From 9157d82cb9213d9071c15203dddf96ae9081dfbe Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 29 Oct 2014 19:05:37 +0000
Subject: [PATCH] JAL-353 updated patch for undo successive remove redundant
 sequences

---
 .gitignore                            |    1 +
 src/jalview/commands/EditCommand.java |   20 ++++++++++++++++++--
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 9841761..c47ff62 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@
 /classes
 .externalToolBuilders/Jalview Release indices [Builder].launch
 /.DS_Store
+.DS_Store
 /.com.apple.timemachine.supported
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index da2b552..b39d1dd 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -20,9 +20,15 @@
  */
 package jalview.commands;
 
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.Hashtable;
+import java.util.List;
 
 /**
  * 
@@ -353,6 +359,8 @@ public class EditCommand implements CommandI
           List<SequenceI> sequences;
           synchronized (sequences = command.al.getSequences())
           {
+            // int index = command.al.findIndex(command.seqs[i]);
+            // sequences.add(index, command.seqs[i]);
             sequences.add(command.alIndex[i] < 0 ? 0 : command.alIndex[i], command.seqs[i]);
           }
         }
@@ -396,9 +404,13 @@ public class EditCommand implements CommandI
                       + command.number);
             }
             if (command.seqs[i].getStart() == start)
+            {
               newstart--;
+            }
             else
+            {
               newend++;
+            }
           }
         }
         command.string[i] = null;
@@ -702,10 +714,12 @@ public class EditCommand implements CommandI
       {
         temp = new Annotation[aSize + command.number];
         if (annotations[a].padGaps)
+        {
           for (int aa = 0; aa < temp.length; aa++)
           {
             temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
           }
+        }
       }
       else
       {
@@ -784,8 +798,10 @@ public class EditCommand implements CommandI
           int copylen = Math.min(command.position,
                   annotations[a].annotations.length);
           if (copylen > 0)
+           {
             System.arraycopy(annotations[a].annotations, 0, temp, 0,
                     copylen); // command.position);
+          }
 
           Annotation[] deleted = new Annotation[command.number];
           if (copylen >= command.position)
-- 
1.7.10.2