*/
package jalview.commands;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import java.util.Map;
*/
public class EditCommandTest
{
+ private static Comparator<SequenceFeature> BY_DESCRIPTION = new Comparator<SequenceFeature>()
+ {
+
+ @Override
+ public int compare(SequenceFeature o1, SequenceFeature o2)
+ {
+ return o1.getDescription().compareTo(o2.getDescription());
+ }
+ };
+
+ private EditCommand testee;
+
+ private SequenceI[] seqs;
+
+ private Alignment al;
+
/*
* compute n(n+1)/2 e.g.
* func(5) = 5 + 4 + 3 + 2 + 1 = 15
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private EditCommand testee;
-
- private SequenceI[] seqs;
-
- private Alignment al;
-
@BeforeMethod(alwaysRun = true)
public void setUp()
{
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);
}
/**
- * Test a Paste action, where this adds sequences to an alignment.
+ * Test a Paste action, followed by Undo and Redo
*/
@Test(groups = { "Functional" }, enabled = false)
- // TODO fix so it works
- public void testPaste_addToAlignment()
+ public void testPaste_undo_redo()
{
+ // TODO code this test properly, bearing in mind that:
+ // Paste action requires something on the clipboard (Cut/Copy)
+ // - EditCommand.paste doesn't add sequences to the alignment
+ // ... that is done in AlignFrame.paste()
+ // ... unless as a Redo
+ // ...
+
SequenceI[] newSeqs = new SequenceI[2];
newSeqs[0] = new Sequence("newseq0", "ACEFKL");
newSeqs[1] = new Sequence("newseq1", "JWMPDH");
- Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al);
- EditCommand.paste(ec, new AlignmentI[] { al });
+ new EditCommand("Paste", Action.PASTE, newSeqs, 0, al.getWidth(), al);
assertEquals(6, al.getSequences().size());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals("ACEFKL", seqs[4].getSequenceAsString());
{
// seem to need a dataset sequence on the edited sequence here
seqs[1].createDatasetSequence();
- new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] },
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ // NB command.number holds end position for a Replace command
+ new EditCommand("", Action.REPLACE, "Z-xY", new SequenceI[] { seqs[1] },
4, 8, al);
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
+ // Dataset Sequence should always be uppercase
+ assertEquals("fghjZxYopq".toUpperCase(Locale.ROOT),
+ seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
- seqs[1] = new Sequence("seq1", "fghjZXYnopq");
+ }
+
+ /**
+ * Test the replace command (used to manually edit a sequence)
+ */
+ @Test(groups = { "Functional" })
+ public void testReplace_withGaps()
+ {
+ SequenceI seq = new Sequence("seq", "ABC--DEF");
+ seq.createDatasetSequence();
+ assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ /*
+ * replace C- with XYZ
+ * NB arg4 = start column of selection for edit (base 0)
+ * arg5 = column after end of selection for edit
+ */
+ EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ",
+ new SequenceI[]
+ { seq }, 2, 4, al);
+ assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(8, seq.getEnd());
+ // Dataset sequence always uppercase
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
+ seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(8, seq.getDatasetSequence().getEnd());
+
+ /*
+ * undo the edit
+ */
+ AlignmentI[] views = new AlignmentI[] {
+ new Alignment(new SequenceI[]
+ { seq }) };
+ edit.undoCommand(views);
+
+ assertEquals("ABC--DEF", seq.getSequenceAsString());
+ assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ assertEquals(6, seq.getDatasetSequence().getEnd());
+
+ /*
+ * redo the edit
+ */
+ edit.doCommand(views);
+
+ assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(8, seq.getEnd());
+ // dataset sequence should be Uppercase
+ assertEquals("ABxyZDEF".toUpperCase(Locale.ROOT),
+ seq.getDatasetSequence().getSequenceAsString());
+ assertEquals(8, seq.getDatasetSequence().getEnd());
+
+ }
+
+ /**
+ * Test replace command when it doesn't cause a sequence edit (see comment in
+ */
+ @Test(groups = { "Functional" })
+ public void testReplaceFirstResiduesWithGaps()
+ {
+ // test replace when gaps are inserted at start. Start/end should change
+ // w.r.t. original edited sequence.
+ SequenceI dsseq = seqs[1].getDatasetSequence();
+ EditCommand edit = new EditCommand("", Action.REPLACE, "----",
+ new SequenceI[]
+ { seqs[1] }, 0, 4, al);
+
+ // trimmed start
+ assertEquals("----klmnopq", seqs[1].getSequenceAsString());
+ // and ds is preserved
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // and it is unchanged and UPPERCASE !
+ 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());
+
+ AlignmentI[] views = new AlignmentI[] { new Alignment(seqs) };
+ // and undo
+ edit.undoCommand(views);
+
+ // dataset sequence unchanged
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // restore sequence
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ // and start/end numbering also restored
+ assertEquals(1, seqs[1].getStart());
+ assertEquals(11, seqs[1].getEnd());
+
+ // now redo
+ edit.undoCommand(views);
+
+ // and repeat asserts for the original edit
+
+ // trimmed start
+ assertEquals("----klmnopq", seqs[1].getSequenceAsString());
+ // and ds is preserved
+ assertTrue(dsseq == seqs[1].getDatasetSequence());
+ // and it is unchanged AND UPPERCASE !
+ 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'
/*
* 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++)
+
+ /*
+ * create a new alignment with shared dataset sequence
+ */
+ AlignmentI copy = new Alignment(
+ new SequenceI[]
+ { alignment.getDataset().getSequenceAt(0).deriveSequence() });
+ SequenceI copySeq0 = copy.getSequenceAt(0);
+
+ 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,
- 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);
// sanity check
List<SequenceFeature> sfs = seq0.getSequenceFeatures();
assertEquals(func(5), sfs.size());
+ assertEquals(sfs, copySeq0.getSequenceFeatures());
+ String copySequenceFeatures = copySeq0.getSequenceFeatures().toString();
/*
- * 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 };
{
for (int to = from; to < seq0.getLength(); to++)
{
- testee.appendEdit(Action.CUT, sqs, from, (to - from + 1),
- alignment, true);
+ 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();
- sfs = seq0.getSequenceFeatures();
+ verifyCut(seq0, from, to, msg, start);
/*
- * confirm the number of features has reduced by the
- * number of features within the cut region i.e. by
- * func(length of cut)
+ * verify copy alignment dataset sequence unaffected
*/
- String msg = String.format("Cut %d-%d ", from, to);
- if (to - from == 4)
- {
- // all columns were cut
- assertTrue(sfs.isEmpty());
- }
- else
- {
- assertEquals(msg + "wrong number of features left", func(5)
- - func(to - from + 1), sfs.size());
- }
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
/*
- * inspect individual features
+ * verify any new dataset sequence was added to the
+ * alignment dataset
*/
- for (SequenceFeature sf : sfs)
- {
- checkFeatureRelocation(sf, from + 1, to + 1, from > 0);
- }
+ assertEquals("Wrong Dataset size after " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
/*
- * undo ready for next cut
+ * undo and verify all restored
*/
- testee.undoCommand(new AlignmentI[] { alignment });
+ AlignmentI[] views = new AlignmentI[] { alignment };
+ ec.undoCommand(views);
sfs = seq0.getSequenceFeatures();
assertEquals("After undo of " + msg, func(5), sfs.size());
verifyUndo(from, to, sfs);
+
+ /*
+ * verify copy alignment dataset sequence still unaffected
+ * and alignment dataset has shrunk (if it was added to)
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * redo and verify
+ */
+ ec.doCommand(views);
+ verifyCut(seq0, from, to, msg, start);
+
+ /*
+ * verify copy alignment dataset sequence unaffected
+ * and any new dataset sequence readded to alignment dataset
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after Redo of " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * undo ready for next cut
+ */
+ ec.undoCommand(views);
+
+ /*
+ * final verify that copy alignment dataset sequence is still unaffected
+ * and that alignment dataset has shrunk
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+ assertEquals("Wrong Dataset size after final Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
}
}
}
/**
+ * Verify by inspection that the sequence features left on the sequence after
+ * a cut match the expected results. The trick to this is that we can parse
+ * each feature's original start-end positions from its description.
+ *
+ * @param seq0
+ * @param from
+ * @param to
+ * @param msg
+ * @param seqStart
+ */
+ protected void verifyCut(SequenceI seq0, int from, int to,
+ final String msg, int seqStart)
+ {
+ List<SequenceFeature> sfs;
+ sfs = seq0.getSequenceFeatures();
+
+ Collections.sort(sfs, BY_DESCRIPTION);
+
+ /*
+ * confirm the number of features has reduced by the
+ * number of features within the cut region i.e. by
+ * func(length of cut); exception is a cut at start or end of sequence,
+ * which retains the original coordinates, dataset sequence
+ * and all its features
+ */
+ boolean datasetRetained = from == 0 || to == 4;
+ if (datasetRetained)
+ {
+ // dataset and all features retained
+ assertEquals(msg, func(5), sfs.size());
+ }
+ else if (to - from == 4)
+ {
+ // all columns were cut
+ assertTrue(sfs.isEmpty());
+ }
+ else
+ {
+ // failure in checkFeatureRelocation is more informative!
+ assertEquals(msg + "wrong number of features left",
+ func(5) - func(to - from + 1), sfs.size());
+ }
+
+ /*
+ * inspect individual features
+ */
+ for (SequenceFeature sf : sfs)
+ {
+ verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained,
+ seqStart);
+ }
+ }
+
+ /**
* Check that after Undo, every feature has start/end that match its original
* "start" and "end" properties
*
{
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 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 checkFeatureRelocation(SequenceFeature sf, int from, int to,
- boolean newDataset)
+ private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
+ 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",
sf.getDescription(), sf.getBegin(), sf.getEnd(), from, to);
- if (oldTo < from)
+ if (!newDataset)
+ {
+ // dataset retained with all features unchanged
+ assertEquals("0: " + msg, oldFrom, sf.getBegin());
+ assertEquals("0: " + msg, oldTo, sf.getEnd());
+ }
+ 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,
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());
}
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)
*/
SequenceFeature sf = sfs.get(0);
assertEquals(10, sf.getBegin());
assertEquals(11, sf.getEnd());
-
- // TODO add further cases including Undo - see JAL-2541
}
}
git://source.jalview.org / jalview.git / blobdiff