From 73ffad785a317d4014bc448ea4d8a7303e8a4350 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 24 Jul 2009 15:10:05 +0000
Subject: [PATCH] implement new insert annotation row method and ensure group
 annotation rows are removed when groups are removed

---
 src/jalview/datamodel/Alignment.java |   47 ++++++++++++++++++++++++++--------
 1 file changed, 36 insertions(+), 11 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 7fcbda2..afe7032 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -25,6 +25,10 @@ import jalview.analysis.*;
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
+/**
+ * @author JimP
+ *
+ */
 public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
@@ -352,6 +356,14 @@ public class Alignment implements AlignmentI
   {
     if (groups.contains(g))
     {
+      if (annotations!=null && annotations.length>0)
+      {
+        if (g.hasAnnotationRows())
+        {  // remove any annotation references. 
+          deleteAnnotation(g.getConsensus());// todo - create=false flag so we don't create another object unnecessarily
+          deleteAnnotation(g.getConservationRow());
+        }
+      }
       groups.removeElement(g);
     }
   }
@@ -606,14 +618,19 @@ public class Alignment implements AlignmentI
     return swap;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param aa
-   *                DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation)
    */
   public void addAnnotation(AlignmentAnnotation aa)
   {
+    addAnnotation(aa, -1);
+  }
+  
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation, int)
+   */
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
     int aSize = 1;
     if (annotations != null)
     {
@@ -621,16 +638,24 @@ public class Alignment implements AlignmentI
     }
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-    temp[aSize - 1] = aa;
-
     int i = 0;
-
+    if (pos==-1 || pos>=aSize) {
+      temp[aSize - 1] = aa;
+    } else {
+      temp[pos] = aa;
+    }
     if (aSize > 1)
     {
-      for (i = 0; i < (aSize - 1); i++)
+      int p=0;
+      for (i = 0; i < (aSize-1); i++,p++)
       {
-        temp[i] = annotations[i];
+        if (p==pos)
+        {
+          p++;
+        }
+        if (p<temp.length) {
+          temp[p] = annotations[i];
+        }
       }
     }
 
-- 
1.7.10.2