test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.analysis.scoremodels;
  22
  23 import static org.testng.Assert.assertEquals;
  24
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.AlignFrame;
  29 import jalview.gui.JvOptionPane;
  30 import jalview.io.DataSourceType;
  31 import jalview.io.FileLoader;
  32
  33 import java.util.Arrays;
  34
  35 import org.testng.Assert;
  36 import org.testng.annotations.BeforeClass;
  37 import org.testng.annotations.Test;
  38
  39 public class FeatureDistanceModelTest
  40 {
  41
  42   @BeforeClass(alwaysRun = true)
  43   public void setUpJvOptionPane()
  44   {
  45     JvOptionPane.setInteractiveMode(false);
  46     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  47   }
  48
  49   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";
  50
  51   int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
  52
  53   int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
  54
  55   int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
  56
  57   /**
  58    * <pre>
  59    * Load test alignment and add features to sequences:
  60    *      FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE
  61    *  sf1     X          X          X
  62    *  sf2                X                     X
  63    *  sf3                                      X
  64    * </pre>
  65    *
  66    * @return
  67    */
  68   public AlignFrame getTestAlignmentFrame()
  69   {
  70     AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
  71             alntestFile, DataSourceType.PASTE);
  72     AlignmentI al = alf.getViewport().getAlignment();
  73     Assert.assertEquals(al.getHeight(), 4);
  74     Assert.assertEquals(al.getWidth(), 5);
  75     for (int i = 0; i < 4; i++)
  76     {
  77       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
  78       if (sf1[i * 2] > 0)
  79       {
  80         ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
  81                 sf1[i * 2], sf1[i * 2 + 1], "sf1"));
  82       }
  83       if (sf2[i * 2] > 0)
  84       {
  85         ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
  86                 sf2[i * 2], sf2[i * 2 + 1], "sf2"));
  87       }
  88       if (sf3[i * 2] > 0)
  89       {
  90         ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
  91                 sf3[i * 2], sf3[i * 2 + 1], "sf3"));
  92       }
  93     }
  94     alf.setShowSeqFeatures(true);
  95     alf.getFeatureRenderer().setVisible("sf1");
  96     alf.getFeatureRenderer().setVisible("sf2");
  97     alf.getFeatureRenderer().setVisible("sf3");
  98     alf.getFeatureRenderer().findAllFeatures(true);
  99     Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
 100             .size(), 3, "Number of feature types");
 101     Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
 102     return alf;
 103   }
 104
 105   @Test(groups = { "Functional" })
 106   public void testFeatureScoreModel() throws Exception
 107   {
 108     AlignFrame alf = getTestAlignmentFrame();
 109     FeatureDistanceModel fsm = new FeatureDistanceModel();
 110     Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 111             .getAlignPanel()));
 112     alf.selectAllSequenceMenuItem_actionPerformed(null);
 113
 114     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
 115             true));
 116     Assert.assertTrue(dm[0][2] == 0f,
 117             "FER1_MESCR (0) should be identical with RAPSA (2)");
 118     Assert.assertTrue(dm[0][1] > dm[0][2],
 119             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
 120   }
 121
 122   @Test(groups = { "Functional" })
 123   public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
 124   {
 125     AlignFrame alf = getTestAlignmentFrame();
 126     // hiding first two columns shouldn't affect the tree
 127     alf.getViewport().hideColumns(0, 1);
 128     FeatureDistanceModel fsm = new FeatureDistanceModel();
 129     Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 130             .getAlignPanel()));
 131     alf.selectAllSequenceMenuItem_actionPerformed(null);
 132     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
 133             true));
 134     Assert.assertTrue(dm[0][2] == 0f,
 135             "FER1_MESCR (0) should be identical with RAPSA (2)");
 136     Assert.assertTrue(dm[0][1] > dm[0][2],
 137             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
 138   }
 139
 140   @Test(groups = { "Functional" })
 141   public void testFeatureScoreModel_HiddenColumns() throws Exception
 142   {
 143     AlignFrame alf = getTestAlignmentFrame();
 144     // hide columns and check tree changes
 145     alf.getViewport().hideColumns(3, 4);
 146     alf.getViewport().hideColumns(0, 1);
 147     FeatureDistanceModel fsm = new FeatureDistanceModel();
 148     Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 149             .getAlignPanel()));
 150     alf.selectAllSequenceMenuItem_actionPerformed(null);
 151     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
 152             true));
 153     Assert.assertTrue(
 154             dm[0][2] == 0f,
 155             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
 156     Assert.assertTrue(
 157             dm[0][1] == 0f,
 158             "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
 159     for (int s = 0; s < 3; s++)
 160     {
 161       Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns "
 162               + alf.getViewport().getAlignment().getSequenceAt(s).getName()
 163               + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
 164     }
 165   }
 166
 167   /**
 168    * Check findFeatureAt doesn't return contact features except at contact
 169    * points TODO:move to under the FeatureRendererModel test suite
 170    */
 171   @Test(groups = { "Functional" })
 172   public void testFindFeatureAt_PointFeature() throws Exception
 173   {
 174     String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
 175             + "c CCCCCCGGGGGGCCCCCC\n";
 176     AlignFrame af = new jalview.io.FileLoader(false)
 177             .LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
 178     SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
 179     SequenceFeature sf = null;
 180     sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
 181     aseq.addSequenceFeature(sf);
 182     Assert.assertTrue(sf.isContactFeature());
 183     af.refreshFeatureUI(true);
 184     af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
 185     Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
 186             .size(), 1, "Should be just one feature type displayed");
 187     // step through and check for pointwise feature presence/absence
 188     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
 189             .size(), 0);
 190     // step through and check for pointwise feature presence/absence
 191     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
 192             .size(), 1);
 193     // step through and check for pointwise feature presence/absence
 194     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
 195             .size(), 0);
 196     // step through and check for pointwise feature presence/absence
 197     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
 198             .size(), 0);
 199     // step through and check for pointwise feature presence/absence
 200     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
 201             .size(), 1);
 202     // step through and check for pointwise feature presence/absence
 203     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
 204             .size(), 0);
 205   }
 206
 207   @Test(groups = { "Functional" })
 208   public void testFindDistances() throws Exception
 209   {
 210     String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
 211     AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
 212             DataSourceType.PASTE);
 213     SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
 214     SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
 215
 216     /*
 217      * set domain and variant features thus:
 218      *     ----5
 219      *  s1 ddd..
 220      *  s1 .vvv.
 221      *  s1 ..vvv
 222      *  s2 .ddd.
 223      *  s2 vv..v
 224      *  The number of unshared feature types per column is
 225      *     20120 (two features of the same type doesn't affect score)
 226      *  giving an average (pairwise distance) of 5/5 or 1.0
 227      */
 228     s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
 229             null));
 230     s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
 231             null));
 232     s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
 233             null));
 234     s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
 235             null));
 236     s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
 237             null));
 238     s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
 239             null));
 240     alf.setShowSeqFeatures(true);
 241     alf.getFeatureRenderer().findAllFeatures(true);
 242
 243     FeatureDistanceModel fsm = new FeatureDistanceModel();
 244     Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 245             .getAlignPanel()));
 246     alf.selectAllSequenceMenuItem_actionPerformed(null);
 247
 248     float[][] distances = fsm.findDistances(alf.getViewport()
 249             .getAlignmentView(true));
 250     assertEquals(distances.length, 2);
 251     assertEquals(distances[0][0], 0f);
 252     assertEquals(distances[1][1], 0f);
 253     // these left to fail pending resolution of
 254     // JAL-2424 (dividing score by 6, not 5)
 255     assertEquals(distances[0][1], 1f);
 256     assertEquals(distances[1][0], 1f);
 257   }
 258
 259 }