import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.Finder;
+import jalview.api.AlignViewControllerI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import java.util.Arrays;
import java.util.BitSet;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignViewControllerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testFindColumnsWithFeature()
{
- SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
- SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
- SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
- SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+ SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
/*
* features start/end are base 1
null));
seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
0f, null));
+ // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+ seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
+ 0f, null));
/*
- * select the first three columns --> Metal in seq1 2-3
+ * select the first five columns --> Metal in seq1 cols 4-5
*/
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(0); // base 0
- sg.setEndRes(2);
+ sg.setEndRes(4);
sg.addSequence(seq1, false);
sg.addSequence(seq2, false);
sg.addSequence(seq3, false);
bs);
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
+ assertTrue(bs.get(3)); // base 0
+ assertTrue(bs.get(4));
/*
- * select the first four columns: Metal in seq1 2:4, seq2 4:4
+ * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
*/
- sg.setEndRes(3);
+ sg.setEndRes(6);
bs.clear();
seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
assertEquals(2, seqCount);
- assertEquals(3, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
+ assertEquals(4, bs.cardinality());
assertTrue(bs.get(3));
+ assertTrue(bs.get(4));
+ assertTrue(bs.get(5));
+ assertTrue(bs.get(6));
/*
- * select column 11: Metal in seq3 only
+ * select column 14: Metal in seq3 only
*/
- sg.setStartRes(10);
- sg.setEndRes(10);
+ sg.setStartRes(13);
+ sg.setEndRes(13);
bs.clear();
seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(1, bs.cardinality());
- assertTrue(bs.get(10));
+ assertTrue(bs.get(13));
/*
- * select columns 16-20: no Metal feature
+ * select columns 18-20: no Metal feature
*/
- sg.setStartRes(15);
+ sg.setStartRes(17);
sg.setEndRes(19);
bs.clear();
seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
assertEquals(0, bs.cardinality());
/*
+ * columns 11-13 should not match disulfide bond at 8/12
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(12);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * columns 6-18 should match disulfide bond at columns 9, 14
+ */
+ sg.setStartRes(5);
+ sg.setEndRes(17);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(8));
+ assertTrue(bs.get(13));
+
+ /*
* look for a feature that isn't there
*/
sg.setStartRes(0);
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
}
+
+ /**
+ * shameless copy of test data from findFeature for testing mark columns from
+ * highlight
+ */
+ @Test(groups = "Functional")
+ public void testSelectColumnsWithHighlight()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
+ + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+
+ SearchResultsI sr = new SearchResults();
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ SequenceI seq1 = sqs[0];
+ SequenceI seq2 = sqs[1];
+ SequenceI seq3 = sqs[2];
+ SequenceI seq4 = sqs[3];
+
+ /*
+ * features start/end are base 1
+ */
+ sr.addResult(seq1, 2, 4);
+ sr.addResult(seq2, 4, 10);
+ sr.addResult(seq3, 11, 15);
+
+ /*
+ * test Match/Find works first
+ */
+ Finder f = new Finder(af.getViewport().getAlignment(), null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("M+");
+ assertEquals(
+ "Finder found different set of results to manually created SearchResults",
+ sr, f.getSearchResults());
+
+ /*
+ * now check simple mark columns from find operation
+ */
+ af.getViewport().setSearchResults(sr);
+ AlignViewControllerI avc = af.avc;
+
+ avc.markHighlightedColumns(false, false, false);
+ assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
+ .getViewport().getColumnSelection().getSelectedRanges()
+ .toArray(), new int[][] { { 1, 14 } }));
+ }
}
git://source.jalview.org / jalview.git / blobdiff