From 4f42212c4d9a825aac6300ac9e3e3c5349040360 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 31 Oct 2005 15:52:04 +0000
Subject: [PATCH] DisplayId can be dbref and or jvsuffix

---
 src/jalview/datamodel/Sequence.java  |   62 ++++++++++++++++++++++------------
 src/jalview/datamodel/SequenceI.java |    8 ++++-
 2 files changed, 47 insertions(+), 23 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 586280b..c24dc02 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -31,13 +31,14 @@ import java.util.*;
  */
 public class Sequence implements SequenceI
 {
-    protected String name;
-    protected String sequence;
-    protected String description;
-    protected int start;
-    protected int end;
-    protected String displayId;
-    protected Color color = Color.white;
+    SequenceI datasetSequence;
+    String name;
+    String sequence;
+    String description;
+    int start;
+    int end;
+    String displayId;
+    Color color = Color.white;
     String pdbId;
     String vamsasId;
     Vector dbrefs;
@@ -62,8 +63,6 @@ public class Sequence implements SequenceI
       this.end = end;
 
       checkValidRange();
-
-      setDisplayId();
     }
 
     void checkValidRange()
@@ -88,7 +87,6 @@ public class Sequence implements SequenceI
         this.end = endRes;
       }
 
-      setDisplayId();
     }
 
     /**
@@ -165,17 +163,26 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getDisplayId()
+    public String getDisplayId(boolean dbref, boolean jvsuffix)
     {
-        return displayId;
-    }
+      StringBuffer result = new StringBuffer();
+      if (dbref && dbrefs != null)
+      {
+        for (int i = 0; i < dbrefs.size(); i++)
+        {
+          DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);
+          result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");
+        }
+      }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setDisplayId()
-    {
-        displayId = name + "/" + start + "-" + end;
+      result.append(name);
+
+      if (jvsuffix)
+      {
+        result.append("/" + start + "-" + end);
+      }
+
+      return result.toString();
     }
 
     /**
@@ -186,7 +193,6 @@ public class Sequence implements SequenceI
     public void setName(String name)
     {
         this.name = name;
-        setDisplayId();
     }
 
     /**
@@ -207,7 +213,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)
     {
         this.start = start;
-        setDisplayId();
     }
 
     /**
@@ -228,7 +233,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)
     {
         this.end = end;
-        setDisplayId();
     }
 
     /**
@@ -531,6 +535,10 @@ public class Sequence implements SequenceI
       vamsasId = id;
     }
 
+    public void setDBRef(Vector dbref)
+    {
+      dbrefs = dbref;
+    }
     public Vector getDBRef()
     {
       return dbrefs;
@@ -544,4 +552,14 @@ public class Sequence implements SequenceI
       dbrefs.addElement(entry);
     }
 
+    public void setDatasetSequence(SequenceI seq)
+    {
+      datasetSequence = seq;
+    }
+
+    public SequenceI getDatasetSequence()
+    {
+      return datasetSequence;
+    }
+
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 186179b..fe2a859 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -64,7 +64,7 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getDisplayId();
+    public String getDisplayId(boolean dbref, boolean jvsuffix);
 
     /**
      * DOCUMENT ME!
@@ -237,9 +237,15 @@ public interface SequenceI
 
     public void setVamsasId(String id);
 
+    public void setDBRef(Vector dbs);
+
     public Vector getDBRef();
 
     public void addDBRef(DBRefEntry entry);
 
     public void addSequenceFeature(SequenceFeature sf);
+
+    public void setDatasetSequence(SequenceI seq);
+
+    public SequenceI getDatasetSequence();
 }
-- 
1.7.10.2