X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModelTest.java;fp=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureDistanceModelTest.java;h=1300fa211652e5822ab393a60c4137a1066d2b03;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=a1623f62b7ea4a080ca6cae82a64bd60e5064a50;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java index a1623f6..1300fa2 100644 --- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java +++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java @@ -75,8 +75,8 @@ public class FeatureDistanceModelTest */ public AlignFrame getTestAlignmentFrame() { - AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded( - alntestFile, DataSourceType.PASTE); + AlignFrame alf = new FileLoader(false) + .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE); AlignmentI al = alf.getViewport().getAlignment(); Assert.assertEquals(al.getHeight(), 4); Assert.assertEquals(al.getWidth(), 5); @@ -104,8 +104,9 @@ public class FeatureDistanceModelTest alf.getFeatureRenderer().setVisible("sf2"); alf.getFeatureRenderer().setVisible("sf3"); alf.getFeatureRenderer().findAllFeatures(true); - Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes() - .size(), 3, "Number of feature types"); + Assert.assertEquals( + alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3, + "Number of feature types"); assertTrue(alf.getCurrentView().areFeaturesDisplayed()); return alf; } @@ -119,8 +120,7 @@ public class FeatureDistanceModelTest alf.getCurrentView().getAlignPanel()); alf.selectAllSequenceMenuItem_actionPerformed(null); - MatrixI dm = sm.findDistances( - alf.getViewport().getAlignmentView(true), + MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true), SimilarityParams.Jalview); assertEquals(dm.getValue(0, 2), 0d, "FER1_MESCR (0) should be identical with RAPSA (2)"); @@ -138,8 +138,7 @@ public class FeatureDistanceModelTest sm = ScoreModels.getInstance().getScoreModel(sm.getName(), alf.getCurrentView().getAlignPanel()); alf.selectAllSequenceMenuItem_actionPerformed(null); - MatrixI dm = sm.findDistances( - alf.getViewport().getAlignmentView(true), + MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true), SimilarityParams.Jalview); assertEquals(dm.getValue(0, 2), 0d, "FER1_MESCR (0) should be identical with RAPSA (2)"); @@ -159,22 +158,20 @@ public class FeatureDistanceModelTest sm = ScoreModels.getInstance().getScoreModel(sm.getName(), alf.getCurrentView().getAlignPanel()); alf.selectAllSequenceMenuItem_actionPerformed(null); - MatrixI dm = sm.findDistances( - alf.getViewport().getAlignmentView(true), + MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true), SimilarityParams.Jalview); - assertEquals( - dm.getValue(0, 2), - 0d, + assertEquals(dm.getValue(0, 2), 0d, "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)"); - assertEquals( - dm.getValue(0, 1), - 0d, + assertEquals(dm.getValue(0, 1), 0d, "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)"); for (int s = 0; s < 3; s++) { - assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns " - + alf.getViewport().getAlignment().getSequenceAt(s).getName() - + "(" + s + ") should still be distinct from FER1_MAIZE (3)"); + assertTrue(dm.getValue(s, 3) > 0d, + "After hiding last two columns " + + alf.getViewport().getAlignment().getSequenceAt(s) + .getName() + + "(" + s + + ") should still be distinct from FER1_MAIZE (3)"); } } @@ -196,26 +193,33 @@ public class FeatureDistanceModelTest 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"); + 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().findFeaturesAtColumn(aseq, 1) - .size(), 0); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(), + 0); // step through and check for pointwise feature presence/absence - Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2) - .size(), 1); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(), + 1); // step through and check for pointwise feature presence/absence - Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3) - .size(), 0); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(), + 0); // step through and check for pointwise feature presence/absence - Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4) - .size(), 0); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(), + 0); // step through and check for pointwise feature presence/absence - Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5) - .size(), 1); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(), + 1); // step through and check for pointwise feature presence/absence - Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6) - .size(), 0); + Assert.assertEquals( + af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(), + 0); } @Test(groups = { "Functional" }) @@ -239,18 +243,18 @@ public class FeatureDistanceModelTest * 20120 (two features of the same type doesn't affect score) * giving an average (pairwise distance) of 5/5 or 1.0 */ - s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f, - null)); - s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f, - null)); - s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f, - null)); - s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f, - null)); - s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f, - null)); - s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f, - null)); + s1.addSequenceFeature( + new SequenceFeature("domain", null, 1, 3, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("variant", null, 2, 4, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("variant", null, 3, 5, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("domain", null, 2, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("variant", null, 1, 2, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("variant", null, 5, 5, 0f, null)); alf.setShowSeqFeatures(true); alf.getFeatureRenderer().findAllFeatures(true); @@ -259,8 +263,7 @@ public class FeatureDistanceModelTest alf.getCurrentView().getAlignPanel()); alf.selectAllSequenceMenuItem_actionPerformed(null); - AlignmentView alignmentView = alf.getViewport() - .getAlignmentView(true); + AlignmentView alignmentView = alf.getViewport().getAlignmentView(true); MatrixI distances = sm.findDistances(alignmentView, SimilarityParams.Jalview); assertEquals(distances.width(), 2); @@ -303,7 +306,7 @@ public class FeatureDistanceModelTest assertEquals(distances.getValue(1, 1), 0d); assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6 assertEquals(distances.getValue(1, 0), 13d / 6); - + /* * exclude gaps * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6 @@ -339,12 +342,16 @@ public class FeatureDistanceModelTest SequenceI s1 = new Sequence("s1", "FR K S"); SequenceI s2 = new Sequence("s2", "FS L"); - s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null)); - s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f, - null)); - s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null)); - s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null)); - s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("chain", null, 1, 4, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("domain", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("chain", null, 1, 3, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("metal", null, 1, 3, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("Pfam", null, 1, 3, 0f, null)); AlignmentI al = new Alignment(new SequenceI[] { s1, s2 }); AlignFrame af = new AlignFrame(al, 300, 300); af.setShowSeqFeatures(true);