X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModelTest.java;h=1da23eadd9178ad844445fc7ceea80feb8c2ce7a;hb=19424d4e1623bfcdcf30567f7a233fe81c4a9e4e;hp=2dc2ac3c359cb87c38da3c5e7433a32e2b527449;hpb=08c587d9947f357382199bdb6900c263efc62739;p=jalview.git diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java index 2dc2ac3..1da23ea 100644 --- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java +++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java @@ -24,14 +24,26 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; import jalview.io.FileLoader; import jalview.io.FormatAdapter; -import org.testng.AssertJUnit; +import java.util.Arrays; + +import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class FeatureScoreModelTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + 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"; int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 }; @@ -40,14 +52,13 @@ public class FeatureScoreModelTest int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 }; - @Test(groups = { "Functional" }) - public void testFeatureScoreModel() throws Exception + public AlignFrame getTestAlignmentFrame() { AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( alntestFile, FormatAdapter.PASTE); AlignmentI al = alf.getViewport().getAlignment(); - AssertJUnit.assertEquals(4, al.getHeight()); - AssertJUnit.assertEquals(5, al.getWidth()); + Assert.assertEquals(al.getHeight(), 4); + Assert.assertEquals(al.getWidth(), 5); for (int i = 0; i < 4; i++) { SequenceI ds = al.getSequenceAt(i).getDatasetSequence(); @@ -72,21 +83,111 @@ public class FeatureScoreModelTest alf.getFeatureRenderer().setVisible("sf2"); alf.getFeatureRenderer().setVisible("sf3"); alf.getFeatureRenderer().findAllFeatures(true); - AssertJUnit.assertEquals("Number of feature types", 3, alf - .getFeatureRenderer().getDisplayedFeatureTypes().size()); - AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed()); + Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes() + .size(), 3, "Number of feature types"); + Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed()); + return alf; + } + + @Test(groups = { "Functional" }) + public void testFeatureScoreModel() throws Exception + { + AlignFrame alf = getTestAlignmentFrame(); + FeatureScoreModel fsm = new FeatureScoreModel(); + Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView() + .getAlignPanel())); + alf.selectAllSequenceMenuItem_actionPerformed(null); + float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView( + true)); + Assert.assertTrue(dm[0][2] == 0f, + "FER1_MESCR (0) should be identical with RAPSA (2)"); + Assert.assertTrue(dm[0][1] > dm[0][2], + "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)"); + } + + @Test(groups = { "Functional" }) + public void testFeatureScoreModel_hiddenFirstColumn() throws Exception + { + AlignFrame alf = getTestAlignmentFrame(); + // hiding first two columns shouldn't affect the tree + alf.getViewport().hideColumns(0, 1); FeatureScoreModel fsm = new FeatureScoreModel(); - AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf - .getCurrentView().getAlignPanel())); + Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView() + .getAlignPanel())); alf.selectAllSequenceMenuItem_actionPerformed(null); float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView( true)); - AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)", - dm[0][2] == 0f); - AssertJUnit - .assertTrue( - "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)", - dm[0][1] > dm[0][2]); + Assert.assertTrue(dm[0][2] == 0f, + "FER1_MESCR (0) should be identical with RAPSA (2)"); + Assert.assertTrue(dm[0][1] > dm[0][2], + "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)"); + } + @Test(groups = { "Functional" }) + public void testFeatureScoreModel_HiddenColumns() throws Exception + { + AlignFrame alf = getTestAlignmentFrame(); + // hide columns and check tree changes + alf.getViewport().hideColumns(3, 4); + alf.getViewport().hideColumns(0, 1); + FeatureScoreModel fsm = new FeatureScoreModel(); + Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView() + .getAlignPanel())); + alf.selectAllSequenceMenuItem_actionPerformed(null); + float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView( + true)); + Assert.assertTrue( + dm[0][2] == 0f, + "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)"); + Assert.assertTrue( + dm[0][1] == 0f, + "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)"); + for (int s = 0; s < 3; s++) + { + Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns " + + alf.getViewport().getAlignment().getSequenceAt(s).getName() + + "(" + s + ") should still be distinct from FER1_MAIZE (3)"); + } + } + + /** + * Check findFeatureAt doesn't return contact features except at contact + * points TODO:move to under the FeatureRendererModel test suite + */ + @Test(groups = { "Functional" }) + public void testFindFeatureAt_PointFeature() throws Exception + { + String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n" + + "c CCCCCCGGGGGGCCCCCC\n"; + AlignFrame af = new jalview.io.FileLoader(false) + .LoadFileWaitTillLoaded(alignment, FormatAdapter.PASTE); + SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0); + SequenceFeature sf = null; + sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, ""); + aseq.addSequenceFeature(sf); + Assert.assertTrue(sf.isContactFeature()); + af.refreshFeatureUI(true); + af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond")); + Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes() + .size(), 1, "Should be just one feature type displayed"); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6) + .size(), 0); } + }