From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 14 Sep 2017 15:10:36 +0000 (+0100)
Subject: JAL-2541 test with seq start > 1 (and fix Undo bug this uncovered)
X-Git-Tag: Release_2_11_1_0~98^2~23^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f9a10c9d8e8173c7387a9a2dd2547c2e9e6c6be3;p=jalview.git

JAL-2541 test with seq start > 1 (and fix Undo bug this uncovered)
---

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 9be8d3f..8c53128 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1163,7 +1163,8 @@ public class EditCommand implements CommandI
        * shift right any features that start at the cut position,
        * unless they were truncated
        */
-      List<SequenceFeature> sfs = seq.findFeatures(start, start);
+      List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
+              start);
       for (SequenceFeature sf : sfs)
       {
         if (sf.getBegin() == start)
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 111adba..dbc659e 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -746,11 +746,15 @@ public class EditCommandTest
      * create a sequence features on each subrange of 1-5
      */
     SequenceI seq0 = new Sequence("seq", "ABCDE");
+    int start = 8;
+    int end = 12;
+    seq0.setStart(start);
+    seq0.setEnd(end);
     AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
     alignment.setDataset(null);
-    for (int from = 1; from <= seq0.getLength(); from++)
+    for (int from = start; from <= end; from++)
     {
-      for (int to = from; to <= seq0.getLength(); to++)
+      for (int to = from; to <= end; to++)
       {
         String desc = String.format("%d-%d", from, to);
         SequenceFeature sf = new SequenceFeature("test", desc, from, to,
@@ -765,7 +769,7 @@ public class EditCommandTest
     assertEquals(func(5), sfs.size());
 
     /*
-     * now perform all possible cuts of subranges of 1-5 (followed by Undo)
+     * now perform all possible cuts of subranges of columns 1-5
      * and validate the resulting remaining sequence features!
      */
     SequenceI[] sqs = new SequenceI[] { seq0 };
@@ -778,10 +782,10 @@ public class EditCommandTest
                 - from + 1), alignment);
         final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
 
-        verifyCut(seq0, from, to, msg);
+        verifyCut(seq0, from, to, msg, start);
 
         /*
-         * undo and verify
+         * undo and verify all restored
          */
         AlignmentI[] views = new AlignmentI[] { alignment };
         ec.undoCommand(views);
@@ -793,7 +797,7 @@ public class EditCommandTest
          * redo and verify
          */
         ec.doCommand(views);
-        verifyCut(seq0, from, to, msg);
+        verifyCut(seq0, from, to, msg, start);
 
         /*
          * undo ready for next cut
@@ -812,9 +816,10 @@ public class EditCommandTest
    * @param from
    * @param to
    * @param msg
+   * @param seqStart
    */
   protected void verifyCut(SequenceI seq0, int from, int to,
-          final String msg)
+          final String msg, int seqStart)
   {
     List<SequenceFeature> sfs;
     sfs = seq0.getSequenceFeatures();
@@ -851,7 +856,8 @@ public class EditCommandTest
      */
     for (SequenceFeature sf : sfs)
     {
-      verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained);
+      verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained,
+              seqStart);
     }
   }
 
@@ -882,18 +888,21 @@ public class EditCommandTest
    * 
    * @param sf
    * @param from
-   *          start of cut (first residue cut)
+   *          start of cut (first residue cut 1..)
    * @param to
-   *          end of cut (last residue cut)
+   *          end of cut (last residue cut 1..)
    * @param newDataset
+   * @param seqStart
    */
   private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
-          boolean newDataset)
+ boolean newDataset, int seqStart)
   {
     // TODO handle the gapped sequence case as well
     int cutSize = to - from + 1;
     final int oldFrom = ((Integer) sf.getValue("from")).intValue();
     final int oldTo = ((Integer) sf.getValue("to")).intValue();
+    final int oldFromPosition = oldFrom - seqStart + 1; // 1..
+    final int oldToPosition = oldTo - seqStart + 1; // 1..
 
     String msg = String.format(
             "Feature %s relocated to %d-%d after cut of %d-%d",
@@ -904,13 +913,13 @@ public class EditCommandTest
       assertEquals("0: " + msg, oldFrom, sf.getBegin());
       assertEquals("0: " + msg, oldTo, sf.getEnd());
     }
-    else if (oldTo < from)
+    else if (oldToPosition < from)
     {
       // before cut region so unchanged
       assertEquals("1: " + msg, oldFrom, sf.getBegin());
       assertEquals("2: " + msg, oldTo, sf.getEnd());
     }
-    else if (oldFrom > to)
+    else if (oldFromPosition > to)
     {
       // follows cut region - shift by size of cut
       assertEquals("3: " + msg, newDataset ? oldFrom - cutSize : oldFrom,
@@ -918,21 +927,22 @@ public class EditCommandTest
       assertEquals("4: " + msg, newDataset ? oldTo - cutSize : oldTo,
               sf.getEnd());
     }
-    else if (oldFrom < from && oldTo > to)
+    else if (oldFromPosition < from && oldToPosition > to)
     {
       // feature encloses cut region - shrink it right
       assertEquals("5: " + msg, oldFrom, sf.getBegin());
       assertEquals("6: " + msg, oldTo - cutSize, sf.getEnd());
     }
-    else if (oldFrom < from)
+    else if (oldFromPosition < from)
     {
       // feature overlaps left side of cut region - truncated right
-      assertEquals("7: " + msg, from - 1, sf.getEnd());
+      assertEquals("7: " + msg, from - 1 + seqStart - 1, sf.getEnd());
     }
-    else if (oldTo > to)
+    else if (oldToPosition > to)
     {
       // feature overlaps right side of cut region - truncated left
-      assertEquals("8: " + msg, newDataset ? from : to + 1, sf.getBegin());
+      assertEquals("8: " + msg, newDataset ? from + seqStart - 1 : to + 1,
+              sf.getBegin());
       assertEquals("9: " + msg, newDataset ? from + oldTo - to - 1 : oldTo,
               sf.getEnd());
     }