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.schemes.Colour;
  38
  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 Colour(0x93b1d1));
  71     assertEquals(colours.get("ASX-MOTIF").getColour(), new Colour(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" + "GFF\n"
 157             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 158             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 159     FeaturesFile featuresFile = new FeaturesFile(gffData,
 160             FormatAdapter.PASTE);
 161     assertTrue("Failed to parse features file",
 162             featuresFile.parse(al.getDataset(), colours, true));
 163
 164     // verify colours read or synthesized
 165     colours = af.getFeatureRenderer().getFeatureColours();
 166     assertEquals("1 feature group colours not found", 1, colours.size());
 167     assertEquals(colours.get("METAL").getColour(), new Colour(0xcc9900));
 168
 169     // verify feature on FER_CAPAA
 170     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 171             .getSequenceFeatures();
 172     assertEquals(1, sfs.length);
 173     SequenceFeature sf = sfs[0];
 174     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 175     assertEquals(44, sf.begin);
 176     assertEquals(45, sf.end);
 177     assertEquals("uniprot", sf.featureGroup);
 178     assertEquals("METAL", sf.type);
 179     assertEquals(4f, sf.getScore(), 0.001f);
 180
 181     // verify feature on FER1_SOLLC
 182     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 183     assertEquals(1, sfs.length);
 184     sf = sfs[0];
 185     assertEquals("uniprot", sf.description);
 186     assertEquals(55, sf.begin);
 187     assertEquals(130, sf.end);
 188     assertEquals("uniprot", sf.featureGroup);
 189     assertEquals("Pfam", sf.type);
 190     assertEquals(2f, sf.getScore(), 0.001f);
 191   }
 192
 193   public static AlignmentI readAlignmentFile(File f) throws IOException
 194   {
 195     System.out.println("Reading file: " + f);
 196     String ff = f.getPath();
 197     FormatAdapter rf = new FormatAdapter();
 198
 199     AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
 200             new IdentifyFile().identify(ff, FormatAdapter.FILE));
 201
 202     al.setDataset(null); // creates dataset sequences
 203     assertNotNull("Couldn't read supplied alignment data.", al);
 204     return al;
 205   }
 206
 207   /**
 208    * Test various ways of describing a feature colour scheme
 209    *
 210    * @throws Exception
 211    */
 212   @Test(groups = { "Functional" })
 213   public void testParseGraduatedColourScheme() throws Exception
 214   {
 215     FeaturesFile ff = new FeaturesFile();
 216
 217     // colour by label:
 218     FeatureColourI gc = ff.parseGraduatedColourScheme(
 219             "BETA-TURN-IR\t9a6a94", "label");
 220     assertTrue(gc.isColourByLabel());
 221     assertEquals(Colour.white, gc.getMinColour());
 222     assertEquals(Colour.black, gc.getMaxColour());
 223     assertTrue(gc.isAutoScaled());
 224
 225     // using colour name, rgb, etc:
 226     String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
 227     gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
 228     assertFalse(gc.isColourByLabel());
 229     assertEquals(Colour.blue, gc.getMinColour());
 230     assertEquals(new Colour(255, 0, 255), gc.getMaxColour());
 231     assertFalse(gc.isAutoScaled());
 232     // assertFalse(gc.getTolow());
 233     assertEquals(20.0f, gc.getMin(), 0.001f);
 234     assertEquals(95.0f, gc.getMax(), 0.001f);
 235     assertTrue(gc.isBelowThreshold());
 236     assertEquals(66.0f, gc.getThreshold(), 0.001f);
 237
 238     // inverse gradient high to low:
 239     spec = "blue|255,0,255|95.0|20.0|below|66.0";
 240     gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
 241     assertTrue(gc.isAutoScaled());
 242     // assertTrue(gc..getTolow());
 243   }
 244
 245   /**
 246    * Test parsing a features file with GFF formatted content only
 247    *
 248    * @throws Exception
 249    */
 250   @Test(groups = { "Functional" })
 251   public void testParse_pureGff3() throws Exception
 252   {
 253     File f = new File("examples/uniref50.fa");
 254     AlignmentI al = readAlignmentFile(f);
 255     AlignFrame af = new AlignFrame(al, 500, 500);
 256     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 257             .getFeatureColours();
 258     // GFF3 uses '=' separator for name/value pairs in colum 9
 259     String gffData = "##gff-version 3\n"
 260             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 261             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 262             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 263     FeaturesFile featuresFile = new FeaturesFile(gffData,
 264             FormatAdapter.PASTE);
 265     assertTrue("Failed to parse features file",
 266             featuresFile.parse(al.getDataset(), colours, true));
 267
 268     // verify feature on FER_CAPAA
 269     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 270             .getSequenceFeatures();
 271     assertEquals(1, sfs.length);
 272     SequenceFeature sf = sfs[0];
 273     // description parsed from Note attribute
 274     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 275     assertEquals(39, sf.begin);
 276     assertEquals(39, sf.end);
 277     assertEquals("uniprot", sf.featureGroup);
 278     assertEquals("METAL", sf.type);
 279     assertEquals(
 280             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 281             sf.getValue("ATTRIBUTES"));
 282
 283     // verify feature on FER1_SOLLC1
 284     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 285     assertEquals(1, sfs.length);
 286     sf = sfs[0];
 287     // ID used for description if available
 288     assertEquals("$23", sf.description);
 289     assertEquals(55, sf.begin);
 290     assertEquals(130, sf.end);
 291     assertEquals("uniprot", sf.featureGroup);
 292     assertEquals("Pfam", sf.type);
 293     assertEquals(3f, sf.getScore(), 0.001f);
 294   }
 295
 296   /**
 297    * Test parsing a features file with Jalview format features (but no colour
 298    * descriptors or startgroup to give the hint not to parse as GFF)
 299    *
 300    * @throws Exception
 301    */
 302   @Test(groups = { "Functional" })
 303   public void testParse_jalviewFeaturesOnly() throws Exception
 304   {
 305     File f = new File("examples/uniref50.fa");
 306     AlignmentI al = readAlignmentFile(f);
 307     AlignFrame af = new AlignFrame(al, 500, 500);
 308     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 309             .getFeatureColours();
 310
 311     /*
 312      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 313      */
 314     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 315             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 316     FeaturesFile featuresFile = new FeaturesFile(featureData,
 317             FormatAdapter.PASTE);
 318     assertTrue("Failed to parse features file",
 319             featuresFile.parse(al.getDataset(), colours, true));
 320
 321     // verify FER_CAPAA feature
 322     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 323             .getSequenceFeatures();
 324     assertEquals(1, sfs.length);
 325     SequenceFeature sf = sfs[0];
 326     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 327     assertEquals(39, sf.begin);
 328     assertEquals(39, sf.end);
 329     assertEquals("METAL", sf.type);
 330
 331     // verify FER1_SOLLC feature
 332     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 333     assertEquals(1, sfs.length);
 334     sf = sfs[0];
 335     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 336     assertEquals(86, sf.begin);
 337     assertEquals(87, sf.end);
 338     assertEquals("METALLIC", sf.type);
 339   }
 340
 341   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 342   {
 343     assertEquals("no sequences extracted from GFF3 file", 2,
 344             dataset.getHeight());
 345
 346     SequenceI seq1 = dataset.findName("seq1");
 347     SequenceI seq2 = dataset.findName("seq2");
 348     assertNotNull(seq1);
 349     assertNotNull(seq2);
 350     assertFalse(
 351             "Failed to replace dummy seq1 with real sequence",
 352             seq1 instanceof SequenceDummy
 353                     && ((SequenceDummy) seq1).isDummy());
 354     assertFalse(
 355             "Failed to replace dummy seq2 with real sequence",
 356             seq2 instanceof SequenceDummy
 357                     && ((SequenceDummy) seq2).isDummy());
 358     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 359     assertFalse("dummy replacement buggy for seq1",
 360             placeholderseq.equals(seq1.getSequenceAsString()));
 361     assertFalse("dummy replacement buggy for seq2",
 362             placeholderseq.equals(seq2.getSequenceAsString()));
 363     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 364     assertEquals("Wrong number of features", 3,
 365             seq1.getSequenceFeatures().length);
 366     assertNull(seq2.getSequenceFeatures());
 367     assertEquals(
 368             "Wrong number of features",
 369             0,
 370             seq2.getSequenceFeatures() == null ? 0 : seq2
 371                     .getSequenceFeatures().length);
 372     assertTrue(
 373             "Expected at least one CDNA/Protein mapping for seq1",
 374             dataset.getCodonFrame(seq1) != null
 375                     && dataset.getCodonFrame(seq1).size() > 0);
 376
 377   }
 378
 379   @Test(groups = { "Functional" })
 380   public void readGff3File() throws IOException
 381   {
 382     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 383             FormatAdapter.FILE);
 384     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 385     gffreader.addProperties(dataset);
 386     checkDatasetfromSimpleGff3(dataset);
 387   }
 388
 389   @Test(groups = { "Functional" })
 390   public void simpleGff3FileClass() throws IOException
 391   {
 392     AlignmentI dataset = new Alignment(new SequenceI[] {});
 393     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 394             FormatAdapter.FILE);
 395
 396     boolean parseResult = ffile.parse(dataset, null, false, false);
 397     assertTrue("return result should be true", parseResult);
 398     checkDatasetfromSimpleGff3(dataset);
 399   }
 400
 401   @Test(groups = { "Functional" })
 402   public void simpleGff3FileLoader() throws IOException
 403   {
 404     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 405             simpleGffFile, FormatAdapter.FILE);
 406     assertTrue(
 407             "Didn't read the alignment into an alignframe from Gff3 File",
 408             af != null);
 409     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 410   }
 411
 412   @Test(groups = { "Functional" })
 413   public void simpleGff3RelaxedIdMatching() throws IOException
 414   {
 415     AlignmentI dataset = new Alignment(new SequenceI[] {});
 416     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 417             FormatAdapter.FILE);
 418
 419     boolean parseResult = ffile.parse(dataset, null, false, true);
 420     assertTrue("return result (relaxedID matching) should be true",
 421             parseResult);
 422     checkDatasetfromSimpleGff3(dataset);
 423   }
 424
 425   @Test(groups = { "Functional" })
 426   public void testPrintJalviewFormat() throws Exception
 427   {
 428     File f = new File("examples/uniref50.fa");
 429     AlignmentI al = readAlignmentFile(f);
 430     AlignFrame af = new AlignFrame(al, 500, 500);
 431     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 432             .getFeatureColours();
 433     String features = "METAL\tcc9900\n"
 434             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 435             + "Pfam\tred\n"
 436             + "STARTGROUP\tuniprot\n"
 437             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 438             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 439             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 440             + "ENDGROUP\tuniprot\n";
 441     FeaturesFile featuresFile = new FeaturesFile(features,
 442             FormatAdapter.PASTE);
 443     featuresFile.parse(al.getDataset(), colours, false);
 444
 445     /*
 446      * first with no features displayed
 447      */
 448     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 449     Map<String, FeatureColourI> visible = fr
 450             .getDisplayedFeatureCols();
 451     String exported = featuresFile.printJalviewFormat(
 452             al.getSequencesArray(), visible);
 453     String expected = "No Features Visible";
 454     assertEquals(expected, exported);
 455
 456     /*
 457      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 458      */
 459     fr.setVisible("METAL");
 460     fr.setVisible("GAMMA-TURN");
 461     visible = fr.getDisplayedFeatureCols();
 462     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 463             visible);
 464     expected = "METAL\tcc9900\n"
 465             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 466             + "\nSTARTGROUP\tuniprot\n"
 467             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 468             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 469             + "ENDGROUP\tuniprot\n";
 470     assertEquals(expected, exported);
 471
 472     /*
 473      * now set Pfam visible
 474      */
 475     fr.setVisible("Pfam");
 476     visible = fr.getDisplayedFeatureCols();
 477     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 478             visible);
 479     /*
 480      * note the order of feature types is uncontrolled - derives from
 481      * FeaturesDisplayed.featuresDisplayed which is a HashSet
 482      */
 483     expected = "METAL\tcc9900\n"
 484             + "Pfam\tff0000\n"
 485             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 486             + "\nSTARTGROUP\tuniprot\n"
 487             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 488             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 489             + "<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"
 490             + "ENDGROUP\tuniprot\n";
 491     assertEquals(expected, exported);
 492   }
 493 }