X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=ca72942e48234b6ade1b7c31f492172c335b0909;hb=b46b15a5edcd1fa2cd670503287ec753e46245f3;hp=b054ea1958b853212c5bf5a0c533362311cf7fe6;hpb=a2435635b288c8fa08f7f345b9e906c056514ff0;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index b054ea1..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
@@ -33,8 +33,7 @@ public class SequenceFeature
     public float score;
     public String type;
     public String description;
-    public String status;
-    Hashtable otherDetails;
+    public Hashtable otherDetails;
     public java.util.Vector links;
 
     // Feature group can be set from a features file
@@ -52,11 +51,12 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
+      setValue("status", status);
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
     }
+
     public SequenceFeature(String type,
                            String desc,
                            int begin, int end,
@@ -65,7 +65,6 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
       this.begin = begin;
       this.end = end;
       this.score = score;
@@ -74,13 +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+status).equals
-         (sf.type+sf.description+sf.status))
+      if(!(type+description+featureGroup).equals
+         (sf.type+sf.description+sf.featureGroup))
         return false;
 
       return true;
@@ -147,21 +146,6 @@ public class SequenceFeature
       description = desc;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getStatus()
-    {
-        return status;
-    }
-
-    public void setStatus(String status)
-    {
-      this.status = status;
-    }
-
     public String getFeatureGroup()
     {
       return featureGroup;
@@ -211,11 +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);
+        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);
+    }
+
+    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;
+    }
+
 }