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package jalview.controller; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.analysis.Finder; |
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import jalview.api.AlignViewControllerI; |
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import jalview.api.FeatureColourI; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.SearchResults; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.schemes.FeatureColour; |
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import java.awt.Color; |
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import java.util.Arrays; |
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import java.util.BitSet; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (103) |
Complexity: 3 |
Complexity Density: 0.03 |
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public class AlignViewControllerTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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| 100% |
Uncovered Elements: 0 (79) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
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@Test(groups = "Functional")... |
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public void testFindColumnsWithFeature() |
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{ |
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SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa"); |
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SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa"); |
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SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa"); |
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SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa"); |
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seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f, |
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null)); |
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seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f, |
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null)); |
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seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, |
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10f, |
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null)); |
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seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15, |
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10f, null)); |
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seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", |
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8, 12, 0f, null)); |
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SequenceGroup sg = new SequenceGroup(); |
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sg.setStartRes(0); |
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sg.setEndRes(4); |
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sg.addSequence(seq1, false); |
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sg.addSequence(seq2, false); |
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sg.addSequence(seq3, false); |
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sg.addSequence(seq4, false); |
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AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1, |
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seq2, seq3, seq4 }), 100, 100); |
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af.getFeatureRenderer().findAllFeatures(true); |
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AlignViewController avc = new AlignViewController(af, af.getViewport(), |
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af.alignPanel); |
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BitSet bs = new BitSet(); |
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int seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
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assertEquals(1, seqCount); |
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assertEquals(2, bs.cardinality()); |
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assertTrue(bs.get(3)); |
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assertTrue(bs.get(4)); |
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sg.setEndRes(6); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
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assertEquals(2, seqCount); |
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assertEquals(4, bs.cardinality()); |
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assertTrue(bs.get(3)); |
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assertTrue(bs.get(4)); |
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assertTrue(bs.get(5)); |
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assertTrue(bs.get(6)); |
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sg.setStartRes(13); |
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sg.setEndRes(13); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
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assertEquals(1, seqCount); |
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assertEquals(1, bs.cardinality()); |
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assertTrue(bs.get(13)); |
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sg.setStartRes(17); |
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sg.setEndRes(19); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
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assertEquals(0, seqCount); |
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assertEquals(0, bs.cardinality()); |
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FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f); |
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fc.setAboveThreshold(true); |
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fc.setThreshold(5f); |
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af.getFeatureRenderer().setColour("Metal", fc); |
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sg.setStartRes(0); |
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sg.setEndRes(6); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
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assertEquals(1, seqCount); |
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assertEquals(2, bs.cardinality()); |
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assertTrue(bs.get(5)); |
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assertTrue(bs.get(6)); |
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sg.setStartRes(10); |
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sg.setEndRes(12); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); |
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assertEquals(0, seqCount); |
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assertEquals(0, bs.cardinality()); |
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sg.setStartRes(5); |
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sg.setEndRes(17); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); |
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assertEquals(1, seqCount); |
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assertEquals(2, bs.cardinality()); |
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assertTrue(bs.get(8)); |
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assertTrue(bs.get(13)); |
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sg.setStartRes(0); |
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sg.setEndRes(19); |
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bs.clear(); |
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seqCount = avc.findColumnsWithFeature("Pfam", sg, bs); |
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assertEquals(0, seqCount); |
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assertEquals(0, bs.cardinality()); |
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} |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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@Test(groups = "Functional")... |
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public void testSelectColumnsWithHighlight() |
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{ |
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AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
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"seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n" |
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+ "seq3 aaaaaaaaaaMMMMMaaaaa\n" |
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+ "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE); |
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SearchResultsI sr = new SearchResults(); |
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SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); |
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SequenceI seq1 = sqs[0]; |
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SequenceI seq2 = sqs[1]; |
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SequenceI seq3 = sqs[2]; |
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SequenceI seq4 = sqs[3]; |
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sr.addResult(seq1, 2, 4); |
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sr.addResult(seq2, 4, 10); |
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sr.addResult(seq3, 11, 15); |
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Finder f = new Finder(af.getViewport().getAlignment(), null); |
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f.setFindAll(true); |
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f.setCaseSensitive(true); |
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f.find("M+"); |
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assertEquals( |
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"Finder found different set of results to manually created SearchResults", |
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sr, f.getSearchResults()); |
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af.getViewport().setSearchResults(sr); |
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AlignViewControllerI avc = af.avc; |
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avc.markHighlightedColumns(false, false, false); |
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assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af |
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.getViewport().getColumnSelection().getSelectedRanges() |
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.toArray(), new int[][] { { 1, 14 } })); |
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} |
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} |