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