X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=48057b8401c00221761871deb7cf2fe2e12a0015;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=80dfda54c35e56f521e290d007226b9b0d011e0a;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 80dfda5..48057b8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -42,9 +42,12 @@ public class Sequence implements SequenceI
     String vamsasId;
     Vector dbrefs;
 
+    /** This annotation is displayed below the alignment but the
+     * positions are tied to the residues of this sequence */
+    Vector annotation;
 
     /** DOCUMENT ME!! */
-    public Vector sequenceFeatures;
+    public SequenceFeature [] sequenceFeatures;
 
     /**
      * Creates a new Sequence object.
@@ -66,9 +69,9 @@ public class Sequence implements SequenceI
       checkValidRange();
     }
 
-    static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+    com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
                         "[/][0-9]{1,}[-][0-9]{1,}$");
-    static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+    com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
                         "[0-9]{1,}$");
 
     void parseId()
@@ -133,25 +136,40 @@ public class Sequence implements SequenceI
      *
      * @param v DOCUMENT ME!
      */
-    public void setSequenceFeatures(Vector v)
+    public void setSequenceFeatures(SequenceFeature [] features)
     {
-        sequenceFeatures = v;
+        sequenceFeatures = features;
     }
 
     public void addSequenceFeature(SequenceFeature sf)
     {
       if(sequenceFeatures==null)
-        sequenceFeatures = new Vector();
+      {
+        sequenceFeatures = new SequenceFeature[0];
+      }
+
+      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+      temp[sequenceFeatures.length] = sf;
 
-      sequenceFeatures.addElement(sf);
+
+      sequenceFeatures = temp;
     }
 
+    SequenceFeature [] sfarray;
+
+        public SequenceFeature[] getsfarray()
+        {
+          return sfarray;
+        }
+
+
     /**
      * DOCUMENT ME!
      *
      * @return DOCUMENT ME!
      */
-    public Vector getSequenceFeatures()
+    public SequenceFeature [] getSequenceFeatures()
     {
         return sequenceFeatures;
     }
@@ -574,4 +592,24 @@ public class Sequence implements SequenceI
       return datasetSequence;
     }
 
+    public AlignmentAnnotation [] getAnnotation()
+    {
+      if(annotation==null)
+        return null;
+
+      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
+      for(int r = 0; r<ret.length; r++)
+        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+
+      return ret;
+    }
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    {
+      if(this.annotation==null)
+        this.annotation = new Vector();
+
+      this.annotation.addElement( annotation );
+    }
+
 }