X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=ebdff92bb896cd11255b7c8dd8959fa0d2b48339;hb=cd1ded4a9a6f3478f3b704c9c97fd323ac5dbdd7;hp=cc5d760532264f639847d70ff24264e640683f83;hpb=28c732f6b0a3a43029bcc529fef8ac1174befa69;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc5d760..ebdff92 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -2,7 +2,7 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 import java.awt.*;
-import java.util.StringTokenizer;
+import java.util.*;
 import MCview.*;
 
 
@@ -10,19 +10,38 @@ public class Sequence implements SequenceI
 {
   protected String   name;
   protected String   sequence;
+  protected String description;
   protected int      start;
   protected int      end;
-  protected String   description;
-  protected int      charHeight;
   protected String   displayId;
   protected Color    color = Color.white;
+  String pdbId;
   PDBfile pdb;
-   public int maxchain = -1;
 
+   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)
+   {
+     sequenceFeatures = v;
+   }
+
+   public Vector getSequenceFeatures()
+   {return sequenceFeatures; }
+
+   public void setPDBId(String id)
+   {
+     pdbId = id;
+   }
+   public String getPDBId()
+   {
+     return pdbId;
+   }
+
    public void setPDBfile(PDBfile pdb)
    {
      this.pdb = pdb;
@@ -120,6 +139,8 @@ public class Sequence implements SequenceI
     return this.sequence;
   }
   public String getSequence(int start,int end) {
+    if(end>=sequence.length())
+      end = sequence.length()-1;
     return this.sequence.substring(start,end);
   }
 
@@ -144,19 +165,18 @@ public class Sequence implements SequenceI
 
     while (i< sequence.length() && j <= end && j <= pos) {
 
-      String s = sequence.substring(i,i+1);
+      char c = sequence.charAt(i);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         j++;
-      }
+
       i++;
     }
-    if (j == end && j < pos) {
+    if (j == end && j < pos)
       return end+1;
-    } else {
-
+    else
       return i;
-    }
+
   }
 
   public int findPosition(int i) {
@@ -164,12 +184,12 @@ public class Sequence implements SequenceI
     int j   = 0;
     int pos = start;
 
-    while (j < i) {
-      String s = sequence.substring(j,j+1);
-
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+    while (j < i && j<sequence.length())
+    {
+      char c = sequence.charAt(j);
+      if (!jalview.util.Comparison.isGap((c)))
         pos++;
-      }
+
       j++;
     }
     return pos;