From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 15 Jun 2006 12:51:52 +0000 (+0000)
Subject: Maintain status and position only for uniprot parsing
X-Git-Tag: Release_2_1~350
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=62f21e48108443babb5c855967c6d388f23904d4;p=jalview.git

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
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -146,7 +146,7 @@ public class Sequence implements SequenceI
         sequenceFeatures = features;
     }
 
-    public void addSequenceFeature(SequenceFeature sf)
+    public synchronized void addSequenceFeature(SequenceFeature sf)
     {
       if(sequenceFeatures==null)
       {
@@ -165,7 +165,6 @@ public class Sequence implements SequenceI
       System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
       temp[sequenceFeatures.length] = sf;
 
-
       sequenceFeatures = temp;
     }
 
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 3d8744f..ef391eb 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -51,9 +51,7 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      if(status!=null)
-        setValue("status", status);
-
+      setValue("status", status);
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
@@ -75,13 +73,13 @@ public class SequenceFeature
 
     public boolean equals(SequenceFeature sf)
     {
-      if(begin != sf.begin
-      || end != sf.end)
-     return false;
-
+      if (begin != sf.begin
+          || end != sf.end
+          || score != sf.score)
+        return false;
 
-      if(!(type+description).equals
-         (sf.type+sf.description))
+      if(!(type+description+featureGroup).equals
+         (sf.type+sf.description+sf.featureGroup))
         return false;
 
       return true;
@@ -197,11 +195,42 @@ public class SequenceFeature
      */
     public void setValue(String key, Object value)
     {
-      if(otherDetails == null)
-        otherDetails = new Hashtable();
+      if(value!=null)
+      {
+        if (otherDetails == null)
+          otherDetails = new Hashtable();
+
+        otherDetails.put(key, value);
+      }
+    }
+
+
+    /*
+     * The following methods are added to maintain
+     * the castor Uniprot mapping file for the moment.
+     */
+    public void setStatus(String status)
+    {
+      setValue("status", status);
+    }
 
-      otherDetails.put(key, value);
+    public String getStatus()
+    {
+      if (otherDetails != null)
+        return otherDetails.get("status").toString();
+      else
+        return null;
     }
 
+    public void setPosition(int pos)
+    {
+      begin = pos;
+      end = pos;
+    }
+
+    public int getPosition()
+    {
+      return begin;
+    }
 
 }