Maintain status and position only for uniprot parsing

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 09c9a69..0dec805 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -146,7 +146,7 @@ public class Sequence implements SequenceI
         sequenceFeatures = features;\r
     }\r
 \r
-    public void addSequenceFeature(SequenceFeature sf)\r
+    public synchronized void addSequenceFeature(SequenceFeature sf)\r
     {\r
       if(sequenceFeatures==null)\r
       {\r
@@ -165,7 +165,6 @@ public class Sequence implements SequenceI
       System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);\r
       temp[sequenceFeatures.length] = sf;\r
 \r
-\r
       sequenceFeatures = temp;\r
     }\r
 \r

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 3d8744f..ef391eb 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -51,9 +51,7 @@ public class SequenceFeature
     {\r
       this.type = type;\r
       this.description = desc;\r
-      if(status!=null)\r
-        setValue("status", status);\r
-\r
+      setValue("status", status);\r
       this.begin = begin;\r
       this.end = end;\r
       this.featureGroup = featureGroup;\r
@@ -75,13 +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).equals\r
-         (sf.type+sf.description))\r
+      if(!(type+description+featureGroup).equals\r
+         (sf.type+sf.description+sf.featureGroup))\r
         return false;\r
 \r
       return true;\r
@@ -197,11 +195,42 @@ public class SequenceFeature
      */\r
     public void setValue(String key, Object value)\r
     {\r
-      if(otherDetails == null)\r
-        otherDetails = new Hashtable();\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
-      otherDetails.put(key, value);\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