X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=7df3eaf5c7c1dd18cc0be284cab4cf8634bf9991;hb=b0a90dcb797054f5e01a3b10969e782ef3aafa4a;hp=be2e1c063521fe55fd9a6f1a052c1dd17dc7dc3c;hpb=7abeaf76ba3913ccb95139df58b353bdde49429c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index be2e1c0..7df3eaf 100755
--- 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;
@@ -169,6 +168,44 @@ public class Sequence implements SequenceI
     sequenceFeatures = temp;
   }
 
+  public void deleteFeature(SequenceFeature sf)
+  {
+    if(sequenceFeatures==null)
+      return;
+
+    int index=0;
+    for (index = 0; index < sequenceFeatures.length; index++)
+    {
+      if (sequenceFeatures[index].equals(sf))
+      {
+        break;
+      }
+    }
+
+
+    if(index==sequenceFeatures.length)
+      return;
+
+    int sfLength = sequenceFeatures.length;
+    if(sfLength<2)
+    {
+      sequenceFeatures = null;
+    }
+    else
+    {
+      SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+      if(index<sfLength)
+        System.arraycopy(sequenceFeatures,
+                         index + 1,
+                         temp,
+                         index, sequenceFeatures.length - index -1);
+
+      sequenceFeatures = temp;
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -356,6 +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;
   }
@@ -534,7 +572,6 @@ public class Sequence implements SequenceI
 
     if (i >= sequence.length())
     {
-      length = i - sequence.length() + 1;
       tmp = new StringBuffer(sequence);
     }
     else
@@ -559,26 +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;
@@ -604,9 +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;