DisplayId can be dbref and or jvsuffix

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 186179b..fe2a859 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -64,7 +64,7 @@ public interface SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getDisplayId();\r
+    public String getDisplayId(boolean dbref, boolean jvsuffix);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -237,9 +237,15 @@ public interface SequenceI
 \r
     public void setVamsasId(String id);\r
 \r
+    public void setDBRef(Vector dbs);\r
+\r
     public Vector getDBRef();\r
 \r
     public void addDBRef(DBRefEntry entry);\r
 \r
     public void addSequenceFeature(SequenceFeature sf);\r
+\r
+    public void setDatasetSequence(SequenceI seq);\r
+\r
+    public SequenceI getDatasetSequence();\r
 }\r