X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=ca72942e48234b6ade1b7c31f492172c335b0909;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=f8444a09f8c07b4f64fdab05fce14b2c897f3d30;hpb=d9462b7299f6c5d7025369d55bba347aee04a81d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index f8444a0..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
@@ -18,6 +18,8 @@
  */
 package jalview.datamodel;
 
+import java.util.Hashtable;
+
 /**
  * DOCUMENT ME!
  *
@@ -26,12 +28,13 @@ package jalview.datamodel;
  */
 public class SequenceFeature
 {
-    public int position;
     public int begin;
     public int end;
+    public float score;
     public String type;
     public String description;
-    public String status;
+    public Hashtable otherDetails;
+    public java.util.Vector links;
 
     // Feature group can be set from a features file
     // as a group of features between STARTGROUP and ENDGROUP markers
@@ -48,41 +51,41 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
-      this.position = begin;
+      setValue("status", status);
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
     }
 
-    public boolean equals(SequenceFeature sf)
+    public SequenceFeature(String type,
+                           String desc,
+                           int begin, int end,
+                           float score,
+                           String featureGroup)
     {
-      if(begin != sf.begin
-      || end != sf.end)
-     return false;
+      this.type = type;
+      this.description = desc;
+      this.begin = begin;
+      this.end = end;
+      this.score = score;
+      this.featureGroup = featureGroup;
+    }
 
+    public boolean equals(SequenceFeature sf)
+    {
+      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;
     }
 
 
-    public int getPosition()
-    {
-      return position;
-    }
-
-    public void setPosition(int pos)
-    {
-      position = pos;
-      begin = pos;
-      end = pos;
-    }
-
-
     /**
      * DOCUMENT ME!
      *
@@ -143,30 +146,91 @@ public class SequenceFeature
       description = desc;
     }
 
+    public String getFeatureGroup()
+    {
+      return featureGroup;
+    }
+
+    public void setFeatureGroup(String featureGroup)
+    {
+      this.featureGroup = featureGroup;
+    }
+
+    public void addLink(String labelLink)
+    {
+      if(links==null)
+        links = new java.util.Vector();
+
+      links.insertElementAt(labelLink,0);
+    }
+
+    public float getScore()
+    {
+      return score;
+    }
+
+    public void setScore(float value)
+    {
+      score = value;
+    }
+
     /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * Used for getting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key String
      */
-    public String getStatus()
+    public Object getValue(String key)
+    {
+      if(otherDetails==null)
+        return null;
+      else
+        return otherDetails.get(key);
+    }
+
+    /**
+     * Used for setting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key   eg STRAND
+     * @param value eg +
+     */
+    public void setValue(String key, Object value)
     {
-        return status;
+      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)
     {
-      this.status = status;
+      setValue("status", status);
     }
 
-    public String getFeatureGroup()
+    public String getStatus()
     {
-      return featureGroup;
+      if (otherDetails != null)
+        return otherDetails.get("status").toString();
+      else
+        return null;
     }
 
-    public void setFeatureGroup(String featureGroup)
+    public void setPosition(int pos)
     {
-      this.featureGroup = featureGroup;
+      begin = pos;
+      end = pos;
     }
 
+    public int getPosition()
+    {
+      return begin;
+    }
 
 }