test/jalview/datamodel/SequenceFeatureTest.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.datamodel;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertNull;
  26 import static org.testng.AssertJUnit.assertSame;
  27 import static org.testng.AssertJUnit.assertTrue;
  28
  29 import java.util.ArrayList;
  30 import java.util.List;
  31
  32 import org.testng.annotations.BeforeClass;
  33 import org.testng.annotations.Test;
  34
  35 import jalview.gui.JvOptionPane;
  36 import jalview.util.MapList;
  37
  38 public class SequenceFeatureTest
  39 {
  40
  41   @BeforeClass(alwaysRun = true)
  42   public void setUpJvOptionPane()
  43   {
  44     JvOptionPane.setInteractiveMode(false);
  45     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  46   }
  47
  48   @Test(groups = { "Functional" })
  49   public void testCopyConstructors()
  50   {
  51     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
  52             "group");
  53     sf1.setValue("STRAND", "+");
  54     sf1.setValue("Note", "Testing");
  55     Integer count = Integer.valueOf(7);
  56     sf1.setValue("Count", count);
  57
  58     SequenceFeature sf2 = new SequenceFeature(sf1);
  59     assertEquals("type", sf2.getType());
  60     assertEquals("desc", sf2.getDescription());
  61     assertEquals(22, sf2.getBegin());
  62     assertEquals(33, sf2.getEnd());
  63     assertEquals(12.5f, sf2.getScore());
  64     assertEquals("+", sf2.getValue("STRAND"));
  65     assertEquals("Testing", sf2.getValue("Note"));
  66     // shallow clone of otherDetails map - contains the same object values!
  67     assertSame(count, sf2.getValue("Count"));
  68
  69     /*
  70      * copy constructor modifying begin/end/group/score
  71      */
  72     SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
  73     assertEquals("type", sf3.getType());
  74     assertEquals("desc", sf3.getDescription());
  75     assertEquals(11, sf3.getBegin());
  76     assertEquals(14, sf3.getEnd());
  77     assertEquals(17.4f, sf3.getScore());
  78     assertEquals("+", sf3.getValue("STRAND"));
  79     assertEquals("Testing", sf3.getValue("Note"));
  80     // shallow clone of otherDetails map - contains the same object values!
  81     assertSame(count, sf3.getValue("Count"));
  82
  83     /*
  84      * copy constructor modifying type/begin/end/group/score
  85      */
  86     SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
  87             "group3", -9.1f);
  88     assertEquals("Disulfide bond", sf4.getType());
  89     assertTrue(sf4.isContactFeature());
  90     assertEquals("desc", sf4.getDescription());
  91     assertEquals(12, sf4.getBegin());
  92     assertEquals(15, sf4.getEnd());
  93     assertEquals(-9.1f, sf4.getScore());
  94     assertEquals("+", sf4.getValue("STRAND"));
  95     assertEquals("Testing", sf4.getValue("Note"));
  96     // shallow clone of otherDetails map - contains the same object values!
  97     assertSame(count, sf4.getValue("Count"));
  98   }
  99
 100   /**
 101    * Tests for retrieving a 'miscellaneous details' property value, with or
 102    * without a supplied default
 103    */
 104   @Test(groups = { "Functional" })
 105   public void testGetValue()
 106   {
 107     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 108             "group");
 109     sf1.setValue("STRAND", "+");
 110     assertEquals("+", sf1.getValue("STRAND"));
 111     assertNull(sf1.getValue("strand")); // case-sensitive
 112     assertEquals(".", sf1.getValue("unknown", "."));
 113     Integer i = Integer.valueOf(27);
 114     assertSame(i, sf1.getValue("Unknown", i));
 115   }
 116
 117   /**
 118    * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
 119    */
 120   @Test(groups = { "Functional" })
 121   public void testGetStrand()
 122   {
 123     SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 124             "group");
 125     assertEquals(0, sf.getStrand());
 126     sf.setValue("STRAND", "+");
 127     assertEquals(1, sf.getStrand());
 128     sf.setValue("STRAND", "-");
 129     assertEquals(-1, sf.getStrand());
 130     sf.setValue("STRAND", ".");
 131     assertEquals(0, sf.getStrand());
 132   }
 133
 134   /**
 135    * Tests for equality, and that equal objects have the same hashCode
 136    */
 137   @Test(groups = { "Functional" })
 138   public void testEqualsAndHashCode()
 139   {
 140     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 141             "group");
 142     sf1.setValue("ID", "id");
 143     sf1.setValue("Name", "name");
 144     sf1.setValue("Parent", "parent");
 145     sf1.setStrand("+");
 146     sf1.setPhase("1");
 147     SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 148             "group");
 149     sf2.setValue("ID", "id");
 150     sf2.setValue("Name", "name");
 151     sf2.setValue("Parent", "parent");
 152     sf2.setStrand("+");
 153     sf2.setPhase("1");
 154
 155     assertFalse(sf1.equals(null));
 156     assertTrue(sf1.equals(sf2));
 157     assertTrue(sf2.equals(sf1));
 158     assertEquals(sf1.hashCode(), sf2.hashCode());
 159
 160     // changing type breaks equals:
 161     SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 162             "group");
 163     SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, 12.5f,
 164             "group");
 165     assertFalse(sf3.equals(sf4));
 166
 167     // changing description breaks equals:
 168     String restores = sf2.getDescription();
 169     sf2.setDescription("Desc");
 170     assertFalse(sf1.equals(sf2));
 171     sf2.setDescription(restores);
 172
 173     // changing score breaks equals:
 174     float restoref = sf2.getScore();
 175     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
 176             sf2.getFeatureGroup(), 10f);
 177     assertFalse(sf1.equals(sf2));
 178     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
 179             sf2.getFeatureGroup(), restoref);
 180
 181     // NaN doesn't match a number
 182     restoref = sf2.getScore();
 183     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
 184             sf2.getFeatureGroup(), Float.NaN);
 185     assertFalse(sf1.equals(sf2));
 186
 187     // NaN matches NaN
 188     sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
 189             sf1.getFeatureGroup(), Float.NaN);
 190     assertTrue(sf1.equals(sf2));
 191     sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
 192             sf1.getFeatureGroup(), restoref);
 193     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
 194             sf2.getFeatureGroup(), restoref);
 195
 196     // changing start position breaks equals:
 197     int restorei = sf2.getBegin();
 198     sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(),
 199             sf2.getScore());
 200     assertFalse(sf1.equals(sf2));
 201     sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
 202             sf2.getFeatureGroup(), sf2.getScore());
 203
 204     // changing end position breaks equals:
 205     restorei = sf2.getEnd();
 206     sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
 207             sf2.getFeatureGroup(), sf2.getScore());
 208     assertFalse(sf1.equals(sf2));
 209     sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
 210             sf2.getFeatureGroup(), sf2.getScore());
 211
 212     // changing feature group breaks equals:
 213     restores = sf2.getFeatureGroup();
 214     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group",
 215             sf2.getScore());
 216     assertFalse(sf1.equals(sf2));
 217     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores,
 218             sf2.getScore());
 219
 220     // changing ID breaks equals:
 221     restores = (String) sf2.getValue("ID");
 222     sf2.setValue("ID", "id2");
 223     assertFalse(sf1.equals(sf2));
 224     sf2.setValue("ID", restores);
 225
 226     // changing Name breaks equals:
 227     restores = (String) sf2.getValue("Name");
 228     sf2.setValue("Name", "Name");
 229     assertFalse(sf1.equals(sf2));
 230     sf2.setValue("Name", restores);
 231
 232     // changing Parent breaks equals:
 233     restores = (String) sf1.getValue("Parent");
 234     sf1.setValue("Parent", "Parent");
 235     assertFalse(sf1.equals(sf2));
 236     sf1.setValue("Parent", restores);
 237
 238     // changing strand breaks equals:
 239     restorei = sf2.getStrand();
 240     sf2.setStrand("-");
 241     assertFalse(sf1.equals(sf2));
 242     sf2.setStrand(restorei == 1 ? "+" : "-");
 243
 244     // changing phase breaks equals:
 245     restores = sf1.getPhase();
 246     sf1.setPhase("2");
 247     assertFalse(sf1.equals(sf2));
 248     sf1.setPhase(restores);
 249
 250     // restore equality as sanity check:
 251     assertTrue(sf1.equals(sf2));
 252     assertTrue(sf2.equals(sf1));
 253     assertEquals(sf1.hashCode(), sf2.hashCode());
 254
 255     // changing status doesn't change equals:
 256     sf1.setStatus("new");
 257     assertTrue(sf1.equals(sf2));
 258   }
 259
 260   @Test(groups = { "Functional" })
 261   public void testIsContactFeature()
 262   {
 263     SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 264             "group");
 265     assertFalse(sf.isContactFeature());
 266     sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
 267     assertFalse(sf.isContactFeature());
 268     sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
 269     assertFalse(sf.isContactFeature());
 270     sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
 271             "group");
 272     assertTrue(sf.isContactFeature());
 273     sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
 274             "group");
 275     assertTrue(sf.isContactFeature());
 276     sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
 277             "group");
 278     assertTrue(sf.isContactFeature());
 279     sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
 280             "group");
 281     assertTrue(sf.isContactFeature());
 282   }
 283
 284   @Test(groups = { "Functional" })
 285   public void testGetDetailsReport()
 286   {
 287     SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
 288     String seqName = seq.getName();
 289
 290     // single locus, no group, no score
 291     SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
 292             null);
 293     String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
 294             + "<tr><td>Type</td><td>variant</td><td></td></tr>"
 295             + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
 296     assertEquals(expected, sf.getDetailsReport(seqName, null));
 297
 298     // contact feature
 299     sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
 300             null);
 301     expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
 302             + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
 303             + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
 304     assertEquals(expected, sf.getDetailsReport(seqName, null));
 305
 306     sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
 307     sf.setValue("Parent", "ENSG001");
 308     sf.setValue("Child", "ENSP002");
 309     expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
 310             + "<tr><td>Type</td><td>variant</td><td></td></tr>"
 311             + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
 312             + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
 313             + "<tr><td>Group</td><td>group</td><td></td></tr>"
 314             + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
 315             + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
 316     assertEquals(expected, sf.getDetailsReport(seqName, null));
 317
 318     /*
 319      * feature with embedded html link in description
 320      */
 321     String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
 322     sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
 323     expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
 324             + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
 325             + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
 326             + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
 327     assertEquals(expected, sf.getDetailsReport(seqName, null));
 328   }
 329
 330   /**
 331    * Feature details report for a virtual feature should include original and
 332    * mapped locations, and also derived peptide consequence if it can be
 333    * determined
 334    */
 335   @Test(groups = { "Functional" })
 336   public void testGetDetailsReport_virtualFeature()
 337   {
 338     SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
 339     SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
 340     MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
 341             3, 1);
 342     Mapping mapping = new Mapping(seq, map);
 343     List<SequenceFeature> features = new ArrayList<>();
 344     // vary ttg (Leu) to ttc (Phe)
 345     SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
 346             null);
 347     sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
 348     features.add(sf);
 349
 350     MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
 351
 352     String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
 353             + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
 354             + "<tr><td>Type</td><td>variant</td><td></td></tr>"
 355             + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
 356             + "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
 357             + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
 358             + "</table>";
 359
 360     assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
 361
 362
 363     /*
 364      * exon feature extending beyond mapped range; mapped location should be
 365      * restricted to peptide mapped range limit i.e. 10-13
 366      */
 367     SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230, null);
 368     features.add(sf2);
 369     expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
 370             + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
 371             + "<tr><td>Type</td><td>exon</td><td></td></tr>"
 372             + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
 373             + "</table>";
 374     assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
 375   }
 376 }