From e39c567c1a0c8deeb68797abc14111967d9ddb91 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 16 Nov 2017 18:40:50 +0000
Subject: [PATCH] JAL-2822 rejig new dataset after edit computation so it
 works for test cases

---
 src/jalview/commands/EditCommand.java |   31 +++++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 894dc75..874948f 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -762,7 +762,7 @@ public class EditCommand implements CommandI
 
       Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
       Range afterEditedPositions = command.seqs[i]
-              .findPositions(start + end + 1, command.seqs[i].getLength());
+              .findPositions(end + 1, command.seqs[i].getLength());
       
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
@@ -770,8 +770,6 @@ public class EditCommand implements CommandI
       String nogaprep = jalview.analysis.AlignSeq.extractGaps(
               jalview.util.Comparison.GapChars,
               new String(command.string[i]));
-      int ipos = command.seqs[i].findPosition(start)
-              - command.seqs[i].getStart();
       if (end < oldstring.length())
       {
         tmp.append(oldstring.substring(end));
@@ -813,9 +811,22 @@ public class EditCommand implements CommandI
           // first edit the original dataset sequence string
           SequenceI oldds = command.seqs[i].getDatasetSequence();
           String osp = oldds.getSequenceAsString();
-
-          String fullseq = osp.substring(0, ipos) + nogaprep
-                  + osp.substring(ipos + nogaprep.length());
+          int beforeStartOfEdit = -oldds.getStart() + 1
+                  + (beforeEditedPositions == null
+                          ? ((afterEditedPositions != null)
+                                  ? afterEditedPositions.getBegin() - 1
+                                  : oldstartend.getBegin()
+                                          + nogapold.length())
+                          : beforeEditedPositions.getEnd()
+                  );
+          int afterEndOfEdit = -oldds.getStart() + 1
+                  + ((afterEditedPositions == null)
+                  ? oldstartend.getEnd()
+                          : afterEditedPositions.getBegin() - 1);
+          String fullseq = osp.substring(0,
+                  beforeStartOfEdit)
+                  + nogaprep
+                  + osp.substring(afterEndOfEdit);
 
           // and check if new sequence data is different..
           if (!fullseq.equalsIgnoreCase(osp))
@@ -830,6 +841,14 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = command.seqs[i].getDatasetSequence();
+
+            // And preserve start/end for good-measure
+
+            if (command.oldStartEnd == null)
+            {
+              command.oldStartEnd = new Range[command.seqs.length];
+            }
+            command.oldStartEnd[i] = oldstartend;
             // TODO: JAL-1131 ensure newly created dataset sequence is added to
             // the set of
             // dataset sequences associated with the alignment.
-- 
1.7.10.2