X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=8928425f607b54b4cff148bc8d93d3b19ec9e921;hb=5d2e589a842cf831e4fdeff6b8ed7e7ce6729fd5;hp=aad8014f54d59742706e62cdf867c9eea7aeb0f5;hpb=cc36a8838d643b1866e14f16366a0d0625aab7a1;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aad8014..8928425 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,18 +1,40 @@
 package jalview.datamodel;
 
-
+import jalview.analysis.*;
 import java.awt.*;
+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;
+  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)
+   {
+     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)
   {
@@ -69,6 +91,8 @@ 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);
   }
 
@@ -93,19 +117,18 @@ 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) {
@@ -113,21 +136,40 @@ 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;
   }
+
+  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)
+  {
+    sequence = sequence.substring(0,i) + sequence.substring(j);
   }
 
   public void insertCharAt(int i, char c)