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 import static org.testng.Assert.assertTrue;
  25
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.gui.AlignFrame;
  30 import jalview.gui.JvOptionPane;
  31 import jalview.io.DataSourceType;
  32 import jalview.io.FileLoader;
  33 import jalview.math.MatrixI;
  34
  35 import java.util.Arrays;
  36
  37 import org.testng.Assert;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.Test;
  40
  41 public class FeatureDistanceModelTest
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   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";
  52
  53   int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
  54
  55   int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
  56
  57   int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
  58
  59   /**
  60    * <pre>
  61    * Load test alignment and add features to sequences:
  62    *      FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE
  63    *  sf1     X          X          X
  64    *  sf2                X                     X
  65    *  sf3                                      X
  66    * </pre>
  67    *
  68    * @return
  69    */
  70   public AlignFrame getTestAlignmentFrame()
  71   {
  72     AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
  73             alntestFile, DataSourceType.PASTE);
  74     AlignmentI al = alf.getViewport().getAlignment();
  75     Assert.assertEquals(al.getHeight(), 4);
  76     Assert.assertEquals(al.getWidth(), 5);
  77     for (int i = 0; i < 4; i++)
  78     {
  79       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
  80       if (sf1[i * 2] > 0)
  81       {
  82         ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
  83                 sf1[i * 2], sf1[i * 2 + 1], "sf1"));
  84       }
  85       if (sf2[i * 2] > 0)
  86       {
  87         ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
  88                 sf2[i * 2], sf2[i * 2 + 1], "sf2"));
  89       }
  90       if (sf3[i * 2] > 0)
  91       {
  92         ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
  93                 sf3[i * 2], sf3[i * 2 + 1], "sf3"));
  94       }
  95     }
  96     alf.setShowSeqFeatures(true);
  97     alf.getFeatureRenderer().setVisible("sf1");
  98     alf.getFeatureRenderer().setVisible("sf2");
  99     alf.getFeatureRenderer().setVisible("sf3");
 100     alf.getFeatureRenderer().findAllFeatures(true);
 101     Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
 102             .size(), 3, "Number of feature types");
 103     assertTrue(alf.getCurrentView().areFeaturesDisplayed());
 104     return alf;
 105   }
 106
 107   @Test(groups = { "Functional" })
 108   public void testFeatureScoreModel() throws Exception
 109   {
 110     AlignFrame alf = getTestAlignmentFrame();
 111     FeatureDistanceModel fsm = new FeatureDistanceModel();
 112     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 113             .getAlignPanel()));
 114     alf.selectAllSequenceMenuItem_actionPerformed(null);
 115
 116     MatrixI dm = fsm
 117             .findDistances(alf.getViewport().getAlignmentView(
 118             true));
 119     assertEquals(dm.getValue(0, 2), 0d,
 120             "FER1_MESCR (0) should be identical with RAPSA (2)");
 121     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
 122             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
 123   }
 124
 125   @Test(groups = { "Functional" })
 126   public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
 127   {
 128     AlignFrame alf = getTestAlignmentFrame();
 129     // hiding first two columns shouldn't affect the tree
 130     alf.getViewport().hideColumns(0, 1);
 131     FeatureDistanceModel fsm = new FeatureDistanceModel();
 132     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 133             .getAlignPanel()));
 134     alf.selectAllSequenceMenuItem_actionPerformed(null);
 135     MatrixI dm = fsm
 136             .findDistances(alf.getViewport().getAlignmentView(
 137             true));
 138     assertEquals(dm.getValue(0, 2), 0d,
 139             "FER1_MESCR (0) should be identical with RAPSA (2)");
 140     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
 141             "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
 142   }
 143
 144   @Test(groups = { "Functional" })
 145   public void testFeatureScoreModel_HiddenColumns() throws Exception
 146   {
 147     AlignFrame alf = getTestAlignmentFrame();
 148     // hide columns and check tree changes
 149     alf.getViewport().hideColumns(3, 4);
 150     alf.getViewport().hideColumns(0, 1);
 151     FeatureDistanceModel fsm = new FeatureDistanceModel();
 152     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 153             .getAlignPanel()));
 154     alf.selectAllSequenceMenuItem_actionPerformed(null);
 155     MatrixI dm = fsm
 156             .findDistances(alf.getViewport().getAlignmentView(
 157             true));
 158     assertEquals(
 159             dm.getValue(0, 2),
 160             0d,
 161             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
 162     assertEquals(
 163             dm.getValue(0, 1),
 164             0d,
 165             "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
 166     for (int s = 0; s < 3; s++)
 167     {
 168       assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
 169               + alf.getViewport().getAlignment().getSequenceAt(s).getName()
 170               + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
 171     }
 172   }
 173
 174   /**
 175    * Check findFeatureAt doesn't return contact features except at contact
 176    * points TODO:move to under the FeatureRendererModel test suite
 177    */
 178   @Test(groups = { "Functional" })
 179   public void testFindFeatureAt_PointFeature() throws Exception
 180   {
 181     String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
 182             + "c CCCCCCGGGGGGCCCCCC\n";
 183     AlignFrame af = new jalview.io.FileLoader(false)
 184             .LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
 185     SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
 186     SequenceFeature sf = null;
 187     sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
 188     aseq.addSequenceFeature(sf);
 189     assertTrue(sf.isContactFeature());
 190     af.refreshFeatureUI(true);
 191     af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
 192     Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
 193             .size(), 1, "Should be just one feature type displayed");
 194     // step through and check for pointwise feature presence/absence
 195     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
 196             .size(), 0);
 197     // step through and check for pointwise feature presence/absence
 198     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
 199             .size(), 1);
 200     // step through and check for pointwise feature presence/absence
 201     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
 202             .size(), 0);
 203     // step through and check for pointwise feature presence/absence
 204     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
 205             .size(), 0);
 206     // step through and check for pointwise feature presence/absence
 207     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
 208             .size(), 1);
 209     // step through and check for pointwise feature presence/absence
 210     Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
 211             .size(), 0);
 212   }
 213
 214   @Test(groups = { "Functional" })
 215   public void testFindDistances() throws Exception
 216   {
 217     String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
 218     AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
 219             DataSourceType.PASTE);
 220     SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
 221     SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
 222
 223     /*
 224      * set domain and variant features thus:
 225      *     ----5
 226      *  s1 ddd..
 227      *  s1 .vvv.
 228      *  s1 ..vvv
 229      *  s2 .ddd.
 230      *  s2 vv..v
 231      *  The number of unshared feature types per column is
 232      *     20120 (two features of the same type doesn't affect score)
 233      *  giving an average (pairwise distance) of 5/5 or 1.0
 234      */
 235     s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
 236             null));
 237     s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
 238             null));
 239     s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
 240             null));
 241     s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
 242             null));
 243     s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
 244             null));
 245     s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
 246             null));
 247     alf.setShowSeqFeatures(true);
 248     alf.getFeatureRenderer().findAllFeatures(true);
 249
 250     FeatureDistanceModel fsm = new FeatureDistanceModel();
 251     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
 252             .getAlignPanel()));
 253     alf.selectAllSequenceMenuItem_actionPerformed(null);
 254
 255     MatrixI distances = fsm.findDistances(alf.getViewport()
 256             .getAlignmentView(true));
 257     assertEquals(distances.width(), 2);
 258     assertEquals(distances.height(), 2);
 259     assertEquals(distances.getValue(0, 0), 0d);
 260     assertEquals(distances.getValue(1, 1), 0d);
 261     // these left to fail pending resolution of
 262     // JAL-2424 (dividing score by 6, not 5)
 263     assertEquals(distances.getValue(0, 1), 1f);
 264     assertEquals(distances.getValue(1, 0), 1f);
 265   }
 266
 267 }