test/jalview/ext/ensembl/EnsemblGeneTest.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.ext.ensembl;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertSame;
  26 import static org.testng.AssertJUnit.assertTrue;
  27
  28 import jalview.api.FeatureSettingsModelI;
  29 import jalview.datamodel.SequenceDummy;
  30 import jalview.datamodel.SequenceFeature;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.gui.JvOptionPane;
  33 import jalview.io.gff.SequenceOntologyFactory;
  34 import jalview.io.gff.SequenceOntologyLite;
  35 import jalview.util.MapList;
  36
  37 import java.awt.Color;
  38 import java.util.List;
  39
  40 import org.testng.annotations.AfterClass;
  41 import org.testng.annotations.BeforeClass;
  42 import org.testng.annotations.Test;
  43
  44 public class EnsemblGeneTest
  45 {
  46
  47   @BeforeClass(alwaysRun = true)
  48   public void setUpJvOptionPane()
  49   {
  50     JvOptionPane.setInteractiveMode(false);
  51     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  52   }
  53
  54   @BeforeClass(alwaysRun = true)
  55   public void setUp()
  56   {
  57     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  58   }
  59
  60   @AfterClass(alwaysRun = true)
  61   public void tearDown()
  62   {
  63     SequenceOntologyFactory.setInstance(null);
  64   }
  65
  66   /**
  67    * Test that the gene part of genomic sequence is uniquely identified by a
  68    * 'gene' features (or subtype) with the correct gene ID
  69    */
  70   @Test(groups = "Functional")
  71   public void testGetGenomicRangesFromFeatures()
  72   {
  73     EnsemblGene testee = new EnsemblGene();
  74     SequenceI genomic = new SequenceDummy("chr7");
  75     genomic.setStart(10000);
  76     genomic.setEnd(50000);
  77     String geneId = "ABC123";
  78
  79     // gene at (start+10000) length 501
  80     SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
  81             null);
  82     sf.setValue("ID", "gene:" + geneId);
  83     sf.setStrand("+");
  84     genomic.addSequenceFeature(sf);
  85
  86     // gene at (start + 10500) length 101
  87     // should be ignored - the first 'gene' found defines the whole range
  88     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
  89     sf.setValue("ID", "gene:" + geneId);
  90     sf.setStrand("+");
  91     genomic.addSequenceFeature(sf);
  92
  93     MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
  94             23);
  95     List<int[]> fromRanges = ranges.getFromRanges();
  96     assertEquals(1, fromRanges.size());
  97     assertEquals(20000, fromRanges.get(0)[0]);
  98     assertEquals(20500, fromRanges.get(0)[1]);
  99     // to range should start from given start numbering
 100     List<int[]> toRanges = ranges.getToRanges();
 101     assertEquals(1, toRanges.size());
 102     assertEquals(23, toRanges.get(0)[0]);
 103     assertEquals(523, toRanges.get(0)[1]);
 104   }
 105
 106   /**
 107    * Test variant using a sub-type of gene from the Sequence Ontology
 108    */
 109   @Test(groups = "Functional")
 110   public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
 111   {
 112     EnsemblGene testee = new EnsemblGene();
 113     SequenceI genomic = new SequenceDummy("chr7");
 114     genomic.setStart(10000);
 115     genomic.setEnd(50000);
 116     String geneId = "ABC123";
 117
 118     // gene at (start+10000) length 501
 119     SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
 120             20500, 0f, null);
 121     sf.setValue("ID", "gene:" + geneId);
 122     sf.setStrand("-");
 123     genomic.addSequenceFeature(sf);
 124
 125     // gene at (start + 10500) length 101
 126     // should be ignored - the first 'gene' found defines the whole range
 127     // (real data would only have one such feature)
 128     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
 129     sf.setValue("ID", "gene:" + geneId);
 130     sf.setStrand("+");
 131     genomic.addSequenceFeature(sf);
 132
 133     MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
 134             23);
 135     List<int[]> fromRanges = ranges.getFromRanges();
 136     assertEquals(1, fromRanges.size());
 137     // from range on reverse strand:
 138     assertEquals(20500, fromRanges.get(0)[0]);
 139     assertEquals(20000, fromRanges.get(0)[1]);
 140     // to range should start from given start numbering
 141     List<int[]> toRanges = ranges.getToRanges();
 142     assertEquals(1, toRanges.size());
 143     assertEquals(23, toRanges.get(0)[0]);
 144     assertEquals(523, toRanges.get(0)[1]);
 145   }
 146
 147   /**
 148    * Test the method that extracts transcript (or subtype) features with a
 149    * specified gene as parent
 150    */
 151   @Test(groups = "Functional")
 152   public void testGetTranscriptFeatures()
 153   {
 154     SequenceI genomic = new SequenceDummy("chr7");
 155     genomic.setStart(10000);
 156     genomic.setEnd(50000);
 157     String geneId = "ABC123";
 158
 159     // transcript feature
 160     SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
 161             20500, 0f, null);
 162     sf1.setValue("Parent", "gene:" + geneId);
 163     sf1.setValue("transcript_id", "transcript1");
 164     genomic.addSequenceFeature(sf1);
 165
 166     // transcript sub-type feature
 167     SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, 20500,
 168             0f, null);
 169     sf2.setValue("Parent", "gene:" + geneId);
 170     sf2.setValue("transcript_id", "transcript2");
 171     genomic.addSequenceFeature(sf2);
 172
 173     // NMD_transcript_variant treated like transcript in Ensembl
 174     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
 175             20000, 20500, 0f, null);
 176     sf3.setValue("Parent", "gene:" + geneId);
 177     sf3.setValue("transcript_id", "transcript3");
 178     genomic.addSequenceFeature(sf3);
 179
 180     // transcript for a different gene - ignored
 181     SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
 182             0f, null);
 183     sf4.setValue("Parent", "gene:XYZ");
 184     sf4.setValue("transcript_id", "transcript4");
 185     genomic.addSequenceFeature(sf4);
 186
 187     EnsemblGene testee = new EnsemblGene();
 188
 189     /*
 190      * with no filter
 191      */
 192     List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
 193             genomic);
 194     assertEquals(3, features.size());
 195     assertSame(sf1, features.get(0));
 196     assertSame(sf2, features.get(1));
 197     assertSame(sf3, features.get(2));
 198   }
 199
 200   /**
 201    * Test the method that retains features except for 'gene', or 'transcript'
 202    * with parent other than the given id
 203    */
 204   @Test(groups = "Functional")
 205   public void testRetainFeature()
 206   {
 207     String geneId = "ABC123";
 208     EnsemblGene testee = new EnsemblGene();
 209     SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
 210             null);
 211     sf.setValue("ID", "gene:" + geneId);
 212     assertFalse(testee.retainFeature(sf, geneId));
 213
 214     sf.setType("transcript");
 215     sf.setValue("Parent", "gene:" + geneId);
 216     assertTrue(testee.retainFeature(sf, geneId));
 217
 218     sf.setType("mature_transcript");
 219     sf.setValue("Parent", "gene:" + geneId);
 220     assertTrue(testee.retainFeature(sf, geneId));
 221
 222     sf.setType("NMD_transcript_variant");
 223     sf.setValue("Parent", "gene:" + geneId);
 224     assertTrue(testee.retainFeature(sf, geneId));
 225
 226     sf.setValue("Parent", "gene:XYZ");
 227     assertFalse(testee.retainFeature(sf, geneId));
 228
 229     sf.setType("anything");
 230     assertTrue(testee.retainFeature(sf, geneId));
 231   }
 232
 233   /**
 234    * Test the method that picks out 'gene' (or subtype) features with the
 235    * accession id as ID
 236    */
 237   @Test(groups = "Functional")
 238   public void testIdentifiesSequence()
 239   {
 240     String accId = "ABC123";
 241     EnsemblGene testee = new EnsemblGene();
 242
 243     // gene with no ID not valid
 244     SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
 245     assertFalse(testee.identifiesSequence(sf, accId));
 246
 247     // gene with wrong ID not valid
 248     sf.setValue("ID", "gene:XYZ");
 249     assertFalse(testee.identifiesSequence(sf, accId));
 250
 251     // gene with right ID is valid
 252     sf.setValue("ID", "gene:" + accId);
 253     assertTrue(testee.identifiesSequence(sf, accId));
 254
 255     // gene sub-type with right ID is valid
 256     sf.setType("snRNA_gene");
 257     assertTrue(testee.identifiesSequence(sf, accId));
 258
 259     // transcript not valid:
 260     sf.setType("transcript");
 261     assertFalse(testee.identifiesSequence(sf, accId));
 262
 263     // exon not valid:
 264     sf.setType("exon");
 265     assertFalse(testee.identifiesSequence(sf, accId));
 266   }
 267
 268   /**
 269    * Check behaviour of feature colour scheme for EnsemblGene sequences.
 270    * Currently coded to display exon and sequence_variant (or sub-types) only,
 271    * with sequence_variant in red above exon coloured by label.
 272    */
 273   @Test(groups = "Functional")
 274   public void testGetFeatureColourScheme()
 275   {
 276     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
 277     assertTrue(fc.isFeatureDisplayed("exon"));
 278     assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
 279     assertTrue(fc.isFeatureDisplayed("sequence_variant"));
 280     assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
 281     assertFalse(fc.isFeatureDisplayed("transcript"));
 282     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
 283             .getColour());
 284     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
 285             .getColour());
 286     assertTrue(fc.getFeatureColour("exon").isColourByLabel());
 287     assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
 288     assertEquals(1, fc.compare("sequence_variant", "exon"));
 289     assertEquals(-1, fc.compare("exon", "sequence_variant"));
 290     assertEquals(1, fc.compare("feature_variant", "coding_exon"));
 291     assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
 292     assertEquals(1f, fc.getTransparency());
 293   }
 294 }