test/jalview/io/FeaturesFileTest.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.api.FeatureColourI;
  30 import jalview.api.FeatureRenderer;
  31 import jalview.datamodel.Alignment;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.SequenceDummy;
  34 import jalview.datamodel.SequenceFeature;
  35 import jalview.datamodel.SequenceI;
  36 import jalview.gui.AlignFrame;
  37
  38 import java.awt.Color;
  39 import java.io.File;
  40 import java.io.IOException;
  41 import java.util.Map;
  42
  43 import org.testng.annotations.Test;
  44
  45 public class FeaturesFileTest
  46 {
  47
  48   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  49
  50   @Test(groups = { "Functional" })
  51   public void testParse() throws Exception
  52   {
  53     File f = new File("examples/uniref50.fa");
  54     AlignmentI al = readAlignmentFile(f);
  55     AlignFrame af = new AlignFrame(al, 500, 500);
  56     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  57             .getFeatureColours();
  58     FeaturesFile featuresFile = new FeaturesFile(
  59             "examples/exampleFeatures.txt", FormatAdapter.FILE);
  60     assertTrue("Test " + "Features file test"
  61             + "\nFailed to parse features file.",
  62             featuresFile.parse(al.getDataset(), colours, true));
  63
  64     /*
  65      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  66      * updated - JAL-1904), and verify (some) feature group colours
  67      */
  68     colours = af.getFeatureRenderer().getFeatureColours();
  69     assertEquals("26 feature group colours not found", 26, colours.size());
  70     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
  71     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
  72
  73     /*
  74      * verify (some) features on sequences
  75      */
  76     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
  77             .getSequenceFeatures(); // FER_CAPAA
  78     assertEquals(8, sfs.length);
  79     SequenceFeature sf = sfs[0];
  80     assertEquals("Pfam family%LINK%", sf.description);
  81     assertEquals(0, sf.begin);
  82     assertEquals(0, sf.end);
  83     assertEquals("uniprot", sf.featureGroup);
  84     assertEquals("Pfam", sf.type);
  85     assertEquals(1, sf.links.size());
  86     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
  87             sf.links.get(0));
  88
  89     sf = sfs[1];
  90     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
  91     assertEquals(39, sf.begin);
  92     assertEquals(39, sf.end);
  93     assertEquals("uniprot", sf.featureGroup);
  94     assertEquals("METAL", sf.type);
  95     sf = sfs[2];
  96     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
  97     assertEquals(44, sf.begin);
  98     assertEquals(44, sf.end);
  99     assertEquals("uniprot", sf.featureGroup);
 100     assertEquals("METAL", sf.type);
 101     sf = sfs[3];
 102     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 103     assertEquals(47, sf.begin);
 104     assertEquals(47, sf.end);
 105     assertEquals("uniprot", sf.featureGroup);
 106     assertEquals("METAL", sf.type);
 107     sf = sfs[4];
 108     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 109     assertEquals(77, sf.begin);
 110     assertEquals(77, sf.end);
 111     assertEquals("uniprot", sf.featureGroup);
 112     assertEquals("METAL", sf.type);
 113     sf = sfs[5];
 114     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 115             sf.description);
 116     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 117             sf.links.get(0));
 118     assertEquals(8, sf.begin);
 119     assertEquals(83, sf.end);
 120     assertEquals("uniprot", sf.featureGroup);
 121     assertEquals("Pfam", sf.type);
 122     sf = sfs[6];
 123     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 124     assertEquals(3, sf.begin);
 125     assertEquals(93, sf.end);
 126     assertEquals("uniprot", sf.featureGroup);
 127     assertEquals("Cath", sf.type);
 128     sf = sfs[7];
 129     assertEquals(
 130             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 131             sf.description);
 132     assertEquals(
 133             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 134             sf.links.get(0));
 135     assertEquals(89, sf.begin);
 136     assertEquals(89, sf.end);
 137     assertEquals("netphos", sf.featureGroup);
 138     assertEquals("PHOSPHORYLATION (T)", sf.type);
 139   }
 140
 141   /**
 142    * Test parsing a features file with a mix of Jalview and GFF formatted
 143    * content
 144    *
 145    * @throws Exception
 146    */
 147   @Test(groups = { "Functional" })
 148   public void testParse_mixedJalviewGff() throws Exception
 149   {
 150     File f = new File("examples/uniref50.fa");
 151     AlignmentI al = readAlignmentFile(f);
 152     AlignFrame af = new AlignFrame(al, 500, 500);
 153     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 154             .getFeatureColours();
 155     // GFF2 uses space as name/value separator in column 9
 156     String gffData = "METAL\tcc9900\n"
 157             + "GFF\n"
 158             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 159             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 160     FeaturesFile featuresFile = new FeaturesFile(gffData,
 161             FormatAdapter.PASTE);
 162     assertTrue("Failed to parse features file",
 163             featuresFile.parse(al.getDataset(), colours, true));
 164
 165     // verify colours read or synthesized
 166     colours = af.getFeatureRenderer().getFeatureColours();
 167     assertEquals("1 feature group colours not found", 1, colours.size());
 168     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 169
 170     // verify feature on FER_CAPAA
 171     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 172             .getSequenceFeatures();
 173     assertEquals(1, sfs.length);
 174     SequenceFeature sf = sfs[0];
 175     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 176     assertEquals(44, sf.begin);
 177     assertEquals(45, sf.end);
 178     assertEquals("uniprot", sf.featureGroup);
 179     assertEquals("METAL", sf.type);
 180     assertEquals(4f, sf.getScore(), 0.001f);
 181
 182     // verify feature on FER1_SOLLC
 183     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 184     assertEquals(1, sfs.length);
 185     sf = sfs[0];
 186     assertEquals("uniprot", sf.description);
 187     assertEquals(55, sf.begin);
 188     assertEquals(130, sf.end);
 189     assertEquals("uniprot", sf.featureGroup);
 190     assertEquals("Pfam", sf.type);
 191     assertEquals(2f, sf.getScore(), 0.001f);
 192   }
 193
 194   public static AlignmentI readAlignmentFile(File f) throws IOException
 195   {
 196     System.out.println("Reading file: " + f);
 197     String ff = f.getPath();
 198     FormatAdapter rf = new FormatAdapter();
 199
 200     AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
 201             new IdentifyFile().identify(ff, FormatAdapter.FILE));
 202
 203     al.setDataset(null); // creates dataset sequences
 204     assertNotNull("Couldn't read supplied alignment data.", al);
 205     return al;
 206   }
 207
 208   /**
 209    * Test parsing a features file with GFF formatted content only
 210    *
 211    * @throws Exception
 212    */
 213   @Test(groups = { "Functional" })
 214   public void testParse_pureGff3() throws Exception
 215   {
 216     File f = new File("examples/uniref50.fa");
 217     AlignmentI al = readAlignmentFile(f);
 218     AlignFrame af = new AlignFrame(al, 500, 500);
 219     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 220             .getFeatureColours();
 221     // GFF3 uses '=' separator for name/value pairs in colum 9
 222     String gffData = "##gff-version 3\n"
 223             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 224             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 225             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 226     FeaturesFile featuresFile = new FeaturesFile(gffData,
 227             FormatAdapter.PASTE);
 228     assertTrue("Failed to parse features file",
 229             featuresFile.parse(al.getDataset(), colours, true));
 230
 231     // verify feature on FER_CAPAA
 232     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 233             .getSequenceFeatures();
 234     assertEquals(1, sfs.length);
 235     SequenceFeature sf = sfs[0];
 236     // description parsed from Note attribute
 237     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 238     assertEquals(39, sf.begin);
 239     assertEquals(39, sf.end);
 240     assertEquals("uniprot", sf.featureGroup);
 241     assertEquals("METAL", sf.type);
 242     assertEquals(
 243             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 244             sf.getValue("ATTRIBUTES"));
 245
 246     // verify feature on FER1_SOLLC1
 247     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 248     assertEquals(1, sfs.length);
 249     sf = sfs[0];
 250     // ID used for description if available
 251     assertEquals("$23", sf.description);
 252     assertEquals(55, sf.begin);
 253     assertEquals(130, sf.end);
 254     assertEquals("uniprot", sf.featureGroup);
 255     assertEquals("Pfam", sf.type);
 256     assertEquals(3f, sf.getScore(), 0.001f);
 257   }
 258
 259   /**
 260    * Test parsing a features file with Jalview format features (but no colour
 261    * descriptors or startgroup to give the hint not to parse as GFF)
 262    *
 263    * @throws Exception
 264    */
 265   @Test(groups = { "Functional" })
 266   public void testParse_jalviewFeaturesOnly() throws Exception
 267   {
 268     File f = new File("examples/uniref50.fa");
 269     AlignmentI al = readAlignmentFile(f);
 270     AlignFrame af = new AlignFrame(al, 500, 500);
 271     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 272             .getFeatureColours();
 273
 274     /*
 275      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 276      */
 277     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 278             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 279     FeaturesFile featuresFile = new FeaturesFile(featureData,
 280             FormatAdapter.PASTE);
 281     assertTrue("Failed to parse features file",
 282             featuresFile.parse(al.getDataset(), colours, true));
 283
 284     // verify FER_CAPAA feature
 285     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 286             .getSequenceFeatures();
 287     assertEquals(1, sfs.length);
 288     SequenceFeature sf = sfs[0];
 289     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 290     assertEquals(39, sf.begin);
 291     assertEquals(39, sf.end);
 292     assertEquals("METAL", sf.type);
 293
 294     // verify FER1_SOLLC feature
 295     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 296     assertEquals(1, sfs.length);
 297     sf = sfs[0];
 298     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 299     assertEquals(86, sf.begin);
 300     assertEquals(87, sf.end);
 301     assertEquals("METALLIC", sf.type);
 302   }
 303
 304   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 305   {
 306     assertEquals("no sequences extracted from GFF3 file", 2,
 307             dataset.getHeight());
 308
 309     SequenceI seq1 = dataset.findName("seq1");
 310     SequenceI seq2 = dataset.findName("seq2");
 311     assertNotNull(seq1);
 312     assertNotNull(seq2);
 313     assertFalse(
 314             "Failed to replace dummy seq1 with real sequence",
 315             seq1 instanceof SequenceDummy
 316                     && ((SequenceDummy) seq1).isDummy());
 317     assertFalse(
 318             "Failed to replace dummy seq2 with real sequence",
 319             seq2 instanceof SequenceDummy
 320                     && ((SequenceDummy) seq2).isDummy());
 321     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 322     assertFalse("dummy replacement buggy for seq1",
 323             placeholderseq.equals(seq1.getSequenceAsString()));
 324     assertFalse("dummy replacement buggy for seq2",
 325             placeholderseq.equals(seq2.getSequenceAsString()));
 326     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 327     assertEquals("Wrong number of features", 3,
 328             seq1.getSequenceFeatures().length);
 329     assertNull(seq2.getSequenceFeatures());
 330     assertEquals(
 331             "Wrong number of features",
 332             0,
 333             seq2.getSequenceFeatures() == null ? 0 : seq2
 334                     .getSequenceFeatures().length);
 335     assertTrue(
 336             "Expected at least one CDNA/Protein mapping for seq1",
 337             dataset.getCodonFrame(seq1) != null
 338                     && dataset.getCodonFrame(seq1).size() > 0);
 339
 340   }
 341
 342   @Test(groups = { "Functional" })
 343   public void readGff3File() throws IOException
 344   {
 345     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 346             FormatAdapter.FILE);
 347     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 348     gffreader.addProperties(dataset);
 349     checkDatasetfromSimpleGff3(dataset);
 350   }
 351
 352   @Test(groups = { "Functional" })
 353   public void simpleGff3FileClass() throws IOException
 354   {
 355     AlignmentI dataset = new Alignment(new SequenceI[] {});
 356     FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
 357
 358     boolean parseResult = ffile.parse(dataset, null, false, false);
 359     assertTrue("return result should be true", parseResult);
 360     checkDatasetfromSimpleGff3(dataset);
 361   }
 362
 363   @Test(groups = { "Functional" })
 364   public void simpleGff3FileLoader() throws IOException
 365   {
 366     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 367             simpleGffFile, FormatAdapter.FILE);
 368     assertTrue(
 369             "Didn't read the alignment into an alignframe from Gff3 File",
 370             af != null);
 371     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 372   }
 373
 374   @Test(groups = { "Functional" })
 375   public void simpleGff3RelaxedIdMatching() throws IOException
 376   {
 377     AlignmentI dataset = new Alignment(new SequenceI[] {});
 378     FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
 379
 380     boolean parseResult = ffile.parse(dataset, null, false, true);
 381     assertTrue("return result (relaxedID matching) should be true",
 382             parseResult);
 383     checkDatasetfromSimpleGff3(dataset);
 384   }
 385
 386   @Test(groups = { "Functional" })
 387   public void testPrintJalviewFormat() throws Exception
 388   {
 389     File f = new File("examples/uniref50.fa");
 390     AlignmentI al = readAlignmentFile(f);
 391     AlignFrame af = new AlignFrame(al, 500, 500);
 392     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 393             .getFeatureColours();
 394     String features = "METAL\tcc9900\n"
 395             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 396             + "Pfam\tred\n"
 397             + "STARTGROUP\tuniprot\n"
 398             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 399             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 400             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 401             + "ENDGROUP\tuniprot\n";
 402     FeaturesFile featuresFile = new FeaturesFile(features,
 403             FormatAdapter.PASTE);
 404     featuresFile.parse(al.getDataset(), colours, false);
 405
 406     /*
 407      * first with no features displayed
 408      */
 409     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 410     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
 411     String exported = featuresFile.printJalviewFormat(
 412             al.getSequencesArray(), visible);
 413     String expected = "No Features Visible";
 414     assertEquals(expected, exported);
 415
 416     /*
 417      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 418      */
 419     fr.setVisible("METAL");
 420     fr.setVisible("GAMMA-TURN");
 421     visible = fr.getDisplayedFeatureCols();
 422     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 423             visible);
 424     expected = "METAL\tcc9900\n"
 425             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 426             + "\nSTARTGROUP\tuniprot\n"
 427             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 428             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 429             + "ENDGROUP\tuniprot\n";
 430     assertEquals(expected, exported);
 431
 432     /*
 433      * now set Pfam visible
 434      */
 435     fr.setVisible("Pfam");
 436     visible = fr.getDisplayedFeatureCols();
 437     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 438             visible);
 439     /*
 440      * note the order of feature types is uncontrolled - derives from
 441      * FeaturesDisplayed.featuresDisplayed which is a HashSet
 442      */
 443     expected = "METAL\tcc9900\n"
 444             + "Pfam\tff0000\n"
 445             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 446             + "\nSTARTGROUP\tuniprot\n"
 447             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 448             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 449             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
 450             + "ENDGROUP\tuniprot\n";
 451     assertEquals(expected, exported);
 452   }
 453 }