Align boxes

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b1a1be2..7df3eaf 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -37,7 +37,6 @@ public class Sequence implements SequenceI
   String description;
   int start;
   int end;
-  Color color = Color.white;
   Vector pdbIds;
   String vamsasId;
   DBRefEntry[] dbrefs;
@@ -394,6 +393,7 @@ public class Sequence implements SequenceI
     int nend = findPosition(end) - 1;
     // JBPNote - this is an incomplete copy.
     SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
+    nseq.setDescription(description);
     nseq.setDatasetSequence(getDatasetSequence());
     return nseq;
   }
@@ -596,26 +596,6 @@ public class Sequence implements SequenceI
     insertCharAt(i, 1, c);
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   */
-  public void setColor(Color c)
-  {
-    this.color = c;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color getColor()
-  {
-    return color;
-  }
-
   public String getVamsasId()
   {
     return vamsasId;
@@ -641,9 +621,18 @@ public class Sequence implements SequenceI
     if (dbrefs == null)
       dbrefs = new DBRefEntry[0];
 
-    DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1];
-    System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+    int i, iSize = dbrefs.length;
+
+    for(i=0; i<iSize; i++)
+      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
+      && dbrefs[i].getSource().equals(entry.getSource())
+      && dbrefs[i].getVersion().equals(entry.getVersion()))
+      {
+        return;
+      }
 
+    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, iSize);
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;