--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis.scoremodels;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.math.MatrixI;
+
+import java.util.Arrays;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class FeatureDistanceModelTest
+{
+
+ @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 };
+
+ int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
+
+ int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
+
+ /**
+ * <pre>
+ * Load test alignment and add features to sequences:
+ * FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE
+ * sf1 X X X
+ * sf2 X X
+ * sf3 X
+ * </pre>
+ *
+ * @return
+ */
+ public AlignFrame getTestAlignmentFrame()
+ {
+ AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+ alntestFile, DataSourceType.PASTE);
+ AlignmentI al = alf.getViewport().getAlignment();
+ Assert.assertEquals(al.getHeight(), 4);
+ Assert.assertEquals(al.getWidth(), 5);
+ for (int i = 0; i < 4; i++)
+ {
+ SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
+ if (sf1[i * 2] > 0)
+ {
+ ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
+ sf1[i * 2 + 1], "sf1"));
+ }
+ if (sf2[i * 2] > 0)
+ {
+ ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
+ sf2[i * 2 + 1], "sf2"));
+ }
+ if (sf3[i * 2] > 0)
+ {
+ ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
+ sf3[i * 2 + 1], "sf3"));
+ }
+ }
+ alf.setShowSeqFeatures(true);
+ alf.getFeatureRenderer().setVisible("sf1");
+ alf.getFeatureRenderer().setVisible("sf2");
+ alf.getFeatureRenderer().setVisible("sf3");
+ alf.getFeatureRenderer().findAllFeatures(true);
+ Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
+ .size(), 3, "Number of feature types");
+ assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+ return alf;
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFeatureScoreModel() throws Exception
+ {
+ AlignFrame alf = getTestAlignmentFrame();
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+
+ 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)");
+ assertTrue(dm.getValue(0, 1) > dm.getValue(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);
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+ 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)");
+ assertTrue(dm.getValue(0, 1) > dm.getValue(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);
+ // getName() can become static in Java 8
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+ MatrixI dm = sm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
+ 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,
+ "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)");
+ }
+ }
+
+ /**
+ * 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, DataSourceType.PASTE);
+ SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
+ SequenceFeature sf = null;
+ sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
+ aseq.addSequenceFeature(sf);
+ 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().findFeaturesAtColumn(aseq, 1)
+ .size(), 0);
+ // step through and check for pointwise feature presence/absence
+ 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);
+ // step through and check for pointwise feature presence/absence
+ 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);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
+ .size(), 0);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindDistances() throws Exception
+ {
+ String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
+ AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
+ DataSourceType.PASTE);
+ SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
+
+ /*
+ * set domain and variant features thus:
+ * ----5
+ * s1 ddd..
+ * s1 .vvv.
+ * s1 ..vvv
+ * s2 .ddd.
+ * s2 vv..v
+ * The number of unshared feature types per column is
+ * 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));
+ alf.setShowSeqFeatures(true);
+ alf.getFeatureRenderer().findAllFeatures(true);
+
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+
+ AlignmentView alignmentView = alf.getViewport()
+ .getAlignmentView(true);
+ MatrixI distances = sm.findDistances(alignmentView,
+ SimilarityParams.Jalview);
+ assertEquals(distances.width(), 2);
+ assertEquals(distances.height(), 2);
+ assertEquals(distances.getValue(0, 0), 0d);
+ assertEquals(distances.getValue(1, 1), 0d);
+
+ assertEquals(distances.getValue(0, 1), 1d,
+ "expected identical pairs. (check normalisation for similarity score)");
+ assertEquals(distances.getValue(1, 0), 1d);
+ }
+
+ /**
+ * Verify computed distances with varying parameter options
+ */
+ @Test(groups = "Functional")
+ public void testFindDistances_withParams()
+ {
+ AlignFrame af = setupAlignmentView();
+ AlignViewport viewport = af.getViewport();
+ AlignmentView view = viewport.getAlignmentView(false);
+
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ af.alignPanel);
+
+ /*
+ * feature distance model always normalises by region width
+ * gap-gap is always included (but scores zero)
+ * the only variable parameter is 'includeGaps'
+ */
+
+ /*
+ * include gaps
+ * score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
+ */
+ SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+ MatrixI distances = sm.findDistances(view, params);
+ assertEquals(distances.getValue(0, 0), 0d);
+ 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
+ */
+ params = new SimilarityParams(true, true, false, true);
+ distances = sm.findDistances(view, params);
+ assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
+ }
+
+ /**
+ * <pre>
+ * Set up
+ * column 1 2 3 4 5 6
+ * seq s1 F R - K - S
+ * seq s2 F S - - L
+ * s1 chain c c c c
+ * s1 domain d d d d
+ * s2 chain c c c
+ * s2 metal m m m
+ * s2 Pfam P P P
+ * scores: 3 3 0 2 3 2
+ * </pre>
+ *
+ * @return
+ */
+ protected AlignFrame setupAlignmentView()
+ {
+ /*
+ * for now, using space for gap to match callers of
+ * AlignmentView.getSequenceStrings()
+ * may change this to '-' (with corresponding change to matrices)
+ */
+ 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));
+ AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
+ AlignFrame af = new AlignFrame(al, 300, 300);
+ af.setShowSeqFeatures(true);
+ af.getFeatureRenderer().findAllFeatures(true);
+ return af;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff