X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5db051ac89bd77b7579315aafe526a8b17f3cbe0;hb=116786d279dcb83f05afd625ad6e39627a37e1e8;hp=eceddf11607d4b5a05d8489a0a414313f7f157f5;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index eceddf1..5db051a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -139,6 +139,8 @@ public class Sequence implements SequenceI
     return this.sequence;
   }
   public String getSequence(int start,int end) {
+    if(end>sequence.length())
+      end = sequence.length();
     return this.sequence.substring(start,end);
   }
 
@@ -182,10 +184,9 @@ 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++;
 
@@ -193,6 +194,22 @@ 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);
@@ -200,6 +217,13 @@ public class Sequence implements SequenceI
     sequence = sbuffer.toString();
   }
 
+  public void deleteChars(int i, int j)
+  {
+    StringBuffer sbuffer = new StringBuffer(sequence);
+    sbuffer.delete(i,j);
+    sequence = sbuffer.toString();
+  }
+
   public void insertCharAt(int i, char c)
   {
     insertCharAt(i,c,true);