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package jalview.analysis.scoremodels; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertTrue; |
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import jalview.api.analysis.ScoreModelI; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.AlignViewport; |
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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.math.MatrixI; |
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import java.util.Arrays; |
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import org.testng.Assert; |
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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 (132) |
Complexity: 14 |
Complexity Density: 0.12 |
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public class FeatureDistanceModelTest |
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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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public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n"; |
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int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 }; |
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int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 }; |
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int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 }; |
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@return |
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| 100% |
Uncovered Elements: 0 (28) |
Complexity: 5 |
Complexity Density: 0.25 |
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public AlignFrame getTestAlignmentFrame()... |
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{ |
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AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( |
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alntestFile, DataSourceType.PASTE); |
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AlignmentI al = alf.getViewport().getAlignment(); |
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Assert.assertEquals(al.getHeight(), 4); |
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Assert.assertEquals(al.getWidth(), 5); |
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for (int i = 0; i < 4; i++) |
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{ |
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SequenceI ds = al.getSequenceAt(i).getDatasetSequence(); |
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if (sf1[i * 2] > 0) |
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{ |
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ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2], |
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sf1[i * 2 + 1], "sf1")); |
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} |
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if (sf2[i * 2] > 0) |
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{ |
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ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2], |
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sf2[i * 2 + 1], "sf2")); |
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} |
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if (sf3[i * 2] > 0) |
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{ |
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ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2], |
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sf3[i * 2 + 1], "sf3")); |
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} |
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} |
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alf.setShowSeqFeatures(true); |
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alf.getFeatureRenderer().setVisible("sf1"); |
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alf.getFeatureRenderer().setVisible("sf2"); |
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alf.getFeatureRenderer().setVisible("sf3"); |
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alf.getFeatureRenderer().findAllFeatures(true); |
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Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes() |
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.size(), 3, "Number of feature types"); |
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assertTrue(alf.getCurrentView().areFeaturesDisplayed()); |
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return alf; |
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} |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testFeatureScoreModel() throws Exception |
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{ |
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AlignFrame alf = getTestAlignmentFrame(); |
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ScoreModelI sm = new FeatureDistanceModel(); |
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sm = ScoreModels.getInstance().getScoreModel(sm.getName(), |
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alf.getCurrentView().getAlignPanel()); |
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alf.selectAllSequenceMenuItem_actionPerformed(null); |
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MatrixI dm = sm.findDistances( |
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alf.getViewport().getAlignmentView(true), |
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SimilarityParams.Jalview); |
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assertEquals(dm.getValue(0, 2), 0d, |
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"FER1_MESCR (0) should be identical with RAPSA (2)"); |
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assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2), |
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"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)"); |
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} |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testFeatureScoreModel_hiddenFirstColumn() throws Exception |
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{ |
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AlignFrame alf = getTestAlignmentFrame(); |
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alf.getViewport().hideColumns(0, 1); |
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ScoreModelI sm = new FeatureDistanceModel(); |
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sm = ScoreModels.getInstance().getScoreModel(sm.getName(), |
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alf.getCurrentView().getAlignPanel()); |
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alf.selectAllSequenceMenuItem_actionPerformed(null); |
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MatrixI dm = sm.findDistances( |
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alf.getViewport().getAlignmentView(true), |
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SimilarityParams.Jalview); |
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assertEquals(dm.getValue(0, 2), 0d, |
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"FER1_MESCR (0) should be identical with RAPSA (2)"); |
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assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2), |
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"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)"); |
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} |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testFeatureScoreModel_HiddenColumns() throws Exception |
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{ |
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AlignFrame alf = getTestAlignmentFrame(); |
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alf.getViewport().hideColumns(3, 4); |
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alf.getViewport().hideColumns(0, 1); |
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ScoreModelI sm = new FeatureDistanceModel(); |
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sm = ScoreModels.getInstance().getScoreModel(sm.getName(), |
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alf.getCurrentView().getAlignPanel()); |
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alf.selectAllSequenceMenuItem_actionPerformed(null); |
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MatrixI dm = sm.findDistances( |
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alf.getViewport().getAlignmentView(true), |
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SimilarityParams.Jalview); |
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assertEquals( |
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dm.getValue(0, 2), |
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0d, |
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"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)"); |
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assertEquals( |
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dm.getValue(0, 1), |
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0d, |
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"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)"); |
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for (int s = 0; s < 3; s++) |
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{ |
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assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns " |
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+ alf.getViewport().getAlignment().getSequenceAt(s).getName() |
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+ "(" + s + ") should still be distinct from FER1_MAIZE (3)"); |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (16) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testFindFeatureAt_PointFeature() throws Exception |
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{ |
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String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n" |
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+ "c CCCCCCGGGGGGCCCCCC\n"; |
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AlignFrame af = new jalview.io.FileLoader(false) |
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.LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE); |
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SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0); |
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SequenceFeature sf = null; |
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sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, ""); |
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aseq.addSequenceFeature(sf); |
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assertTrue(sf.isContactFeature()); |
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af.refreshFeatureUI(true); |
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af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond")); |
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Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes() |
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.size(), 1, "Should be just one feature type displayed"); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1) |
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.size(), 0); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2) |
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.size(), 1); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3) |
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.size(), 0); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4) |
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.size(), 0); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5) |
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.size(), 1); |
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Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6) |
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.size(), 0); |
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} |
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| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testFindDistances() throws Exception |
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{ |
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String seqs = ">s1\nABCDE\n>seq2\nABCDE\n"; |
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AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs, |
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DataSourceType.PASTE); |
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SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0); |
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SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1); |
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s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f, |
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null)); |
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s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f, |
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null)); |
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s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f, |
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null)); |
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s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f, |
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null)); |
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s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f, |
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null)); |
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s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f, |
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null)); |
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alf.setShowSeqFeatures(true); |
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alf.getFeatureRenderer().findAllFeatures(true); |
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ScoreModelI sm = new FeatureDistanceModel(); |
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sm = ScoreModels.getInstance().getScoreModel(sm.getName(), |
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alf.getCurrentView().getAlignPanel()); |
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alf.selectAllSequenceMenuItem_actionPerformed(null); |
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AlignmentView alignmentView = alf.getViewport() |
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.getAlignmentView(true); |
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MatrixI distances = sm.findDistances(alignmentView, |
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SimilarityParams.Jalview); |
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assertEquals(distances.width(), 2); |
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assertEquals(distances.height(), 2); |
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assertEquals(distances.getValue(0, 0), 0d); |
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assertEquals(distances.getValue(1, 1), 0d); |
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assertEquals(distances.getValue(0, 1), 1d, |
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"expected identical pairs. (check normalisation for similarity score)"); |
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assertEquals(distances.getValue(1, 0), 1d); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testFindDistances_withParams() |
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{ |
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AlignFrame af = setupAlignmentView(); |
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AlignViewport viewport = af.getViewport(); |
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AlignmentView view = viewport.getAlignmentView(false); |
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ScoreModelI sm = new FeatureDistanceModel(); |
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sm = ScoreModels.getInstance().getScoreModel(sm.getName(), |
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af.alignPanel); |
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SimilarityParamsI params = new SimilarityParams(true, true, true, true); |
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MatrixI distances = sm.findDistances(view, params); |
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assertEquals(distances.getValue(0, 0), 0d); |
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assertEquals(distances.getValue(1, 1), 0d); |
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assertEquals(distances.getValue(0, 1), 13d / 6); |
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assertEquals(distances.getValue(1, 0), 13d / 6); |
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params = new SimilarityParams(true, true, false, true); |
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distances = sm.findDistances(view, params); |
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assertEquals(distances.getValue(0, 1), 6d / 6); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
|
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1 |
protected AlignFrame setupAlignmentView()... |
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{ |
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SequenceI s1 = new Sequence("s1", "FR K S"); |
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SequenceI s2 = new Sequence("s2", "FS L"); |
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s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null)); |
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s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f, |
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null)); |
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s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null)); |
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s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null)); |
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s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null)); |
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AlignmentI al = new Alignment(new SequenceI[] { s1, s2 }); |
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AlignFrame af = new AlignFrame(al, 300, 300); |
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af.setShowSeqFeatures(true); |
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af.getFeatureRenderer().findAllFeatures(true); |
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return af; |
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} |
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} |