Remove position, add score and links

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index f8444a0..dd39f9f 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -26,12 +26,13 @@ package jalview.datamodel;
  */\r
 public class SequenceFeature\r
 {\r
-    public int position;\r
     public int begin;\r
     public int end;\r
+    public float score;\r
     public String type;\r
     public String description;\r
     public String status;\r
+    public java.util.Vector links;\r
 \r
     // Feature group can be set from a features file\r
     // as a group of features between STARTGROUP and ENDGROUP markers\r
@@ -49,11 +50,24 @@ public class SequenceFeature
       this.type = type;\r
       this.description = desc;\r
       this.status = status;\r
-      this.position = begin;\r
       this.begin = begin;\r
       this.end = end;\r
       this.featureGroup = featureGroup;\r
     }\r
+    public SequenceFeature(String type,\r
+                           String desc,\r
+                           int begin, int end,\r
+                           float score,\r
+                           String featureGroup)\r
+    {\r
+      this.type = type;\r
+      this.description = desc;\r
+      this.status = status;\r
+      this.begin = begin;\r
+      this.end = end;\r
+      this.score = score;\r
+      this.featureGroup = featureGroup;\r
+    }\r
 \r
     public boolean equals(SequenceFeature sf)\r
     {\r
@@ -70,19 +84,6 @@ public class SequenceFeature
     }\r
 \r
 \r
-    public int getPosition()\r
-    {\r
-      return position;\r
-    }\r
-\r
-    public void setPosition(int pos)\r
-    {\r
-      position = pos;\r
-      begin = pos;\r
-      end = pos;\r
-    }\r
-\r
-\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -168,5 +169,21 @@ public class SequenceFeature
       this.featureGroup = featureGroup;\r
     }\r
 \r
+    public void addLink(String labelLink)\r
+    {\r
+      if(links==null)\r
+        links = new java.util.Vector();\r
 \r
+      links.insertElementAt(labelLink,0);\r
+    }\r
+\r
+    public float getScore()\r
+    {\r
+      return score;\r
+    }\r
+\r
+    public void setScore(float value)\r
+    {\r
+      score = value;\r
+    }\r
 }\r