From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 1 Mar 2019 09:59:24 +0000 (+0000)
Subject: JAL-3140 update for change to SequenceI api
X-Git-Tag: Release_2_11_0~17^2~92
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6084ed0c6da51ac6569320a33b7f4aa0ec523c80;hp=f0bd9a900c8cf4746b51486b6a7bfc9bef9c0180;p=jalview.git

JAL-3140 update for change to SequenceI api
---

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 1a227c5..f80bd4a 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.Range;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -526,8 +527,8 @@ public class EditCommand implements CommandI
         command.string[i] = sequence.getSequence(command.position,
                 command.position + command.number);
         SequenceI oldds = sequence.getDatasetSequence();
-        Range cutPositions = sequence.findPositions(command.position + 1,
-                command.position + command.number);
+        ContiguousI cutPositions = sequence.findPositions(
+                command.position + 1, command.position + command.number);
         boolean cutIsInternal = cutPositions != null
                 && sequence.getStart() != cutPositions
                 .getBegin() && sequence.getEnd() != cutPositions.getEnd();
@@ -763,9 +764,9 @@ public class EditCommand implements CommandI
        * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
        * 
        */
-
-      Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
-      Range afterEditedPositions = command.seqs[i]
+      ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1,
+              start);
+      ContiguousI afterEditedPositions = command.seqs[i]
               .findPositions(end + 1, command.seqs[i].getLength());
       
       oldstring = command.seqs[i].getSequenceAsString();