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Merge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
[jalview.git]
/
test
/
jalview
/
commands
/
EditCommandTest.java
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");
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] = 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] = 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);
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());
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());
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("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());
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("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());
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());
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());
// 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());
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());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());