleteCharAt(i);
-    sequence = sbuffer.toString();
+    sequence = sequence.substring(0,i) + sequence.substring(i+1);
   }
 
   public void deleteChars(int i, int j)
   {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.delete(i,j);
-    sequence = sbuffer.toString();
+    sequence = sequence.substring(0,i) + sequence.substring(j);
   }
 
   public void insertCharAt(int i, char c)