import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.Finder;
+import jalview.api.AlignViewControllerI;
+import jalview.api.FeatureColourI;
+import jalview.api.FinderI;
+import jalview.datamodel.Alignment;
+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 jalview.schemes.FeatureColour;
+import java.awt.Color;
+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()
{
null));
seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+ seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
+ 10f,
null));
seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
- 0f, null));
+ 10f, null));
// disulfide bond is a 'contact feature' - only select its 'start' and 'end'
- seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
- 0f, null));
+ seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
+ 8, 12, 0f, null));
/*
* select the first five columns --> Metal in seq1 cols 4-5
sg.addSequence(seq3, false);
sg.addSequence(seq4, false);
+ /*
+ * set features visible on a viewport as only visible features are selected
+ */
+ AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
+ seq2, seq3, seq4 }), 100, 100);
+ af.getFeatureRenderer().findAllFeatures(true);
+
+ AlignViewController avc = new AlignViewController(af, af.getViewport(),
+ af.alignPanel);
+
BitSet bs = new BitSet();
- int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
- bs);
+ int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
assertTrue(bs.get(3)); // base 0
*/
sg.setEndRes(6);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(2, seqCount);
assertEquals(4, bs.cardinality());
assertTrue(bs.get(3));
sg.setStartRes(13);
sg.setEndRes(13);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(1, bs.cardinality());
assertTrue(bs.get(13));
sg.setStartRes(17);
sg.setEndRes(19);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
/*
+ * threshold Metal to hide where score < 5
+ * seq1 feature in columns 4-6 is hidden
+ * seq2 feature in columns 6-7 is shown
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(5f);
+ af.getFeatureRenderer().setColour("Metal", fc);
+ sg.setStartRes(0);
+ sg.setEndRes(6);
+ bs.clear();
+ seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(5));
+ assertTrue(bs.get(6));
+
+ /*
* 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);
+ seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
sg.setStartRes(5);
sg.setEndRes(17);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
- sg, bs);
+ seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
assertTrue(bs.get(8));
sg.setStartRes(0);
sg.setEndRes(19);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+ seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
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
+ */
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false, false);
+ 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