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.HashMap;
  43 import java.util.Map;
  44
  45 import org.testng.annotations.BeforeClass;
  46 import org.testng.annotations.Test;
  47
  48 public class FeaturesFileTest
  49 {
  50
  51   @BeforeClass(alwaysRun = true)
  52   public void setUpJvOptionPane()
  53   {
  54     JvOptionPane.setInteractiveMode(false);
  55     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  56   }
  57
  58   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  59
  60   @Test(groups = { "Functional" })
  61   public void testParse() throws Exception
  62   {
  63     File f = new File("examples/uniref50.fa");
  64     AlignmentI al = readAlignmentFile(f);
  65     AlignFrame af = new AlignFrame(al, 500, 500);
  66     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  67             .getFeatureColours();
  68     FeaturesFile featuresFile = new FeaturesFile(
  69             "examples/exampleFeatures.txt", DataSourceType.FILE);
  70     assertTrue("Test " + "Features file test"
  71             + "\nFailed to parse features file.",
  72             featuresFile.parse(al.getDataset(), colours, true));
  73
  74     /*
  75      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  76      * updated - JAL-1904), and verify (some) feature group colours
  77      */
  78     colours = af.getFeatureRenderer().getFeatureColours();
  79     assertEquals("26 feature group colours not found", 26, colours.size());
  80     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
  81     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
  82
  83     /*
  84      * verify (some) features on sequences
  85      */
  86     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
  87             .getSequenceFeatures(); // FER_CAPAA
  88     assertEquals(8, sfs.length);
  89     SequenceFeature sf = sfs[0];
  90     assertEquals("Pfam family%LINK%", sf.description);
  91     assertEquals(0, sf.begin);
  92     assertEquals(0, sf.end);
  93     assertEquals("uniprot", sf.featureGroup);
  94     assertEquals("Pfam", sf.type);
  95     assertEquals(1, sf.links.size());
  96     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
  97             sf.links.get(0));
  98
  99     sf = sfs[1];
 100     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 101     assertEquals(39, sf.begin);
 102     assertEquals(39, sf.end);
 103     assertEquals("uniprot", sf.featureGroup);
 104     assertEquals("METAL", sf.type);
 105     sf = sfs[2];
 106     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 107     assertEquals(44, sf.begin);
 108     assertEquals(44, sf.end);
 109     assertEquals("uniprot", sf.featureGroup);
 110     assertEquals("METAL", sf.type);
 111     sf = sfs[3];
 112     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 113     assertEquals(47, sf.begin);
 114     assertEquals(47, sf.end);
 115     assertEquals("uniprot", sf.featureGroup);
 116     assertEquals("METAL", sf.type);
 117     sf = sfs[4];
 118     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 119     assertEquals(77, sf.begin);
 120     assertEquals(77, sf.end);
 121     assertEquals("uniprot", sf.featureGroup);
 122     assertEquals("METAL", sf.type);
 123     sf = sfs[5];
 124     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 125             sf.description);
 126     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 127             sf.links.get(0));
 128     assertEquals(8, sf.begin);
 129     assertEquals(83, sf.end);
 130     assertEquals("uniprot", sf.featureGroup);
 131     assertEquals("Pfam", sf.type);
 132     sf = sfs[6];
 133     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 134     assertEquals(3, sf.begin);
 135     assertEquals(93, sf.end);
 136     assertEquals("uniprot", sf.featureGroup);
 137     assertEquals("Cath", sf.type);
 138     sf = sfs[7];
 139     assertEquals(
 140             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 141             sf.description);
 142     assertEquals(
 143             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 144             sf.links.get(0));
 145     assertEquals(89, sf.begin);
 146     assertEquals(89, sf.end);
 147     assertEquals("netphos", sf.featureGroup);
 148     assertEquals("PHOSPHORYLATION (T)", sf.type);
 149   }
 150
 151   /**
 152    * Test parsing a features file with a mix of Jalview and GFF formatted
 153    * content
 154    *
 155    * @throws Exception
 156    */
 157   @Test(groups = { "Functional" })
 158   public void testParse_mixedJalviewGff() throws Exception
 159   {
 160     File f = new File("examples/uniref50.fa");
 161     AlignmentI al = readAlignmentFile(f);
 162     AlignFrame af = new AlignFrame(al, 500, 500);
 163     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 164             .getFeatureColours();
 165     // GFF2 uses space as name/value separator in column 9
 166     String gffData = "METAL\tcc9900\n"
 167             + "GFF\n"
 168             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 169             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 170     FeaturesFile featuresFile = new FeaturesFile(gffData,
 171             DataSourceType.PASTE);
 172     assertTrue("Failed to parse features file",
 173             featuresFile.parse(al.getDataset(), colours, true));
 174
 175     // verify colours read or synthesized
 176     colours = af.getFeatureRenderer().getFeatureColours();
 177     assertEquals("1 feature group colours not found", 1, colours.size());
 178     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 179
 180     // verify feature on FER_CAPAA
 181     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 182             .getSequenceFeatures();
 183     assertEquals(1, sfs.length);
 184     SequenceFeature sf = sfs[0];
 185     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 186     assertEquals(44, sf.begin);
 187     assertEquals(45, sf.end);
 188     assertEquals("uniprot", sf.featureGroup);
 189     assertEquals("METAL", sf.type);
 190     assertEquals(4f, sf.getScore(), 0.001f);
 191
 192     // verify feature on FER1_SOLLC
 193     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 194     assertEquals(1, sfs.length);
 195     sf = sfs[0];
 196     assertEquals("uniprot", sf.description);
 197     assertEquals(55, sf.begin);
 198     assertEquals(130, sf.end);
 199     assertEquals("uniprot", sf.featureGroup);
 200     assertEquals("Pfam", sf.type);
 201     assertEquals(2f, sf.getScore(), 0.001f);
 202   }
 203
 204   public static AlignmentI readAlignmentFile(File f) throws IOException
 205   {
 206     System.out.println("Reading file: " + f);
 207     String ff = f.getPath();
 208     FormatAdapter rf = new FormatAdapter();
 209
 210     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 211             new IdentifyFile().identify(ff, DataSourceType.FILE));
 212
 213     al.setDataset(null); // creates dataset sequences
 214     assertNotNull("Couldn't read supplied alignment data.", al);
 215     return al;
 216   }
 217
 218   /**
 219    * Test parsing a features file with GFF formatted content only
 220    *
 221    * @throws Exception
 222    */
 223   @Test(groups = { "Functional" })
 224   public void testParse_pureGff3() throws Exception
 225   {
 226     File f = new File("examples/uniref50.fa");
 227     AlignmentI al = readAlignmentFile(f);
 228     AlignFrame af = new AlignFrame(al, 500, 500);
 229     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 230             .getFeatureColours();
 231     // GFF3 uses '=' separator for name/value pairs in colum 9
 232     String gffData = "##gff-version 3\n"
 233             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 234             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 235             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 236     FeaturesFile featuresFile = new FeaturesFile(gffData,
 237             DataSourceType.PASTE);
 238     assertTrue("Failed to parse features file",
 239             featuresFile.parse(al.getDataset(), colours, true));
 240
 241     // verify feature on FER_CAPAA
 242     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 243             .getSequenceFeatures();
 244     assertEquals(1, sfs.length);
 245     SequenceFeature sf = sfs[0];
 246     // description parsed from Note attribute
 247     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 248     assertEquals(39, sf.begin);
 249     assertEquals(39, sf.end);
 250     assertEquals("uniprot", sf.featureGroup);
 251     assertEquals("METAL", sf.type);
 252     assertEquals(
 253             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 254             sf.getValue("ATTRIBUTES"));
 255
 256     // verify feature on FER1_SOLLC1
 257     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 258     assertEquals(1, sfs.length);
 259     sf = sfs[0];
 260     // ID used for description if available
 261     assertEquals("$23", sf.description);
 262     assertEquals(55, sf.begin);
 263     assertEquals(130, sf.end);
 264     assertEquals("uniprot", sf.featureGroup);
 265     assertEquals("Pfam", sf.type);
 266     assertEquals(3f, sf.getScore(), 0.001f);
 267   }
 268
 269   /**
 270    * Test parsing a features file with Jalview format features (but no colour
 271    * descriptors or startgroup to give the hint not to parse as GFF)
 272    *
 273    * @throws Exception
 274    */
 275   @Test(groups = { "Functional" })
 276   public void testParse_jalviewFeaturesOnly() throws Exception
 277   {
 278     File f = new File("examples/uniref50.fa");
 279     AlignmentI al = readAlignmentFile(f);
 280     AlignFrame af = new AlignFrame(al, 500, 500);
 281     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 282             .getFeatureColours();
 283
 284     /*
 285      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 286      */
 287     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 288             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 289     FeaturesFile featuresFile = new FeaturesFile(featureData,
 290             DataSourceType.PASTE);
 291     assertTrue("Failed to parse features file",
 292             featuresFile.parse(al.getDataset(), colours, true));
 293
 294     // verify FER_CAPAA feature
 295     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
 296             .getSequenceFeatures();
 297     assertEquals(1, sfs.length);
 298     SequenceFeature sf = sfs[0];
 299     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 300     assertEquals(39, sf.begin);
 301     assertEquals(39, sf.end);
 302     assertEquals("METAL", sf.type);
 303
 304     // verify FER1_SOLLC feature
 305     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 306     assertEquals(1, sfs.length);
 307     sf = sfs[0];
 308     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 309     assertEquals(86, sf.begin);
 310     assertEquals(87, sf.end);
 311     assertEquals("METALLIC", sf.type);
 312   }
 313
 314   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 315   {
 316     assertEquals("no sequences extracted from GFF3 file", 2,
 317             dataset.getHeight());
 318
 319     SequenceI seq1 = dataset.findName("seq1");
 320     SequenceI seq2 = dataset.findName("seq2");
 321     assertNotNull(seq1);
 322     assertNotNull(seq2);
 323     assertFalse(
 324             "Failed to replace dummy seq1 with real sequence",
 325             seq1 instanceof SequenceDummy
 326                     && ((SequenceDummy) seq1).isDummy());
 327     assertFalse(
 328             "Failed to replace dummy seq2 with real sequence",
 329             seq2 instanceof SequenceDummy
 330                     && ((SequenceDummy) seq2).isDummy());
 331     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 332     assertFalse("dummy replacement buggy for seq1",
 333             placeholderseq.equals(seq1.getSequenceAsString()));
 334     assertFalse("dummy replacement buggy for seq2",
 335             placeholderseq.equals(seq2.getSequenceAsString()));
 336     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 337     assertEquals("Wrong number of features", 3,
 338             seq1.getSequenceFeatures().length);
 339     assertNull(seq2.getSequenceFeatures());
 340     assertEquals(
 341             "Wrong number of features",
 342             0,
 343             seq2.getSequenceFeatures() == null ? 0 : seq2
 344                     .getSequenceFeatures().length);
 345     assertTrue(
 346             "Expected at least one CDNA/Protein mapping for seq1",
 347             dataset.getCodonFrame(seq1) != null
 348                     && dataset.getCodonFrame(seq1).size() > 0);
 349
 350   }
 351
 352   @Test(groups = { "Functional" })
 353   public void readGff3File() throws IOException
 354   {
 355     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 356             DataSourceType.FILE);
 357     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 358     gffreader.addProperties(dataset);
 359     checkDatasetfromSimpleGff3(dataset);
 360   }
 361
 362   @Test(groups = { "Functional" })
 363   public void simpleGff3FileClass() throws IOException
 364   {
 365     AlignmentI dataset = new Alignment(new SequenceI[] {});
 366     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 367             DataSourceType.FILE);
 368
 369     boolean parseResult = ffile.parse(dataset, null, false, false);
 370     assertTrue("return result should be true", parseResult);
 371     checkDatasetfromSimpleGff3(dataset);
 372   }
 373
 374   @Test(groups = { "Functional" })
 375   public void simpleGff3FileLoader() throws IOException
 376   {
 377     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 378             simpleGffFile, DataSourceType.FILE);
 379     assertTrue(
 380             "Didn't read the alignment into an alignframe from Gff3 File",
 381             af != null);
 382     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 383   }
 384
 385   @Test(groups = { "Functional" })
 386   public void simpleGff3RelaxedIdMatching() throws IOException
 387   {
 388     AlignmentI dataset = new Alignment(new SequenceI[] {});
 389     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 390             DataSourceType.FILE);
 391
 392     boolean parseResult = ffile.parse(dataset, null, false, true);
 393     assertTrue("return result (relaxedID matching) should be true",
 394             parseResult);
 395     checkDatasetfromSimpleGff3(dataset);
 396   }
 397
 398   @Test(groups = { "Functional" })
 399   public void testPrintJalviewFormat() throws Exception
 400   {
 401     File f = new File("examples/uniref50.fa");
 402     AlignmentI al = readAlignmentFile(f);
 403     AlignFrame af = new AlignFrame(al, 500, 500);
 404     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 405             .getFeatureColours();
 406     String features = "METAL\tcc9900\n"
 407             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 408             + "Pfam\tred\n"
 409             + "STARTGROUP\tuniprot\n"
 410             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 411             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 412             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 413             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 414             + "ENDGROUP\tuniprot\n";
 415     FeaturesFile featuresFile = new FeaturesFile(features,
 416             DataSourceType.PASTE);
 417     featuresFile.parse(al.getDataset(), colours, false);
 418
 419     /*
 420      * first with no features displayed, exclude non-positional features
 421      */
 422     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 423     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
 424     String exported = featuresFile.printJalviewFormat(
 425             al.getSequencesArray(), visible, false);
 426     String expected = "No Features Visible";
 427     assertEquals(expected, exported);
 428
 429     /*
 430      * include non-positional features
 431      */
 432     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 433             visible, true);
 434     expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n";
 435     assertEquals(expected, exported);
 436
 437     /*
 438      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 439      */
 440     fr.setVisible("METAL");
 441     fr.setVisible("GAMMA-TURN");
 442     visible = fr.getDisplayedFeatureCols();
 443     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 444             visible, false);
 445     expected = "METAL\tcc9900\n"
 446             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 447             + "\nSTARTGROUP\tuniprot\n"
 448             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 449             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 450             + "ENDGROUP\tuniprot\n";
 451     assertEquals(expected, exported);
 452
 453     /*
 454      * now set Pfam visible
 455      */
 456     fr.setVisible("Pfam");
 457     visible = fr.getDisplayedFeatureCols();
 458     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 459             visible, false);
 460     /*
 461      * features are output within group, ordered by sequence and by type
 462      */
 463     expected = "METAL\tcc9900\n"
 464             + "Pfam\tff0000\n"
 465             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 466             + "\nSTARTGROUP\tuniprot\n"
 467             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 468             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 469             + "<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"
 470             + "ENDGROUP\tuniprot\n";
 471     assertEquals(expected, exported);
 472   }
 473
 474   @Test(groups = { "Functional" })
 475   public void testPrintGffFormat() throws Exception
 476   {
 477     File f = new File("examples/uniref50.fa");
 478     AlignmentI al = readAlignmentFile(f);
 479     AlignFrame af = new AlignFrame(al, 500, 500);
 480
 481     /*
 482      * no features
 483      */
 484     FeaturesFile featuresFile = new FeaturesFile();
 485     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 486     Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
 487     String exported = featuresFile.printGffFormat(
 488             al.getSequencesArray(), visible, false);
 489     String gffHeader = "##gff-version 2\n";
 490     assertEquals(gffHeader, exported);
 491     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 492             true);
 493     assertEquals(gffHeader, exported);
 494
 495     /*
 496      * add some features
 497      */
 498     al.getSequenceAt(0).addSequenceFeature(
 499             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 500     al.getSequenceAt(0).addSequenceFeature(
 501             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 502     al.getSequenceAt(1)
 503             .addSequenceFeature(
 504                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 505                             "s3dm"));
 506     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, "Uniprot");
 507     sf.setAttributes("x=y;black=white");
 508     sf.setStrand("+");
 509     sf.setPhase("2");
 510     al.getSequenceAt(1).addSequenceFeature(sf);
 511
 512     /*
 513      * with no features displayed, exclude non-positional features
 514      */
 515     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 516             false);
 517     assertEquals(gffHeader, exported);
 518
 519     /*
 520      * include non-positional features
 521      */
 522     exported = featuresFile.printGffFormat(al.getSequencesArray(),
 523             visible, true);
 524     String expected = gffHeader
 525             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 526     assertEquals(expected, exported);
 527
 528     /*
 529      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 530      */
 531     fr.setVisible("METAL");
 532     fr.setVisible("GAMMA-TURN");
 533     visible = fr.getDisplayedFeatureCols();
 534     exported = featuresFile.printGffFormat(al.getSequencesArray(),
 535             visible, false);
 536     // METAL feature has null group: description used for column 2
 537     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 538             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 539     assertEquals(expected, exported);
 540
 541     /*
 542      * now set Pfam visible
 543      */
 544     fr.setVisible("Pfam");
 545     visible = fr.getDisplayedFeatureCols();
 546     exported = featuresFile.printGffFormat(al.getSequencesArray(),
 547             visible, false);
 548     // Pfam feature columns include strand(+), phase(2), attributes
 549     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 550             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
 551             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
 552     assertEquals(expected, exported);
 553   }
 554 }