package jalview.commands;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
+import java.util.List;
import java.util.Map;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class EditCommandTest
{
+ /*
+ * compute n(n+1)/2 e.g.
+ * func(5) = 5 + 4 + 3 + 2 + 1 = 15
+ */
+ private static int func(int i)
+ {
+ return i * (i + 1) / 2;
+ }
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
assertEquals(ds2, unwound.get(ds2).getDatasetSequence());
assertEquals(ds3, unwound.get(ds3).getDatasetSequence());
}
+
+ /**
+ * Test a cut action's relocation of sequence features
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_withFeatures()
+ {
+ /*
+ * create sequence features before, after and overlapping
+ * a cut of columns/residues 4-7
+ */
+ SequenceI seq0 = seqs[0];
+ 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));
+
+ Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); // cols 3-6 base 0
+ EditCommand.cut(ec, new AlignmentI[] { al });
+
+ List<SequenceFeature> sfs = seq0.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(sfs, true);
+
+ assertEquals(4, sfs.size()); // feature internal to cut has been deleted
+ SequenceFeature sf = sfs.get(0);
+ assertEquals("before", sf.getType());
+ assertEquals(1, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ sf = sfs.get(1);
+ assertEquals("overlap left", sf.getType());
+ assertEquals(2, sf.getBegin());
+ assertEquals(3, sf.getEnd()); // truncated by cut
+ sf = sfs.get(2);
+ assertEquals("overlap right", sf.getType());
+ assertEquals(4, sf.getBegin()); // shifted left by cut
+ assertEquals(5, sf.getEnd()); // truncated by cut
+ sf = sfs.get(3);
+ assertEquals("after", sf.getType());
+ assertEquals(4, sf.getBegin()); // shifted left by cut
+ assertEquals(6, sf.getEnd()); // shifted left by cut
+ }
+
+ /**
+ * Test a cut action's relocation of sequence features, with full coverage of
+ * all possible feature and cut locations for a 5-position ungapped sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_withFeatures_exhaustive()
+ {
+ /*
+ * create a sequence features on each subrange of 1-5
+ */
+ SequenceI seq0 = new Sequence("seq", "ABCDE");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
+ alignment.setDataset(null);
+ for (int from = 1; from <= seq0.getLength(); from++)
+ {
+ for (int to = from; to <= seq0.getLength(); to++)
+ {
+ String desc = String.format("%d-%d", from, to);
+ 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());
+
+ /*
+ * now perform all possible cuts of subranges of 1-5 (followed by Undo)
+ * and validate the resulting remaining sequence features!
+ */
+ SequenceI[] sqs = new SequenceI[] { seq0 };
+
+ // goal is to have this passing for all from/to values!!
+ // for (int from = 0; from < seq0.getLength(); from++)
+ // {
+ // for (int to = from; to < seq0.getLength(); to++)
+ for (int from = 1; from < 3; from++)
+ {
+ for (int to = 2; to < 3; to++)
+ {
+ testee.appendEdit(Action.CUT, sqs, from, (to - from + 1),
+ alignment, true);
+
+ sfs = seq0.getSequenceFeatures();
+
+ /*
+ * confirm the number of features has reduced by the
+ * number of features within the cut region i.e. by
+ * func(length of cut)
+ */
+ String msg = String.format("Cut %d-%d ", from, to);
+ if (to - from == 4)
+ {
+ // all columns cut
+ assertNull(sfs);
+ }
+ else
+ {
+ assertEquals(msg + "wrong number of features left", func(5)
+ - func(to - from + 1), sfs.size());
+ }
+
+ /*
+ * inspect individual features
+ */
+ if (sfs != null)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ checkFeatureRelocation(sf, from + 1, to + 1);
+ }
+ }
+ /*
+ * undo ready for next cut
+ */
+ testee.undoCommand(new AlignmentI[] { alignment });
+ assertEquals(func(5), seq0.getSequenceFeatures().size());
+ }
+ }
+ }
+
+ /**
+ * Helper method to check a feature has been correctly relocated after a cut
+ *
+ * @param sf
+ * @param from
+ * start of cut (first residue cut)
+ * @param to
+ * end of cut (last residue cut)
+ */
+ private void checkFeatureRelocation(SequenceFeature sf, int from, int to)
+ {
+ // TODO handle the gapped sequence case as well
+ int cutSize = to - from + 1;
+ int oldFrom = ((Integer) sf.getValue("from")).intValue();
+ int oldTo = ((Integer) sf.getValue("to")).intValue();
+
+ 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)
+ {
+ // before cut region so unchanged
+ assertEquals("1: " + msg, oldFrom, sf.getBegin());
+ assertEquals("2: " + msg, oldTo, sf.getEnd());
+ }
+ else if (oldFrom > to)
+ {
+ // follows cut region - shift by size of cut
+ assertEquals("3: " + msg, oldFrom - cutSize, sf.getBegin());
+ assertEquals("4: " + msg, oldTo - cutSize, sf.getEnd());
+ }
+ else if (oldFrom < from && oldTo > 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)
+ {
+ // feature overlaps left side of cut region - truncated right
+ assertEquals("7: " + msg, from - 1, sf.getEnd());
+ }
+ else if (oldTo > to)
+ {
+ // feature overlaps right side of cut region - truncated left
+ assertEquals("8: " + msg, from, sf.getBegin());
+ assertEquals("9: " + msg, from + oldTo - to - 1, sf.getEnd());
+ }
+ else
+ {
+ // feature internal to cut - should have been deleted!
+ Assert.fail(msg + " - should have been deleted");
+ }
+ }
+
+ /**
+ * Test a cut action's relocation of sequence features
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_gappedWithFeatures()
+ {
+ /*
+ * create sequence features before, after and overlapping
+ * a cut of columns/residues 4-7
+ */
+ SequenceI seq0 = new Sequence("seq", "A-BCC");
+ seq0.addSequenceFeature(new SequenceFeature("", "", 3, 4, 0f,
+ null));
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
+ // cut columns of A-B
+ Edit ec = testee.new Edit(Action.CUT, seqs, 0, 3, alignment); // cols 0-3
+ // base 0
+ EditCommand.cut(ec, new AlignmentI[] { alignment });
+
+ /*
+ * feature on CC(3-4) should now be on CC(1-2)
+ */
+ List<SequenceFeature> sfs = seq0.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(0);
+ assertEquals(1, sf.getBegin());
+ assertEquals(2, sf.getEnd());
+
+ // TODO add further cases including Undo - see JAL-2541
+ }
}
git://source.jalview.org / jalview.git / blobdiff