From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 1 Jun 2018 13:57:08 +0000 (+0100)
Subject: JAL-1950 JAL-2937 allow copy of group without sequences being also copied to cloned... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3490e38574052242c9440d162a427f7c59234a0a;p=jalview.git

JAL-1950 JAL-2937 allow copy of group without sequences being also copied to cloned group
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index cd2b137..cffe0d9 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -198,11 +198,27 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
+    this(seqsel, true);
+  }
+
+  /**
+   * copy constructor
+   * 
+   * @param seqsel
+   * @param keepsequences
+   *          if false do not add sequences from seqsel to new instance
+   */
+  public SequenceGroup(SequenceGroup seqsel, boolean keepsequences)
+  {
     this();
+
     if (seqsel != null)
     {
       sequences = new ArrayList<>();
-      sequences.addAll(seqsel.sequences);
+      if (keepsequences)
+      {
+        sequences.addAll(seqsel.sequences);
+      }
       if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
@@ -236,8 +252,10 @@ public class SequenceGroup implements AnnotatedCollectionI
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
       hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
       hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
-      if (seqsel.conservationData != null)
+      if (keepsequences && seqsel.conservationData != null)
       {
+        // todo avoid doing this if we don't actually want derived calculations
+        // !
         recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
       }