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 import jalview.gui.JvOptionPane;
  38
  39 import java.awt.Color;
  40 import java.io.File;
  41 import java.io.IOException;
  42 import java.util.Map;
  43
  44 import org.testng.annotations.BeforeClass;
  45 import org.testng.annotations.Test;
  46
  47 public class FeaturesFileTest
  48 {
  49
  50   @BeforeClass(alwaysRun = true)
  51   public void setUpJvOptionPane()
  52   {
  53     JvOptionPane.setInteractiveMode(false);
  54     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  55   }
  56
  57   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  58
  59   @Test(groups = { "Functional" })
  60   public void testParse() throws Exception
  61   {
  62     File f = new File("examples/uniref50.fa");
  63     AlignmentI al = readAlignmentFile(f);
  64     AlignFrame af = new AlignFrame(al, 500, 500);
  65     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  66             .getFeatureColours();
  67     FeaturesFile featuresFile = new FeaturesFile(
  68             "examples/exampleFeatures.txt", DataSourceType.FILE);
  69     assertTrue("Test " + "Features file test"
  70             + "\nFailed to parse features file.",
  71             featuresFile.parse(al.getDataset(), colours, true));
  72
  73     /*
  74      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  75      * updated - JAL-1904), and verify (some) feature group colours
  76      */
  77     colours = af.getFeatureRenderer().getFeatureColours();
  78     assertEquals("27 feature group colours not found", 27, colours.size());
  79     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
  80     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
  81     FeatureColourI kdColour = colours.get("kdHydrophobicity");
  82     assertTrue(kdColour.isGraduatedColour());
  83     assertTrue(kdColour.isAboveThreshold());
  84     assertEquals(-2f, kdColour.getThreshold());
  85
  86     /*
  87      * verify (some) features on sequences
  88      */
  89     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
  90             .getSequenceFeatures(); // FER_CAPAA
  91     assertEquals(8, sfs.length);
  92     SequenceFeature sf = sfs[0];
  93     assertEquals("Pfam family%LINK%", sf.description);
  94     assertEquals(0, sf.begin);
  95     assertEquals(0, sf.end);
  96     assertEquals("uniprot", sf.featureGroup);
  97     assertEquals("Pfam", sf.type);
  98     assertEquals(1, sf.links.size());
  99     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 100             sf.links.get(0));
 101
 102     sf = sfs[1];
 103     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 104     assertEquals(39, sf.begin);
 105     assertEquals(39, sf.end);
 106     assertEquals("uniprot", sf.featureGroup);
 107     assertEquals("METAL", sf.type);
 108     sf = sfs[2];
 109     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 110     assertEquals(44, sf.begin);
 111     assertEquals(44, sf.end);
 112     assertEquals("uniprot", sf.featureGroup);
 113     assertEquals("METAL", sf.type);
 114     sf = sfs[3];
 115     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 116     assertEquals(47, sf.begin);
 117     assertEquals(47, sf.end);
 118     assertEquals("uniprot", sf.featureGroup);
 119     assertEquals("METAL", sf.type);
 120     sf = sfs[4];
 121     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 122     assertEquals(77, sf.begin);
 123     assertEquals(77, sf.end);
 124     assertEquals("uniprot", sf.featureGroup);
 125     assertEquals("METAL", sf.type);
 126     sf = sfs[5];
 127     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 128             sf.description);
 129     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 130             sf.links.get(0));
 131     assertEquals(8, sf.begin);
 132     assertEquals(83, sf.end);
 133     assertEquals("uniprot", sf.featureGroup);
 134     assertEquals("Pfam", sf.type);
 135     sf = sfs[6];
 136     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 137     assertEquals(3, sf.begin);
 138     assertEquals(93, sf.end);
 139     assertEquals("uniprot", sf.featureGroup);
 140     assertEquals("Cath", sf.type);
 141     sf = sfs[7];
 142     assertEquals(
 143             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 144             sf.description);
 145     assertEquals(
 146             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 147             sf.links.get(0));
 148     assertEquals(89, sf.begin);
 149     assertEquals(89, sf.end);
 150     assertEquals("netphos", sf.featureGroup);
 151     assertEquals("PHOSPHORYLATION (T)", sf.type);
 152   }
 153
 154   /**
 155    * Test parsing a features file with a mix of Jalview and GFF formatted
 156    * content
 157    *
 158    * @throws Exception
 159    */
 160   @Test(groups = { "Functional" })
 161   public void testParse_mixedJalviewGff() throws Exception
 162   {
 163     File f = new File("examples/uniref50.fa");
 164     AlignmentI al = readAlignmentFile(f);
 165     AlignFrame af = new AlignFrame(al, 500, 500);
 166     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 167             .getFeatureColours();
 168     // GFF2 uses space as name/value separator in column 9
 169     String gffData = "METAL\tcc9900\n"
 170             + "GFF\n"
 171             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 172             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 173     FeaturesFile featuresFile = new FeaturesFile(gffData,
 174             DataSourceType.PASTE);
 175     assertTrue("Failed to parse features file",
 176             featuresFile.parse(al.getDataset(), colours, true));
 177
 178     // verify colours read or synthesized
 179     colours = af.getFeatureRenderer().getFeatureColours();
 180     assertEquals("1 feature group colours not found", 1, colours.size());
 181     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 182
 183     // verify feature on FER_CAPAA
 184     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 185             .getSequenceFeatures();
 186     assertEquals(1, sfs.length);
 187     SequenceFeature sf = sfs[0];
 188     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 189     assertEquals(44, sf.begin);
 190     assertEquals(45, sf.end);
 191     assertEquals("uniprot", sf.featureGroup);
 192     assertEquals("METAL", sf.type);
 193     assertEquals(4f, sf.getScore(), 0.001f);
 194
 195     // verify feature on FER1_SOLLC
 196     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 197     assertEquals(1, sfs.length);
 198     sf = sfs[0];
 199     assertEquals("uniprot", sf.description);
 200     assertEquals(55, sf.begin);
 201     assertEquals(130, sf.end);
 202     assertEquals("uniprot", sf.featureGroup);
 203     assertEquals("Pfam", sf.type);
 204     assertEquals(2f, sf.getScore(), 0.001f);
 205   }
 206
 207   public static AlignmentI readAlignmentFile(File f) throws IOException
 208   {
 209     System.out.println("Reading file: " + f);
 210     String ff = f.getPath();
 211     FormatAdapter rf = new FormatAdapter();
 212
 213     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 214             new IdentifyFile().identify(ff, DataSourceType.FILE));
 215
 216     al.setDataset(null); // creates dataset sequences
 217     assertNotNull("Couldn't read supplied alignment data.", al);
 218     return al;
 219   }
 220
 221   /**
 222    * Test parsing a features file with GFF formatted content only
 223    *
 224    * @throws Exception
 225    */
 226   @Test(groups = { "Functional" })
 227   public void testParse_pureGff3() throws Exception
 228   {
 229     File f = new File("examples/uniref50.fa");
 230     AlignmentI al = readAlignmentFile(f);
 231     AlignFrame af = new AlignFrame(al, 500, 500);
 232     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 233             .getFeatureColours();
 234     // GFF3 uses '=' separator for name/value pairs in colum 9
 235     String gffData = "##gff-version 3\n"
 236             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 237             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 238             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 239     FeaturesFile featuresFile = new FeaturesFile(gffData,
 240             DataSourceType.PASTE);
 241     assertTrue("Failed to parse features file",
 242             featuresFile.parse(al.getDataset(), colours, true));
 243
 244     // verify feature on FER_CAPAA
 245     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 246             .getSequenceFeatures();
 247     assertEquals(1, sfs.length);
 248     SequenceFeature sf = sfs[0];
 249     // description parsed from Note attribute
 250     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 251     assertEquals(39, sf.begin);
 252     assertEquals(39, sf.end);
 253     assertEquals("uniprot", sf.featureGroup);
 254     assertEquals("METAL", sf.type);
 255     assertEquals(
 256             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 257             sf.getValue("ATTRIBUTES"));
 258
 259     // verify feature on FER1_SOLLC1
 260     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 261     assertEquals(1, sfs.length);
 262     sf = sfs[0];
 263     // ID used for description if available
 264     assertEquals("$23", sf.description);
 265     assertEquals(55, sf.begin);
 266     assertEquals(130, sf.end);
 267     assertEquals("uniprot", sf.featureGroup);
 268     assertEquals("Pfam", sf.type);
 269     assertEquals(3f, sf.getScore(), 0.001f);
 270   }
 271
 272   /**
 273    * Test parsing a features file with Jalview format features (but no colour
 274    * descriptors or startgroup to give the hint not to parse as GFF)
 275    *
 276    * @throws Exception
 277    */
 278   @Test(groups = { "Functional" })
 279   public void testParse_jalviewFeaturesOnly() throws Exception
 280   {
 281     File f = new File("examples/uniref50.fa");
 282     AlignmentI al = readAlignmentFile(f);
 283     AlignFrame af = new AlignFrame(al, 500, 500);
 284     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 285             .getFeatureColours();
 286
 287     /*
 288      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 289      */
 290     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 291             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 292     FeaturesFile featuresFile = new FeaturesFile(featureData,
 293             DataSourceType.PASTE);
 294     assertTrue("Failed to parse features file",
 295             featuresFile.parse(al.getDataset(), colours, true));
 296
 297     // verify FER_CAPAA feature
 298     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 299             .getSequenceFeatures();
 300     assertEquals(1, sfs.length);
 301     SequenceFeature sf = sfs[0];
 302     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 303     assertEquals(39, sf.begin);
 304     assertEquals(39, sf.end);
 305     assertEquals("METAL", sf.type);
 306
 307     // verify FER1_SOLLC feature
 308     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 309     assertEquals(1, sfs.length);
 310     sf = sfs[0];
 311     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 312     assertEquals(86, sf.begin);
 313     assertEquals(87, sf.end);
 314     assertEquals("METALLIC", sf.type);
 315   }
 316
 317   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 318   {
 319     assertEquals("no sequences extracted from GFF3 file", 2,
 320             dataset.getHeight());
 321
 322     SequenceI seq1 = dataset.findName("seq1");
 323     SequenceI seq2 = dataset.findName("seq2");
 324     assertNotNull(seq1);
 325     assertNotNull(seq2);
 326     assertFalse(
 327             "Failed to replace dummy seq1 with real sequence",
 328             seq1 instanceof SequenceDummy
 329                     && ((SequenceDummy) seq1).isDummy());
 330     assertFalse(
 331             "Failed to replace dummy seq2 with real sequence",
 332             seq2 instanceof SequenceDummy
 333                     && ((SequenceDummy) seq2).isDummy());
 334     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 335     assertFalse("dummy replacement buggy for seq1",
 336             placeholderseq.equals(seq1.getSequenceAsString()));
 337     assertFalse("dummy replacement buggy for seq2",
 338             placeholderseq.equals(seq2.getSequenceAsString()));
 339     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 340     assertEquals("Wrong number of features", 3,
 341             seq1.getSequenceFeatures().length);
 342     assertNull(seq2.getSequenceFeatures());
 343     assertEquals(
 344             "Wrong number of features",
 345             0,
 346             seq2.getSequenceFeatures() == null ? 0 : seq2
 347                     .getSequenceFeatures().length);
 348     assertTrue(
 349             "Expected at least one CDNA/Protein mapping for seq1",
 350             dataset.getCodonFrame(seq1) != null
 351                     && dataset.getCodonFrame(seq1).size() > 0);
 352
 353   }
 354
 355   @Test(groups = { "Functional" })
 356   public void readGff3File() throws IOException
 357   {
 358     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 359             DataSourceType.FILE);
 360     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 361     gffreader.addProperties(dataset);
 362     checkDatasetfromSimpleGff3(dataset);
 363   }
 364
 365   @Test(groups = { "Functional" })
 366   public void simpleGff3FileClass() throws IOException
 367   {
 368     AlignmentI dataset = new Alignment(new SequenceI[] {});
 369     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 370             DataSourceType.FILE);
 371
 372     boolean parseResult = ffile.parse(dataset, null, false, false);
 373     assertTrue("return result should be true", parseResult);
 374     checkDatasetfromSimpleGff3(dataset);
 375   }
 376
 377   @Test(groups = { "Functional" })
 378   public void simpleGff3FileLoader() throws IOException
 379   {
 380     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 381             simpleGffFile, DataSourceType.FILE);
 382     assertTrue(
 383             "Didn't read the alignment into an alignframe from Gff3 File",
 384             af != null);
 385     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 386   }
 387
 388   @Test(groups = { "Functional" })
 389   public void simpleGff3RelaxedIdMatching() throws IOException
 390   {
 391     AlignmentI dataset = new Alignment(new SequenceI[] {});
 392     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 393             DataSourceType.FILE);
 394
 395     boolean parseResult = ffile.parse(dataset, null, false, true);
 396     assertTrue("return result (relaxedID matching) should be true",
 397             parseResult);
 398     checkDatasetfromSimpleGff3(dataset);
 399   }
 400
 401   @Test(groups = { "Functional" })
 402   public void testPrintJalviewFormat() throws Exception
 403   {
 404     File f = new File("examples/uniref50.fa");
 405     AlignmentI al = readAlignmentFile(f);
 406     AlignFrame af = new AlignFrame(al, 500, 500);
 407     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 408             .getFeatureColours();
 409     String features = "METAL\tcc9900\n"
 410             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 411             + "Pfam\tred\n"
 412             + "STARTGROUP\tuniprot\n"
 413             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 414             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 415             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 416             + "ENDGROUP\tuniprot\n";
 417     FeaturesFile featuresFile = new FeaturesFile(features,
 418             DataSourceType.PASTE);
 419     featuresFile.parse(al.getDataset(), colours, false);
 420
 421     /*
 422      * first with no features displayed
 423      */
 424     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 425     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
 426     String exported = featuresFile.printJalviewFormat(
 427             al.getSequencesArray(), visible);
 428     String expected = "No Features Visible";
 429     assertEquals(expected, exported);
 430
 431     /*
 432      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 433      */
 434     fr.setVisible("METAL");
 435     fr.setVisible("GAMMA-TURN");
 436     visible = fr.getDisplayedFeatureCols();
 437     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 438             visible);
 439     expected = "METAL\tcc9900\n"
 440             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 441             + "\nSTARTGROUP\tuniprot\n"
 442             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 443             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 444             + "ENDGROUP\tuniprot\n";
 445     assertEquals(expected, exported);
 446
 447     /*
 448      * now set Pfam visible
 449      */
 450     fr.setVisible("Pfam");
 451     visible = fr.getDisplayedFeatureCols();
 452     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 453             visible);
 454     /*
 455      * note the order of feature types is uncontrolled - derives from
 456      * FeaturesDisplayed.featuresDisplayed which is a HashSet
 457      */
 458     expected = "METAL\tcc9900\n"
 459             + "Pfam\tff0000\n"
 460             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 461             + "\nSTARTGROUP\tuniprot\n"
 462             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 463             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 464             + "<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"
 465             + "ENDGROUP\tuniprot\n";
 466     assertEquals(expected, exported);
 467   }
 468 }