*/
EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ",
new SequenceI[]
- { seq }, 2,
- 4, al);
+ { seq }, 2, 4, al);
assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
/*
* undo the edit
*/
- AlignmentI[] views = new AlignmentI[]
- { new Alignment(new SequenceI[] { seq }) };
+ AlignmentI[] views = new AlignmentI[] {
+ new Alignment(new SequenceI[]
+ { seq }) };
edit.undoCommand(views);
assertEquals("ABC--DEF", seq.getSequenceAsString());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged and UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT),
+ dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged AND UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT),
+ dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
* 3 insert gap in a row (aka mouse drag right):
*/
Edit e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { seqs[0] }, 1, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 1, 1, al);
testee.addEdit(e);
SequenceI edited = new Sequence("seq0", "a?bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
edited = new Sequence("seq0", "a??bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 3, 1, al);
+ new SequenceI[]
+ { edited }, 3, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
* Add a non-contiguous edit - should not be merged.
*/
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 5, 2, al);
+ new SequenceI[]
+ { edited }, 5, 2, al);
testee.addEdit(e);
assertEquals(2, testee.getSize());
assertEquals(5, testee.getEdit(1).getPosition());
* Add a Delete after the Insert - should not be merged.
*/
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 6, 2, al);
+ new SequenceI[]
+ { edited }, 6, 2, al);
testee.addEdit(e);
assertEquals(3, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction());
*/
seqs[0].setSequence("a???bcdefghjk");
Edit e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { seqs[0] }, 4, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 4, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
SequenceI edited = new Sequence("seq0", "a??bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 3, 1, al);
+ new SequenceI[]
+ { edited }, 3, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
edited = new Sequence("seq0", "a?bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
* Add a non-contiguous edit - should not be merged.
*/
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(2, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
* Add an Insert after the Delete - should not be merged.
*/
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 1, 1, al);
+ new SequenceI[]
+ { edited }, 1, 1, al);
testee.addEdit(e);
assertEquals(3, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction());
{
seqs[0].setSequence("a???bcdefghjk");
Edit e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { seqs[0] }, 4, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 4, 1, al);
testee.addEdit(e);
seqs[1].setSequence("f??ghjklmnopq");
- Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
- { seqs[1] }, 3, 1, al);
+ Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP,
+ new SequenceI[]
+ { seqs[1] }, 3, 1, al);
testee.addEdit(e2);
assertEquals(2, testee.getSize());
assertSame(e, testee.getEdit(0));
/*
* 2 insert gap in a row (aka mouse drag right), on two sequences:
*/
- Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] {
- seqs[0], seqs[1] }, 1, 1, al);
+ Edit e = new EditCommand().new Edit(Action.INSERT_GAP,
+ new SequenceI[]
+ { seqs[0], seqs[1] }, 1, 1, al);
testee.addEdit(e);
SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk");
seq1edited.setDatasetSequence(seqs[0].getDatasetSequence());
SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq");
seq2edited.setDatasetSequence(seqs[1].getDatasetSequence());
- e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] {
- seq1edited, seq2edited }, 2, 1, al);
+ e = new EditCommand().new Edit(Action.INSERT_GAP,
+ new SequenceI[]
+ { seq1edited, seq2edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
assertEquals(1, testee.getEdit(0).getPosition());
assertEquals(2, testee.getEdit(0).getNumber());
- assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0)
- .getSequences()[0].getDatasetSequence());
- assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0)
- .getSequences()[1].getDatasetSequence());
+ assertEquals(seqs[0].getDatasetSequence(),
+ testee.getEdit(0).getSequences()[0].getDatasetSequence());
+ assertEquals(seqs[1].getDatasetSequence(),
+ testee.getEdit(0).getSequences()[1].getDatasetSequence());
}
/**
* a cut of columns/residues 4-7
*/
SequenceI seq0 = seqs[0]; // abcdefghjk/1-10
- seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f,
- null));
- seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6,
- 0f, null));
- seq0.addSequenceFeature(new SequenceFeature("internal", "", 5, 6, 0f,
- null));
- seq0.addSequenceFeature(new SequenceFeature("overlap right", "", 7, 8,
- 0f, null));
- seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f,
- null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("before", "", 1, 3, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("overlap left", "", 2, 6, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("internal", "", 5, 6, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("overlap right", "", 7, 8, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("after", "", 8, 10, 0f, null));
/*
* add some contact features
*/
- SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5,
- 6, 0f, null);
+ SequenceFeature internalContact = new SequenceFeature("disulphide bond",
+ "", 5, 6, 0f, null);
seq0.addSequenceFeature(internalContact); // should get deleted
SequenceFeature overlapLeftContact = new SequenceFeature(
"disulphide bond", "", 2, 6, 0f, null);
SequenceFeature overlapRightContact = new SequenceFeature(
"disulphide bond", "", 5, 8, 0f, null);
seq0.addSequenceFeature(overlapRightContact); // should get deleted
- SequenceFeature spanningContact = new SequenceFeature(
- "disulphide bond", "", 2, 9, 0f, null);
+ SequenceFeature spanningContact = new SequenceFeature("disulphide bond",
+ "", 2, 9, 0f, null);
seq0.addSequenceFeature(spanningContact); // should get shortened 3'
/*
for (int to = from; to <= end; to++)
{
String desc = String.format("%d-%d", from, to);
- SequenceFeature sf = new SequenceFeature("test", desc, from, to,
- 0f, null);
+ SequenceFeature sf = new SequenceFeature("test", desc, from, to, 0f,
+ null);
sf.setValue("from", Integer.valueOf(from));
sf.setValue("to", Integer.valueOf(to));
seq0.addSequenceFeature(sf);
{
for (int to = from; to < seq0.getLength(); to++)
{
- EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to
- - from + 1), alignment);
+ EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from,
+ (to - from + 1), alignment);
final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0
.getDatasetSequence();
else
{
// failure in checkFeatureRelocation is more informative!
- assertEquals(msg + "wrong number of features left", func(5)
- - func(to - from + 1), sfs.size());
+ assertEquals(msg + "wrong number of features left",
+ func(5) - func(to - from + 1), sfs.size());
}
/*
{
final int oldFrom = ((Integer) sf.getValue("from")).intValue();
final int oldTo = ((Integer) sf.getValue("to")).intValue();
- String msg = String.format(
- "Undo cut of [%d-%d], feature at [%d-%d] ", from + 1, to + 1,
- oldFrom, oldTo);
+ String msg = String.format("Undo cut of [%d-%d], feature at [%d-%d] ",
+ from + 1, to + 1, oldFrom, oldTo);
assertEquals(msg + "start", oldFrom, sf.getBegin());
assertEquals(msg + "end", oldTo, sf.getEnd());
}
* @param seqStart
*/
private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
- boolean newDataset, int seqStart)
+ boolean newDataset, int seqStart)
{
// TODO handle the gapped sequence case as well
int cutSize = to - from + 1;
SequenceI seq0 = new Sequence("seq/8-11", "A-BCC");
seq0.createDatasetSequence();
assertEquals(8, seq0.getStart());
- seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f,
- null));
+ seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f, null));
SequenceI[] seqsArray = new SequenceI[] { seq0 };
AlignmentI alignment = new Alignment(seqsArray);
*/
Edit ec = testee.new Edit(Action.CUT, seqsArray, 0, 3, alignment);
EditCommand.cut(ec, new AlignmentI[] { alignment });
-
+
/*
* feature on CC(10-11) should still be on CC(10-11)
*/
git://source.jalview.org / jalview.git / blobdiff