test/jalview/io/Gff3tests.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.io;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertNotNull;
  26 import static org.testng.AssertJUnit.assertNull;
  27 import static org.testng.AssertJUnit.assertTrue;
  28
  29 import jalview.datamodel.Alignment;
  30 import jalview.datamodel.AlignmentI;
  31 import jalview.datamodel.SequenceDummy;
  32 import jalview.datamodel.SequenceI;
  33 import jalview.gui.AlignFrame;
  34
  35 import java.io.IOException;
  36
  37 import org.testng.annotations.Test;
  38
  39 public class Gff3tests
  40 {
  41
  42   private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
  43           exonerateOutput = "examples/testdata/exonerateoutput.gff",
  44           simpleGff3file = "examples/testdata/simpleGff3.gff";
  45
  46   @Test(groups = { "Functional" })
  47   public void testExonerateImport()
  48   {
  49     // exonerate does not tag sequences after features, so we have a more
  50     // conventional annotation import test here
  51
  52     FileLoader loader = new FileLoader(false);
  53
  54     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
  55             FormatAdapter.FILE);
  56
  57     assertEquals("Unexpected number of DNA protein associations", 0, af
  58             .getViewport().getAlignment().getCodonFrames().size());
  59
  60     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
  61
  62     assertTrue("Expected at least one DNA protein association", af
  63             .getViewport().getAlignment().getDataset().getCodonFrames()
  64             .size() > 0);
  65
  66   }
  67
  68   @Test(groups = { "Functional" })
  69   public void simpleGff3FileIdentify()
  70   {
  71     assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
  72             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
  73   }
  74
  75   @Test(groups = { "Functional" })
  76   public void simpleGff3FileClass() throws IOException
  77   {
  78     AlignmentI dataset = new Alignment(new SequenceI[] {});
  79     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  80             FormatAdapter.FILE);
  81
  82     boolean parseResult = ffile.parse(dataset, null, null, false, false);
  83     assertTrue("return result should be true", parseResult);
  84     checkDatasetfromSimpleGff3(dataset);
  85   }
  86
  87   @Test(groups = { "Functional" })
  88   public void simpleGff3FileLoader() throws IOException
  89   {
  90     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
  91             simpleGff3file, FormatAdapter.FILE);
  92     assertTrue(
  93             "Didn't read the alignment into an alignframe from Gff3 File",
  94             af != null);
  95     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
  96   }
  97
  98   @Test(groups = { "Functional" })
  99   public void simpleGff3RelaxedIdMatching() throws IOException
 100   {
 101     AlignmentI dataset = new Alignment(new SequenceI[] {});
 102     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
 103             FormatAdapter.FILE);
 104
 105     boolean parseResult = ffile.parse(dataset, null, null, false, true);
 106     assertTrue("return result (relaxedID matching) should be true",
 107             parseResult);
 108     checkDatasetfromSimpleGff3(dataset);
 109   }
 110
 111   @Test(groups = { "Functional" })
 112   public void readGff3File() throws IOException
 113   {
 114     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
 115     Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
 116     gff3reader.addProperties(dataset);
 117     checkDatasetfromSimpleGff3(dataset);
 118
 119   }
 120
 121   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 122   {
 123     assertEquals("no sequences extracted from GFF3 file", 2,
 124             dataset.getHeight());
 125
 126     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
 127             .findName("seq2");
 128     assertNotNull(seq1);
 129     assertNotNull(seq2);
 130     assertFalse(
 131             "Failed to replace dummy seq1 with real sequence",
 132             seq1 instanceof SequenceDummy
 133                     && ((SequenceDummy) seq1).isDummy());
 134     assertFalse(
 135             "Failed to replace dummy seq2 with real sequence",
 136             seq2 instanceof SequenceDummy
 137                     && ((SequenceDummy) seq2).isDummy());
 138     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 139     assertFalse("dummy replacement buggy for seq1",
 140             placeholderseq.equals(seq1.getSequenceAsString()));
 141     assertFalse("dummy replacement buggy for seq2",
 142             placeholderseq.equals(seq2.getSequenceAsString()));
 143     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
 144                                                                            // null);
 145     assertEquals("Wrong number of features", 3,
 146             seq1.getSequenceFeatures().length);
 147     assertNull(seq2.getSequenceFeatures());
 148     assertEquals(
 149             "Wrong number of features",
 150             0,
 151             seq2.getSequenceFeatures() == null ? 0 : seq2
 152                     .getSequenceFeatures().length);
 153     assertTrue(
 154             "Expected at least one CDNA/Protein mapping for seq1",
 155             dataset.getCodonFrame(seq1) != null
 156                     && dataset.getCodonFrame(seq1).size() > 0);
 157
 158   }
 159   // @Test(groups ={ "Functional" })
 160   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 161   // {
 162   // fail("Not yet implemented");
 163   // }
 164   //
 165   // @Test(groups ={ "Functional" })
 166   // public final void testAlignFileBooleanStringString()
 167   // {
 168   // fail("Not yet implemented");
 169   // }
 170
 171 }