X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=ab35c386090b7475694a46fcaaa0567f787b9c91;hb=60d2bc892983abad01d082cbff73466f093879f2;hp=d35cbe851af4a23ed6033ae791fb8f87c9968164;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d35cbe8..ab35c38 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -2,69 +2,40 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 import java.awt.*;
-import java.util.StringTokenizer;
+import java.util.*;
 import MCview.*;
 
 
 public class Sequence implements SequenceI
 {
-  protected String   name;
-  protected String   sequence;
-  protected int      start;
-  protected int      end;
-  protected String   description;
-  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)
+  protected String name;
+  protected String sequence;
+  protected String description;
+  protected int start;
+  protected int end;
+  protected String displayId;
+  protected Color color = Color.white;
+  String pdbId;
+
+   public Vector sequenceFeatures = new Vector();
+   public void setSequenceFeatures(Vector v)
    {
-     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);
-     }
+     sequenceFeatures = v;
    }
 
+   public Vector getSequenceFeatures()
+   {return sequenceFeatures; }
+
+   public void setPDBId(String id)
+   {
+     pdbId = id;
+   }
+   public String getPDBId()
+   {
+     return pdbId;
+   }
+
+
   public Sequence(String name, String sequence, int start, int end)
   {
 
@@ -120,6 +91,13 @@ public class Sequence implements SequenceI
     return this.sequence;
   }
   public String getSequence(int start,int end) {
+    // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+    if(start>=sequence.length())
+      return "";
+
+    if(end>=sequence.length())
+      end = sequence.length();
+
     return this.sequence.substring(start,end);
   }
 
@@ -163,10 +141,9 @@ public class Sequence implements SequenceI
     int j   = 0;
     int pos = start;
 
-    while (j < i)
+    while (j < i && j<sequence.length())
     {
       char c = sequence.charAt(j);
-
       if (!jalview.util.Comparison.isGap((c)))
         pos++;
 
@@ -174,11 +151,37 @@ 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();
+    if (i>=sequence.length())
+      return;
+    sequence = sequence.substring(0,i) + sequence.substring(i+1);
+  }
+
+  public void deleteChars(int i, int j)
+  {
+    if (i>=sequence.length())
+      return;
+    if (j>=sequence.length())
+      sequence = sequence.substring(0,i);
+    else
+      sequence = sequence.substring(0,i) + sequence.substring(j);
   }
 
   public void insertCharAt(int i, char c)
@@ -193,7 +196,11 @@ public class Sequence implements SequenceI
     if (i < sequence.length()) {
       sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
     } else {
-      sequence = tmp + String.valueOf(c);
+      // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
+      char[] ch = new char[1+i-sequence.length()];
+      for (int j=0, k=ch.length; j<k; j++)
+        ch[j] = c;
+      sequence = tmp + String.valueOf(ch);
     }
 
   }