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("26 feature group colours not found", 26, colours.size());
  79     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
  80     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
  81
  82     /*
  83      * verify (some) features on sequences
  84      */
  85     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
  86             .getSequenceFeatures(); // FER_CAPAA
  87     assertEquals(8, sfs.length);
  88     SequenceFeature sf = sfs[0];
  89     assertEquals("Pfam family%LINK%", sf.description);
  90     assertEquals(0, sf.begin);
  91     assertEquals(0, sf.end);
  92     assertEquals("uniprot", sf.featureGroup);
  93     assertEquals("Pfam", sf.type);
  94     assertEquals(1, sf.links.size());
  95     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
  96             sf.links.get(0));
  97
  98     sf = sfs[1];
  99     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 100     assertEquals(39, sf.begin);
 101     assertEquals(39, sf.end);
 102     assertEquals("uniprot", sf.featureGroup);
 103     assertEquals("METAL", sf.type);
 104     sf = sfs[2];
 105     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 106     assertEquals(44, sf.begin);
 107     assertEquals(44, sf.end);
 108     assertEquals("uniprot", sf.featureGroup);
 109     assertEquals("METAL", sf.type);
 110     sf = sfs[3];
 111     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 112     assertEquals(47, sf.begin);
 113     assertEquals(47, sf.end);
 114     assertEquals("uniprot", sf.featureGroup);
 115     assertEquals("METAL", sf.type);
 116     sf = sfs[4];
 117     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 118     assertEquals(77, sf.begin);
 119     assertEquals(77, sf.end);
 120     assertEquals("uniprot", sf.featureGroup);
 121     assertEquals("METAL", sf.type);
 122     sf = sfs[5];
 123     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 124             sf.description);
 125     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 126             sf.links.get(0));
 127     assertEquals(8, sf.begin);
 128     assertEquals(83, sf.end);
 129     assertEquals("uniprot", sf.featureGroup);
 130     assertEquals("Pfam", sf.type);
 131     sf = sfs[6];
 132     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 133     assertEquals(3, sf.begin);
 134     assertEquals(93, sf.end);
 135     assertEquals("uniprot", sf.featureGroup);
 136     assertEquals("Cath", sf.type);
 137     sf = sfs[7];
 138     assertEquals(
 139             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 140             sf.description);
 141     assertEquals(
 142             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 143             sf.links.get(0));
 144     assertEquals(89, sf.begin);
 145     assertEquals(89, sf.end);
 146     assertEquals("netphos", sf.featureGroup);
 147     assertEquals("PHOSPHORYLATION (T)", sf.type);
 148   }
 149
 150   /**
 151    * Test parsing a features file with a mix of Jalview and GFF formatted
 152    * content
 153    *
 154    * @throws Exception
 155    */
 156   @Test(groups = { "Functional" })
 157   public void testParse_mixedJalviewGff() throws Exception
 158   {
 159     File f = new File("examples/uniref50.fa");
 160     AlignmentI al = readAlignmentFile(f);
 161     AlignFrame af = new AlignFrame(al, 500, 500);
 162     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 163             .getFeatureColours();
 164     // GFF2 uses space as name/value separator in column 9
 165     String gffData = "METAL\tcc9900\n"
 166             + "GFF\n"
 167             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 168             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 169     FeaturesFile featuresFile = new FeaturesFile(gffData,
 170             DataSourceType.PASTE);
 171     assertTrue("Failed to parse features file",
 172             featuresFile.parse(al.getDataset(), colours, true));
 173
 174     // verify colours read or synthesized
 175     colours = af.getFeatureRenderer().getFeatureColours();
 176     assertEquals("1 feature group colours not found", 1, colours.size());
 177     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 178
 179     // verify feature on FER_CAPAA
 180     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 181             .getSequenceFeatures();
 182     assertEquals(1, sfs.length);
 183     SequenceFeature sf = sfs[0];
 184     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 185     assertEquals(44, sf.begin);
 186     assertEquals(45, sf.end);
 187     assertEquals("uniprot", sf.featureGroup);
 188     assertEquals("METAL", sf.type);
 189     assertEquals(4f, sf.getScore(), 0.001f);
 190
 191     // verify feature on FER1_SOLLC
 192     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 193     assertEquals(1, sfs.length);
 194     sf = sfs[0];
 195     assertEquals("uniprot", sf.description);
 196     assertEquals(55, sf.begin);
 197     assertEquals(130, sf.end);
 198     assertEquals("uniprot", sf.featureGroup);
 199     assertEquals("Pfam", sf.type);
 200     assertEquals(2f, sf.getScore(), 0.001f);
 201   }
 202
 203   public static AlignmentI readAlignmentFile(File f) throws IOException
 204   {
 205     System.out.println("Reading file: " + f);
 206     String ff = f.getPath();
 207     FormatAdapter rf = new FormatAdapter();
 208
 209     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 210             new IdentifyFile().identify(ff, DataSourceType.FILE));
 211
 212     al.setDataset(null); // creates dataset sequences
 213     assertNotNull("Couldn't read supplied alignment data.", al);
 214     return al;
 215   }
 216
 217   /**
 218    * Test parsing a features file with GFF formatted content only
 219    *
 220    * @throws Exception
 221    */
 222   @Test(groups = { "Functional" })
 223   public void testParse_pureGff3() throws Exception
 224   {
 225     File f = new File("examples/uniref50.fa");
 226     AlignmentI al = readAlignmentFile(f);
 227     AlignFrame af = new AlignFrame(al, 500, 500);
 228     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 229             .getFeatureColours();
 230     // GFF3 uses '=' separator for name/value pairs in colum 9
 231     String gffData = "##gff-version 3\n"
 232             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 233             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 234             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 235     FeaturesFile featuresFile = new FeaturesFile(gffData,
 236             DataSourceType.PASTE);
 237     assertTrue("Failed to parse features file",
 238             featuresFile.parse(al.getDataset(), colours, true));
 239
 240     // verify feature on FER_CAPAA
 241     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 242             .getSequenceFeatures();
 243     assertEquals(1, sfs.length);
 244     SequenceFeature sf = sfs[0];
 245     // description parsed from Note attribute
 246     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 247     assertEquals(39, sf.begin);
 248     assertEquals(39, sf.end);
 249     assertEquals("uniprot", sf.featureGroup);
 250     assertEquals("METAL", sf.type);
 251     assertEquals(
 252             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 253             sf.getValue("ATTRIBUTES"));
 254
 255     // verify feature on FER1_SOLLC1
 256     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 257     assertEquals(1, sfs.length);
 258     sf = sfs[0];
 259     // ID used for description if available
 260     assertEquals("$23", sf.description);
 261     assertEquals(55, sf.begin);
 262     assertEquals(130, sf.end);
 263     assertEquals("uniprot", sf.featureGroup);
 264     assertEquals("Pfam", sf.type);
 265     assertEquals(3f, sf.getScore(), 0.001f);
 266   }
 267
 268   /**
 269    * Test parsing a features file with Jalview format features (but no colour
 270    * descriptors or startgroup to give the hint not to parse as GFF)
 271    *
 272    * @throws Exception
 273    */
 274   @Test(groups = { "Functional" })
 275   public void testParse_jalviewFeaturesOnly() throws Exception
 276   {
 277     File f = new File("examples/uniref50.fa");
 278     AlignmentI al = readAlignmentFile(f);
 279     AlignFrame af = new AlignFrame(al, 500, 500);
 280     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 281             .getFeatureColours();
 282
 283     /*
 284      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 285      */
 286     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 287             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 288     FeaturesFile featuresFile = new FeaturesFile(featureData,
 289             DataSourceType.PASTE);
 290     assertTrue("Failed to parse features file",
 291             featuresFile.parse(al.getDataset(), colours, true));
 292
 293     // verify FER_CAPAA feature
 294     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 295             .getSequenceFeatures();
 296     assertEquals(1, sfs.length);
 297     SequenceFeature sf = sfs[0];
 298     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 299     assertEquals(39, sf.begin);
 300     assertEquals(39, sf.end);
 301     assertEquals("METAL", sf.type);
 302
 303     // verify FER1_SOLLC feature
 304     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 305     assertEquals(1, sfs.length);
 306     sf = sfs[0];
 307     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 308     assertEquals(86, sf.begin);
 309     assertEquals(87, sf.end);
 310     assertEquals("METALLIC", sf.type);
 311   }
 312
 313   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 314   {
 315     assertEquals("no sequences extracted from GFF3 file", 2,
 316             dataset.getHeight());
 317
 318     SequenceI seq1 = dataset.findName("seq1");
 319     SequenceI seq2 = dataset.findName("seq2");
 320     assertNotNull(seq1);
 321     assertNotNull(seq2);
 322     assertFalse(
 323             "Failed to replace dummy seq1 with real sequence",
 324             seq1 instanceof SequenceDummy
 325                     && ((SequenceDummy) seq1).isDummy());
 326     assertFalse(
 327             "Failed to replace dummy seq2 with real sequence",
 328             seq2 instanceof SequenceDummy
 329                     && ((SequenceDummy) seq2).isDummy());
 330     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 331     assertFalse("dummy replacement buggy for seq1",
 332             placeholderseq.equals(seq1.getSequenceAsString()));
 333     assertFalse("dummy replacement buggy for seq2",
 334             placeholderseq.equals(seq2.getSequenceAsString()));
 335     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 336     assertEquals("Wrong number of features", 3,
 337             seq1.getSequenceFeatures().length);
 338     assertNull(seq2.getSequenceFeatures());
 339     assertEquals(
 340             "Wrong number of features",
 341             0,
 342             seq2.getSequenceFeatures() == null ? 0 : seq2
 343                     .getSequenceFeatures().length);
 344     assertTrue(
 345             "Expected at least one CDNA/Protein mapping for seq1",
 346             dataset.getCodonFrame(seq1) != null
 347                     && dataset.getCodonFrame(seq1).size() > 0);
 348
 349   }
 350
 351   @Test(groups = { "Functional" })
 352   public void readGff3File() throws IOException
 353   {
 354     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 355             DataSourceType.FILE);
 356     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 357     gffreader.addProperties(dataset);
 358     checkDatasetfromSimpleGff3(dataset);
 359   }
 360
 361   @Test(groups = { "Functional" })
 362   public void simpleGff3FileClass() throws IOException
 363   {
 364     AlignmentI dataset = new Alignment(new SequenceI[] {});
 365     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 366             DataSourceType.FILE);
 367
 368     boolean parseResult = ffile.parse(dataset, null, false, false);
 369     assertTrue("return result should be true", parseResult);
 370     checkDatasetfromSimpleGff3(dataset);
 371   }
 372
 373   @Test(groups = { "Functional" })
 374   public void simpleGff3FileLoader() throws IOException
 375   {
 376     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 377             simpleGffFile, DataSourceType.FILE);
 378     assertTrue(
 379             "Didn't read the alignment into an alignframe from Gff3 File",
 380             af != null);
 381     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 382   }
 383
 384   @Test(groups = { "Functional" })
 385   public void simpleGff3RelaxedIdMatching() throws IOException
 386   {
 387     AlignmentI dataset = new Alignment(new SequenceI[] {});
 388     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 389             DataSourceType.FILE);
 390
 391     boolean parseResult = ffile.parse(dataset, null, false, true);
 392     assertTrue("return result (relaxedID matching) should be true",
 393             parseResult);
 394     checkDatasetfromSimpleGff3(dataset);
 395   }
 396
 397   @Test(groups = { "Functional" })
 398   public void testPrintJalviewFormat() throws Exception
 399   {
 400     File f = new File("examples/uniref50.fa");
 401     AlignmentI al = readAlignmentFile(f);
 402     AlignFrame af = new AlignFrame(al, 500, 500);
 403     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 404             .getFeatureColours();
 405     String features = "METAL\tcc9900\n"
 406             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 407             + "Pfam\tred\n"
 408             + "STARTGROUP\tuniprot\n"
 409             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 410             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 411             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 412             + "ENDGROUP\tuniprot\n";
 413     FeaturesFile featuresFile = new FeaturesFile(features,
 414             DataSourceType.PASTE);
 415     featuresFile.parse(al.getDataset(), colours, false);
 416
 417     /*
 418      * first with no features displayed
 419      */
 420     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 421     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
 422     String exported = featuresFile.printJalviewFormat(
 423             al.getSequencesArray(), visible);
 424     String expected = "No Features Visible";
 425     assertEquals(expected, exported);
 426
 427     /*
 428      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 429      */
 430     fr.setVisible("METAL");
 431     fr.setVisible("GAMMA-TURN");
 432     visible = fr.getDisplayedFeatureCols();
 433     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 434             visible);
 435     expected = "METAL\tcc9900\n"
 436             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 437             + "\nSTARTGROUP\tuniprot\n"
 438             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 439             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 440             + "ENDGROUP\tuniprot\n";
 441     assertEquals(expected, exported);
 442
 443     /*
 444      * now set Pfam visible
 445      */
 446     fr.setVisible("Pfam");
 447     visible = fr.getDisplayedFeatureCols();
 448     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 449             visible);
 450     /*
 451      * note the order of feature types is uncontrolled - derives from
 452      * FeaturesDisplayed.featuresDisplayed which is a HashSet
 453      */
 454     expected = "METAL\tcc9900\n"
 455             + "Pfam\tff0000\n"
 456             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 457             + "\nSTARTGROUP\tuniprot\n"
 458             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 459             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 460             + "<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"
 461             + "ENDGROUP\tuniprot\n";
 462     assertEquals(expected, exported);
 463   }
 464 }