header updated

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index f8444a0..ca72942 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -18,6 +18,8 @@
  */\r
 package jalview.datamodel;\r
 \r
+import java.util.Hashtable;\r
+\r
 /**\r
  * DOCUMENT ME!\r
  *\r
@@ -26,12 +28,13 @@ 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 Hashtable otherDetails;\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
@@ -48,41 +51,41 @@ public class SequenceFeature
     {\r
       this.type = type;\r
       this.description = desc;\r
-      this.status = status;\r
-      this.position = begin;\r
+      setValue("status", status);\r
       this.begin = begin;\r
       this.end = end;\r
       this.featureGroup = featureGroup;\r
     }\r
 \r
-    public boolean equals(SequenceFeature sf)\r
+    public SequenceFeature(String type,\r
+                           String desc,\r
+                           int begin, int end,\r
+                           float score,\r
+                           String featureGroup)\r
     {\r
-      if(begin != sf.begin\r
-      || end != sf.end)\r
-     return false;\r
+      this.type = type;\r
+      this.description = desc;\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
+      if (begin != sf.begin\r
+          || end != sf.end\r
+          || score != sf.score)\r
+        return false;\r
 \r
-      if(!(type+description+status).equals\r
-         (sf.type+sf.description+sf.status))\r
+      if(!(type+description+featureGroup).equals\r
+         (sf.type+sf.description+sf.featureGroup))\r
         return false;\r
 \r
       return true;\r
     }\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
@@ -143,30 +146,91 @@ public class SequenceFeature
       description = desc;\r
     }\r
 \r
+    public String getFeatureGroup()\r
+    {\r
+      return featureGroup;\r
+    }\r
+\r
+    public void setFeatureGroup(String featureGroup)\r
+    {\r
+      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
     /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
+     * Used for getting values which are not in the\r
+     * basic set. eg STRAND, FRAME for GFF file\r
+     * @param key String\r
      */\r
-    public String getStatus()\r
+    public Object getValue(String key)\r
+    {\r
+      if(otherDetails==null)\r
+        return null;\r
+      else\r
+        return otherDetails.get(key);\r
+    }\r
+\r
+    /**\r
+     * Used for setting values which are not in the\r
+     * basic set. eg STRAND, FRAME for GFF file\r
+     * @param key   eg STRAND\r
+     * @param value eg +\r
+     */\r
+    public void setValue(String key, Object value)\r
     {\r
-        return status;\r
+      if(value!=null)\r
+      {\r
+        if (otherDetails == null)\r
+          otherDetails = new Hashtable();\r
+\r
+        otherDetails.put(key, value);\r
+      }\r
     }\r
 \r
+\r
+    /*\r
+     * The following methods are added to maintain\r
+     * the castor Uniprot mapping file for the moment.\r
+     */\r
     public void setStatus(String status)\r
     {\r
-      this.status = status;\r
+      setValue("status", status);\r
     }\r
 \r
-    public String getFeatureGroup()\r
+    public String getStatus()\r
     {\r
-      return featureGroup;\r
+      if (otherDetails != null)\r
+        return otherDetails.get("status").toString();\r
+      else\r
+        return null;\r
     }\r
 \r
-    public void setFeatureGroup(String featureGroup)\r
+    public void setPosition(int pos)\r
     {\r
-      this.featureGroup = featureGroup;\r
+      begin = pos;\r
+      end = pos;\r
     }\r
 \r
+    public int getPosition()\r
+    {\r
+      return begin;\r
+    }\r
 \r
 }\r