From 3c900dfc85fe55b1dcefd318acee9a34f701b8bd Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 2 Oct 2007 16:01:39 +0000
Subject: [PATCH] convenience constructor for duplicating an annotation and
 editing it for hidden columns

---
 src/jalview/datamodel/AlignmentAnnotation.java |   15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 87c113f..b59417a 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -656,6 +656,21 @@ Loading...
     this(label, description, null);
     setScore(score);
   }
+  /**
+   * copy constructor with edit based on the hidden columns marked in colSel
+   * @param alignmentAnnotation
+   * @param colSel
+   */
+  public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+          ColumnSelection colSel)
+  {
+    this(alignmentAnnotation);
+    if (annotations==null)
+    {
+      return;
+    }
+    colSel.makeVisibleAnnotation(this);
+  }
 
   public void setPadGaps(boolean padgaps, char gapchar)
   {
-- 
1.7.10.2