added shiftList to record changes in alignment column positions.

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index dd39f9f..b50c50d 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -18,6 +18,8 @@
  */\r
 package jalview.datamodel;\r
 \r
+import java.util.Hashtable;\r
+\r
 /**\r
  * DOCUMENT ME!\r
  *\r
@@ -31,7 +33,7 @@ public class SequenceFeature
     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
@@ -49,11 +51,12 @@ public class SequenceFeature
     {\r
       this.type = type;\r
       this.description = desc;\r
-      this.status = status;\r
+      setValue("status", status);\r
       this.begin = begin;\r
       this.end = end;\r
       this.featureGroup = featureGroup;\r
     }\r
+\r
     public SequenceFeature(String type,\r
                            String desc,\r
                            int begin, int end,\r
@@ -62,7 +65,6 @@ public class SequenceFeature
     {\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
@@ -71,13 +73,13 @@ public class SequenceFeature
 \r
     public boolean equals(SequenceFeature sf)\r
     {\r
-      if(begin != sf.begin\r
-      || end != sf.end)\r
-     return false;\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
@@ -144,21 +146,6 @@ public class SequenceFeature
       description = desc;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String getStatus()\r
-    {\r
-        return status;\r
-    }\r
-\r
-    public void setStatus(String status)\r
-    {\r
-      this.status = status;\r
-    }\r
-\r
     public String getFeatureGroup()\r
     {\r
       return featureGroup;\r
@@ -186,4 +173,64 @@ public class SequenceFeature
     {\r
       score = value;\r
     }\r
+\r
+    /**\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 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
+      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
+      setValue("status", status);\r
+    }\r
+\r
+    public String getStatus()\r
+    {\r
+      if (otherDetails != null)\r
+        return otherDetails.get("status").toString();\r
+      else\r
+        return null;\r
+    }\r
+\r
+    public void setPosition(int pos)\r
+    {\r
+      begin = pos;\r
+      end = pos;\r
+    }\r
+\r
+    public int getPosition()\r
+    {\r
+      return begin;\r
+    }\r
+\r
 }\r