From ea94f71e4b8bd5ceda06e696f6e92723cc2d9db1 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 1 Jul 2015 14:15:19 +0100
Subject: [PATCH] JAL-1802 handle slide sequences edits in split frame mode

---
 src/jalview/datamodel/Sequence.java |    8 ++++----
 src/jalview/gui/AlignFrame.java     |    7 ++++++-
 src/jalview/util/StringUtils.java   |    2 +-
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 37bb7a9..c78ec22 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,6 +20,9 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
@@ -27,9 +30,6 @@ import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
-import jalview.analysis.AlignSeq;
-import jalview.util.StringUtils;
-
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -768,7 +768,7 @@ public class Sequence extends ASequence implements SequenceI
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
-    if (i >= sequence.length)
+    if (i >= sequence.length || i < 0)
     {
       return;
     }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d2e247f..6ce8140 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1822,9 +1822,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
     }
 
+    /*
+     * just extend the last slide command if compatible; but not if in
+     * SplitFrame mode
+     */
     boolean appendHistoryItem = false;
     Deque<CommandI> historyList = viewport.getHistoryList();
-    if (historyList != null
+    boolean inSplitFrame = getSplitViewContainer() != null;
+    if (!inSplitFrame && historyList != null
             && historyList.size() > 0
             && historyList.peek() instanceof SlideSequencesCommand)
     {
diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index 1325ce5..c55d467 100644
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -66,7 +66,7 @@ public class StringUtils
    */
   public static final char[] deleteChars(char[] in, int from, int to)
   {
-    if (from >= in.length)
+    if (from >= in.length || from < 0)
     {
       return in;
     }
-- 
1.7.10.2