Merge branch 'develop' into documentation/JAL-3111_release_211

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index bbd0334..7b33149 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -240,8 +240,9 @@ li:before {
             <!-- JAL-2864 -->Memory test suite to detect leaks in common
             operations</li>
           <li>
-            <!-- JAL-3140 -->IntervalStoreJ (NCList
-            implementation that alows updates) used for Sequence Feature collections</li>          
+            <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+            implementation that alows updates) used for Sequence Feature collections</li>
+          <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>          
         </ul>
       </td>
     <td align="left" valign="top">
@@ -353,10 +354,14 @@ li:before {
             sequence data at beginning or end of alignment added/removed
             via 'Edit' sequence</li>
           <li>
-            <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+            <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't relocate
             sequence features correctly when start of sequence is
             removed (Known defect since 2.10)</li>
-        </ul><em>New Known Defects</em>
+                                       <li>
+                                               <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
+                                               dialog corrupts dataset sequence
+                                       </li>
+                               </ul><em>New Known Defects</em>
         <ul>
           <li>
             <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li> 
@@ -371,6 +376,12 @@ li:before {
                                                window after dragging left to select columns to left of visible
                                                region
                                        </li>
+                                       <li>
+                                               <!-- JAL-2876 -->Features coloured according to their description
+                                               string and thresholded by score in earlier versions of Jalview are
+                                               not shown as thresholded features in 2.11. To workaround please
+                                               create a Score filter instead.
+                                       </li>
                                </ul>
       </td>
     </tr>
@@ -1457,7 +1468,16 @@ li:before {
               <!-- JAL-2589 -->User defined gap colour not shown in
               overview when features overlaid on alignment
             </li>
-          </ul>
+                                               <li>
+                                                       <!-- JAL-2567 -->Feature settings for different views not
+                                                       recovered correctly from Jalview project file
+                                               </li>
+                                               <li>
+                                                       <!-- JAL-2256 -->Feature colours in overview when first opened
+                                                       (automatically via preferences) are different to the main
+                                                       alignment panel
+                                               </li>
+                                       </ul>
           <em>Data import/export</em>
           <ul>
             <li>

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index b9d32f7..aae72d6 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -838,7 +838,7 @@ public class EditCommand implements CommandI
             // old ds and edited ds are different, so
             // create the new dataset sequence
             SequenceI newds = new Sequence(oldds);
-            newds.setSequence(fullseq);
+            newds.setSequence(fullseq.toUpperCase());
 
             if (command.oldds == null)
             {

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 2160657..348d871 100644 (file)
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -90,11 +90,11 @@ public class EditCommandTest
     testee = new EditCommand();
     seqs = new SequenceI[4];
     seqs[0] = new Sequence("seq0", "abcdefghjk");
-    seqs[0].setDatasetSequence(new Sequence("seq0ds", "abcdefghjk"));
+    seqs[0].setDatasetSequence(new Sequence("seq0ds", "ABCDEFGHJK"));
     seqs[1] = new Sequence("seq1", "fghjklmnopq");
-    seqs[1].setDatasetSequence(new Sequence("seq1ds", "fghjklmnopq"));
+    seqs[1].setDatasetSequence(new Sequence("seq1ds", "FGHJKLMNOPQ"));
     seqs[2] = new Sequence("seq2", "qrstuvwxyz");
-    seqs[2].setDatasetSequence(new Sequence("seq2ds", "qrstuvwxyz"));
+    seqs[2].setDatasetSequence(new Sequence("seq2ds", "QRSTUVWXYZ"));
     seqs[3] = new Sequence("seq3", "1234567890");
     seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890"));
     al = new Alignment(seqs);
@@ -285,7 +285,8 @@ public class EditCommandTest
             4, 8, al);
     assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
     assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
-    assertEquals("fghjZxYopq",
+    // Dataset Sequence should always be uppercase
+    assertEquals("fghjZxYopq".toUpperCase(),
             seqs[1].getDatasetSequence().getSequenceAsString());
     assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
     assertEquals("1234567890", seqs[3].getSequenceAsString());
@@ -315,7 +316,8 @@ public class EditCommandTest
     assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
     assertEquals(1, seq.getStart());
     assertEquals(8, seq.getEnd());
-    assertEquals("ABxyZDEF",
+    // Dataset sequence always uppercase
+    assertEquals("ABxyZDEF".toUpperCase(),
             seq.getDatasetSequence().getSequenceAsString());
     assertEquals(8, seq.getDatasetSequence().getEnd());
 
@@ -340,7 +342,8 @@ public class EditCommandTest
     assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
     assertEquals(1, seq.getStart());
     assertEquals(8, seq.getEnd());
-    assertEquals("ABxyZDEF",
+    // dataset sequence should be Uppercase
+    assertEquals("ABxyZDEF".toUpperCase(),
             seq.getDatasetSequence().getSequenceAsString());
     assertEquals(8, seq.getDatasetSequence().getEnd());
 
@@ -363,8 +366,8 @@ public class EditCommandTest
     assertEquals("----klmnopq", seqs[1].getSequenceAsString());
     // and ds is preserved
     assertTrue(dsseq == seqs[1].getDatasetSequence());
-    // and it is unchanged
-    assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+    // and it is unchanged and UPPERCASE !
+    assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
     // and that alignment sequence start has been adjusted
     assertEquals(5, seqs[1].getStart());
     assertEquals(11, seqs[1].getEnd());
@@ -390,8 +393,8 @@ public class EditCommandTest
     assertEquals("----klmnopq", seqs[1].getSequenceAsString());
     // and ds is preserved
     assertTrue(dsseq == seqs[1].getDatasetSequence());
-    // and it is unchanged
-    assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+    // and it is unchanged AND UPPERCASE !
+    assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
     // and that alignment sequence start has been adjusted
     assertEquals(5, seqs[1].getStart());
     assertEquals(11, seqs[1].getEnd());