From 94e3d91558ad96de545821aeb548934f8c8353a3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 14 Jun 2006 10:17:45 +0000
Subject: [PATCH] Status is now in otherData of feature

---
 src/jalview/appletgui/SeqPanel.java        |    4 ++--
 src/jalview/datamodel/SequenceFeature.java |   26 ++++++--------------------
 src/jalview/gui/AlignmentPanel.java        |    4 ++--
 src/jalview/gui/Jalview2XML.java           |    1 -
 src/jalview/gui/SeqPanel.java              |    4 ++--
 5 files changed, 12 insertions(+), 27 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 4b7a45e..5ff10ce 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -551,9 +551,9 @@ public class SeqPanel
         if (sf.getDescription() != null)
           featureText.append(" " + sf.getDescription());
 
-        if (sf.getStatus() != null && sf.getStatus().length() > 0)
+        if (sf.getValue("status") != null )
         {
-          featureText.append(" (" + sf.getStatus() + ")");
+          featureText.append(" (" + sf.getValue("status") + ")");
         }
         featureText.append("\n");
 
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index b054ea1..3d8744f 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -33,7 +33,6 @@ public class SequenceFeature
     public float score;
     public String type;
     public String description;
-    public String status;
     Hashtable otherDetails;
     public java.util.Vector links;
 
@@ -52,11 +51,14 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
+      if(status!=null)
+        setValue("status", status);
+
       this.begin = begin;
       this.end = end;
       this.featureGroup = featureGroup;
     }
+
     public SequenceFeature(String type,
                            String desc,
                            int begin, int end,
@@ -65,7 +67,6 @@ public class SequenceFeature
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
       this.begin = begin;
       this.end = end;
       this.score = score;
@@ -79,8 +80,8 @@ public class SequenceFeature
      return false;
 
 
-      if(!(type+description+status).equals
-         (sf.type+sf.description+sf.status))
+      if(!(type+description).equals
+         (sf.type+sf.description))
         return false;
 
       return true;
@@ -147,21 +148,6 @@ public class SequenceFeature
       description = desc;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getStatus()
-    {
-        return status;
-    }
-
-    public void setStatus(String status)
-    {
-      this.status = status;
-    }
-
     public String getFeatureGroup()
     {
       return featureGroup;
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 20ed37d..4a7a05d 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1171,9 +1171,9 @@ public class AlignmentPanel extends GAlignmentPanel
                       if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
                         text.append(" " + features[f].getDescription());
 
-                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
+                      if (features[f].getValue("status") != null )
                       {
-                        text.append(" (" + features[f].getStatus() + ")");
+                        text.append(" (" + features[f].getValue("status") + ")");
                       }
                     }
                   }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8ac5e8c..f79a158 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -210,7 +210,6 @@ public class Jalview2XML
                 features.setBegin(sf[index].getBegin());
                 features.setEnd(sf[index].getEnd());
                 features.setDescription(sf[index].getDescription());
-                features.setStatus(sf[index].getStatus());
                 features.setType(sf[index].getType());
                 features.setFeatureGroup(sf[index].getFeatureGroup());
                 jseq.addFeatures(features);
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 79d55fd..d457593 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -569,9 +569,9 @@ public class SeqPanel extends JPanel implements MouseListener,
                         && !features[i].description.equals(features[i].getType()))
                       sbuffer.append("; " + features[i].getDescription());
 
-                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
+                    if (features[i].getValue("status") != null)
                     {
-                      sbuffer.append("; (" + features[i].getStatus() + ")");
+                      sbuffer.append("; (" + features[i].getValue("status") + ")");
                     }
                     if (features[i].links != null)
                       sbuffer.append(" <img src=\"" + linkImageURL + "\">");
-- 
1.7.10.2