X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=ca72942e48234b6ade1b7c31f492172c335b0909;hb=ed8d18abc302ac802ad1d0611f3fe2fef570ab5e;hp=3d8744fc47616c6cfa617090604d872a2ffde693;hpb=94e3d91558ad96de545821aeb548934f8c8353a3;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 3d8744f..ca72942 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -33,7 +33,7 @@ public class SequenceFeature
     public float score;
     public String type;
     public String description;
-    Hashtable otherDetails;
+    public Hashtable otherDetails;
     public java.util.Vector links;
 
     // Feature group can be set from a features file
@@ -51,9 +51,7 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      if(status!=null)
-        setValue("status", status);
-
+      setValue("status", status);
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
@@ -75,13 +73,13 @@ public class SequenceFeature
 
     public boolean equals(SequenceFeature sf)
     {
-      if(begin != sf.begin
-      || end != sf.end)
-     return false;
-
+      if (begin != sf.begin
+          || end != sf.end
+          || score != sf.score)
+        return false;
 
-      if(!(type+description).equals
-         (sf.type+sf.description))
+      if(!(type+description+featureGroup).equals
+         (sf.type+sf.description+sf.featureGroup))
         return false;
 
       return true;
@@ -197,11 +195,42 @@ public class SequenceFeature
      */
     public void setValue(String key, Object value)
     {
-      if(otherDetails == null)
-        otherDetails = new Hashtable();
+      if(value!=null)
+      {
+        if (otherDetails == null)
+          otherDetails = new Hashtable();
+
+        otherDetails.put(key, value);
+      }
+    }
+
+
+    /*
+     * The following methods are added to maintain
+     * the castor Uniprot mapping file for the moment.
+     */
+    public void setStatus(String status)
+    {
+      setValue("status", status);
+    }
 
-      otherDetails.put(key, value);
+    public String getStatus()
+    {
+      if (otherDetails != null)
+        return otherDetails.get("status").toString();
+      else
+        return null;
     }
 
+    public void setPosition(int pos)
+    {
+      begin = pos;
+      end = pos;
+    }
+
+    public int getPosition()
+    {
+      return begin;
+    }
 
 }