From 963abee52aa793415d08bdc0f63d8bd3c9678940 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 7 Jun 2006 12:54:50 +0000
Subject: [PATCH] Remove position, add score and links

---
 src/jalview/datamodel/SequenceFeature.java |   47 +++++++++++++++++++---------
 1 file changed, 32 insertions(+), 15 deletions(-)

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index f8444a0..dd39f9f 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -26,12 +26,13 @@ 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 java.util.Vector links;
 
     // Feature group can be set from a features file
     // as a group of features between STARTGROUP and ENDGROUP markers
@@ -49,11 +50,24 @@ public class SequenceFeature
       this.type = type;
       this.description = desc;
       this.status = status;
-      this.position = begin;
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
     }
+    public SequenceFeature(String type,
+                           String desc,
+                           int begin, int end,
+                           float score,
+                           String featureGroup)
+    {
+      this.type = type;
+      this.description = desc;
+      this.status = status;
+      this.begin = begin;
+      this.end = end;
+      this.score = score;
+      this.featureGroup = featureGroup;
+    }
 
     public boolean equals(SequenceFeature sf)
     {
@@ -70,19 +84,6 @@ public class SequenceFeature
     }
 
 
-    public int getPosition()
-    {
-      return position;
-    }
-
-    public void setPosition(int pos)
-    {
-      position = pos;
-      begin = pos;
-      end = pos;
-    }
-
-
     /**
      * DOCUMENT ME!
      *
@@ -168,5 +169,21 @@ public class SequenceFeature
       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;
+    }
 }
-- 
1.7.10.2