X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=14ce0ff52437a984de51aefedcba554af7c460ce;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=1adff257d1318a19459b6cb4d9a2fbc33feef438;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1adff25..14ce0ff 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,6 +18,10 @@
  */
 package jalview.datamodel;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
 /**
  * DOCUMENT ME!
  *
@@ -26,36 +30,93 @@ package jalview.datamodel;
  */
 public class SequenceFeature
 {
-    int position;
-    int begin;
-    int end;
-    String type;
-    String description;
-    String status;
+    public int begin;
+    public int end;
+    public float score;
+    public String type;
+    public String description;
+    public Hashtable otherDetails;
+    public java.util.Vector links;
+
+    // Feature group can be set from a features file
+    // as a group of features between STARTGROUP and ENDGROUP markers
+    public String featureGroup;
 
     public SequenceFeature()
     {}
-
-    public SequenceFeature(String type, String desc, String status, int begin, int end)
+    /**
+     * Constructs a duplicate feature.
+     * Note: Uses clone on the otherDetails so only shallow copies are made
+     * of additional properties and method will silently fail if unclonable
+     * objects are found in the hash.
+     * @param cpy
+     */
+    public SequenceFeature(SequenceFeature cpy) {
+        if (cpy!=null) {
+            begin = cpy.begin;
+            end = cpy.end;
+            score = cpy.score;
+            if (cpy.type != null)
+              type = new String(cpy.type);
+            if (cpy.description != null)
+              description = new String(cpy.description);
+            if (cpy.featureGroup != null)
+              featureGroup = new String(cpy.featureGroup);
+            if (cpy.otherDetails!=null) {
+                try {
+                    otherDetails = (Hashtable) cpy.otherDetails.clone();
+                } catch (Exception e) {
+                    // Uncloneable objects in the otherDetails - don't complain
+                }
+            }
+            if (cpy.links!=null && cpy.links.size()>0) {
+                links=new Vector();
+                for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {
+                    links.setElementAt(cpy.links.elementAt(i), i);
+                }
+            }
+        }
+    }
+    public SequenceFeature(String type,
+                           String desc,
+                           String status,
+                           int begin, int end,
+                           String featureGroup)
     {
       this.type = type;
       this.description = desc;
-      this.status = status;
-      this.position = begin;
+      setValue("status", status);
       this.begin = begin;
       this.end = end;
+      this.featureGroup = featureGroup;
     }
 
-    public int getPosition()
+    public SequenceFeature(String type,
+                           String desc,
+                           int begin, int end,
+                           float score,
+                           String featureGroup)
     {
-      return position;
+      this.type = type;
+      this.description = desc;
+      this.begin = begin;
+      this.end = end;
+      this.score = score;
+      this.featureGroup = featureGroup;
     }
 
-    public void setPosition(int pos)
+    public boolean equals(SequenceFeature sf)
     {
-      position = pos;
-      begin = pos;
-      end = pos;
+      if (begin != sf.begin
+          || end != sf.end
+          || score != sf.score)
+        return false;
+
+      if(!(type+description+featureGroup).equals
+         (sf.type+sf.description+sf.featureGroup))
+        return false;
+
+      return true;
     }
 
 
@@ -119,19 +180,91 @@ public class SequenceFeature
       description = desc;
     }
 
+    public String getFeatureGroup()
+    {
+      return featureGroup;
+    }
+
+    public void setFeatureGroup(String featureGroup)
+    {
+      this.featureGroup = featureGroup;
+    }
+
+    public void addLink(String labelLink)
+    {
+      if(links==null)
+        links = new java.util.Vector();
+
+      links.insertElementAt(labelLink,0);
+    }
+
+    public float getScore()
+    {
+      return score;
+    }
+
+    public void setScore(float value)
+    {
+      score = value;
+    }
+
     /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * Used for getting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key String
      */
-    public String getStatus()
+    public Object getValue(String key)
     {
-        return status;
+      if(otherDetails==null)
+        return null;
+      else
+        return otherDetails.get(key);
     }
 
+    /**
+     * Used for setting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key   eg STRAND
+     * @param value eg +
+     */
+    public void setValue(String key, Object value)
+    {
+      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)
     {
-      this.status = status;
+      setValue("status", status);
+    }
+
+    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;
     }
 
 }