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.assertTrue;
  27
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.datamodel.Alignment;
  31 import jalview.datamodel.AlignmentI;
  32 import jalview.datamodel.SequenceDummy;
  33 import jalview.datamodel.SequenceFeature;
  34 import jalview.datamodel.SequenceI;
  35 import jalview.datamodel.features.SequenceFeatures;
  36 import jalview.gui.AlignFrame;
  37 import jalview.gui.Desktop;
  38 import jalview.gui.JvOptionPane;
  39 import jalview.structure.StructureSelectionManager;
  40
  41 import java.awt.Color;
  42 import java.io.File;
  43 import java.io.IOException;
  44 import java.util.ArrayList;
  45 import java.util.Arrays;
  46 import java.util.HashMap;
  47 import java.util.List;
  48 import java.util.Map;
  49
  50 import org.testng.annotations.AfterClass;
  51 import org.testng.annotations.BeforeClass;
  52 import org.testng.annotations.Test;
  53
  54 public class FeaturesFileTest
  55 {
  56   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  57
  58   @AfterClass(alwaysRun = true)
  59   public void tearDownAfterClass()
  60   {
  61     /*
  62      * remove any sequence mappings created so they don't pollute other tests
  63      */
  64     StructureSelectionManager ssm = StructureSelectionManager
  65             .getStructureSelectionManager(Desktop.instance);
  66     ssm.resetAll();
  67   }
  68
  69   @BeforeClass(alwaysRun = true)
  70   public void setUpJvOptionPane()
  71   {
  72     JvOptionPane.setInteractiveMode(false);
  73     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  74   }
  75
  76   @Test(groups = { "Functional" })
  77   public void testParse() throws Exception
  78   {
  79     File f = new File("examples/uniref50.fa");
  80     AlignmentI al = readAlignmentFile(f);
  81     AlignFrame af = new AlignFrame(al, 500, 500);
  82     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  83             .getFeatureColours();
  84     FeaturesFile featuresFile = new FeaturesFile(
  85             "examples/exampleFeatures.txt", DataSourceType.FILE);
  86     assertTrue("Test " + "Features file test"
  87             + "\nFailed to parse features file.",
  88             featuresFile.parse(al.getDataset(), colours, true));
  89
  90     /*
  91      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  92      * updated - JAL-1904), and verify (some) feature group colours
  93      */
  94     colours = af.getFeatureRenderer().getFeatureColours();
  95     assertEquals("27 feature group colours not found", 27, colours.size());
  96     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
  97     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
  98     FeatureColourI kdColour = colours.get("kdHydrophobicity");
  99     assertTrue(kdColour.isGraduatedColour());
 100     assertTrue(kdColour.isAboveThreshold());
 101     assertEquals(-2f, kdColour.getThreshold());
 102
 103     /*
 104      * verify (some) features on sequences
 105      */
 106     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 107             .getSequenceFeatures(); // FER_CAPAA
 108     SequenceFeatures.sortFeatures(sfs, true);
 109     assertEquals(8, sfs.size());
 110
 111     /*
 112      * verify (in ascending start position order)
 113      */
 114     SequenceFeature sf = sfs.get(0);
 115     assertEquals("Pfam family%LINK%", sf.description);
 116     assertEquals(0, sf.begin);
 117     assertEquals(0, sf.end);
 118     assertEquals("uniprot", sf.featureGroup);
 119     assertEquals("Pfam", sf.type);
 120     assertEquals(1, sf.links.size());
 121     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 122             sf.links.get(0));
 123
 124     sf = sfs.get(1);
 125     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 126     assertEquals(3, sf.begin);
 127     assertEquals(93, sf.end);
 128     assertEquals("uniprot", sf.featureGroup);
 129     assertEquals("Cath", sf.type);
 130
 131     sf = sfs.get(2);
 132     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 133             sf.description);
 134     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 135             sf.links.get(0));
 136     assertEquals(8, sf.begin);
 137     assertEquals(83, sf.end);
 138     assertEquals("uniprot", sf.featureGroup);
 139     assertEquals("Pfam", sf.type);
 140
 141     sf = sfs.get(3);
 142     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 143     assertEquals(39, sf.begin);
 144     assertEquals(39, sf.end);
 145     assertEquals("uniprot", sf.featureGroup);
 146     assertEquals("METAL", sf.type);
 147
 148     sf = sfs.get(4);
 149     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 150     assertEquals(44, sf.begin);
 151     assertEquals(44, sf.end);
 152     assertEquals("uniprot", sf.featureGroup);
 153     assertEquals("METAL", sf.type);
 154
 155     sf = sfs.get(5);
 156     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 157     assertEquals(47, sf.begin);
 158     assertEquals(47, sf.end);
 159     assertEquals("uniprot", sf.featureGroup);
 160     assertEquals("METAL", sf.type);
 161
 162     sf = sfs.get(6);
 163     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 164     assertEquals(77, sf.begin);
 165     assertEquals(77, sf.end);
 166     assertEquals("uniprot", sf.featureGroup);
 167     assertEquals("METAL", sf.type);
 168
 169     sf = sfs.get(7);
 170     assertEquals(
 171             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 172             sf.description);
 173     assertEquals(
 174             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 175             sf.links.get(0));
 176     assertEquals(89, sf.begin);
 177     assertEquals(89, sf.end);
 178     assertEquals("netphos", sf.featureGroup);
 179     assertEquals("PHOSPHORYLATION (T)", sf.type);
 180   }
 181
 182   /**
 183    * Test parsing a features file with a mix of Jalview and GFF formatted
 184    * content
 185    *
 186    * @throws Exception
 187    */
 188   @Test(groups = { "Functional" })
 189   public void testParse_mixedJalviewGff() throws Exception
 190   {
 191     File f = new File("examples/uniref50.fa");
 192     AlignmentI al = readAlignmentFile(f);
 193     AlignFrame af = new AlignFrame(al, 500, 500);
 194     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 195             .getFeatureColours();
 196     // GFF2 uses space as name/value separator in column 9
 197     String gffData = "METAL\tcc9900\n"
 198             + "GFF\n"
 199             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 200             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 201     FeaturesFile featuresFile = new FeaturesFile(gffData,
 202             DataSourceType.PASTE);
 203     assertTrue("Failed to parse features file",
 204             featuresFile.parse(al.getDataset(), colours, true));
 205
 206     // verify colours read or synthesized
 207     colours = af.getFeatureRenderer().getFeatureColours();
 208     assertEquals("1 feature group colours not found", 1, colours.size());
 209     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 210
 211     // verify feature on FER_CAPAA
 212     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 213             .getSequenceFeatures();
 214     assertEquals(1, sfs.size());
 215     SequenceFeature sf = sfs.get(0);
 216     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 217     assertEquals(44, sf.begin);
 218     assertEquals(45, sf.end);
 219     assertEquals("uniprot", sf.featureGroup);
 220     assertEquals("METAL", sf.type);
 221     assertEquals(4f, sf.getScore(), 0.001f);
 222
 223     // verify feature on FER1_SOLLC
 224     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 225     assertEquals(1, sfs.size());
 226     sf = sfs.get(0);
 227     assertEquals("uniprot", sf.description);
 228     assertEquals(55, sf.begin);
 229     assertEquals(130, sf.end);
 230     assertEquals("uniprot", sf.featureGroup);
 231     assertEquals("Pfam", sf.type);
 232     assertEquals(2f, sf.getScore(), 0.001f);
 233   }
 234
 235   public static AlignmentI readAlignmentFile(File f) throws IOException
 236   {
 237     System.out.println("Reading file: " + f);
 238     String ff = f.getPath();
 239     FormatAdapter rf = new FormatAdapter();
 240
 241     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 242             new IdentifyFile().identify(ff, DataSourceType.FILE));
 243
 244     al.setDataset(null); // creates dataset sequences
 245     assertNotNull("Couldn't read supplied alignment data.", al);
 246     return al;
 247   }
 248
 249   /**
 250    * Test parsing a features file with GFF formatted content only
 251    *
 252    * @throws Exception
 253    */
 254   @Test(groups = { "Functional" })
 255   public void testParse_pureGff3() throws Exception
 256   {
 257     File f = new File("examples/uniref50.fa");
 258     AlignmentI al = readAlignmentFile(f);
 259     AlignFrame af = new AlignFrame(al, 500, 500);
 260     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 261             .getFeatureColours();
 262     // GFF3 uses '=' separator for name/value pairs in colum 9
 263     String gffData = "##gff-version 3\n"
 264             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 265             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 266             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 267     FeaturesFile featuresFile = new FeaturesFile(gffData,
 268             DataSourceType.PASTE);
 269     assertTrue("Failed to parse features file",
 270             featuresFile.parse(al.getDataset(), colours, true));
 271
 272     // verify feature on FER_CAPAA
 273     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 274             .getSequenceFeatures();
 275     assertEquals(1, sfs.size());
 276     SequenceFeature sf = sfs.get(0);
 277     // description parsed from Note attribute
 278     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 279     assertEquals(39, sf.begin);
 280     assertEquals(39, sf.end);
 281     assertEquals("uniprot", sf.featureGroup);
 282     assertEquals("METAL", sf.type);
 283     assertEquals(
 284             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 285             sf.getValue("ATTRIBUTES"));
 286
 287     // verify feature on FER1_SOLLC1
 288     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 289     assertEquals(1, sfs.size());
 290     sf = sfs.get(0);
 291     // ID used for description if available
 292     assertEquals("$23", sf.description);
 293     assertEquals(55, sf.begin);
 294     assertEquals(130, sf.end);
 295     assertEquals("uniprot", sf.featureGroup);
 296     assertEquals("Pfam", sf.type);
 297     assertEquals(3f, sf.getScore(), 0.001f);
 298   }
 299
 300   /**
 301    * Test parsing a features file with Jalview format features (but no colour
 302    * descriptors or startgroup to give the hint not to parse as GFF)
 303    *
 304    * @throws Exception
 305    */
 306   @Test(groups = { "Functional" })
 307   public void testParse_jalviewFeaturesOnly() throws Exception
 308   {
 309     File f = new File("examples/uniref50.fa");
 310     AlignmentI al = readAlignmentFile(f);
 311     AlignFrame af = new AlignFrame(al, 500, 500);
 312     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 313             .getFeatureColours();
 314
 315     /*
 316      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 317      */
 318     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 319             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 320     FeaturesFile featuresFile = new FeaturesFile(featureData,
 321             DataSourceType.PASTE);
 322     assertTrue("Failed to parse features file",
 323             featuresFile.parse(al.getDataset(), colours, true));
 324
 325     // verify FER_CAPAA feature
 326     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 327             .getSequenceFeatures();
 328     assertEquals(1, sfs.size());
 329     SequenceFeature sf = sfs.get(0);
 330     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 331     assertEquals(39, sf.begin);
 332     assertEquals(39, sf.end);
 333     assertEquals("METAL", sf.type);
 334
 335     // verify FER1_SOLLC feature
 336     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 337     assertEquals(1, sfs.size());
 338     sf = sfs.get(0);
 339     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 340     assertEquals(86, sf.begin);
 341     assertEquals(87, sf.end);
 342     assertEquals("METALLIC", sf.type);
 343   }
 344
 345   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 346   {
 347     assertEquals("no sequences extracted from GFF3 file", 2,
 348             dataset.getHeight());
 349
 350     SequenceI seq1 = dataset.findName("seq1");
 351     SequenceI seq2 = dataset.findName("seq2");
 352     assertNotNull(seq1);
 353     assertNotNull(seq2);
 354     assertFalse(
 355             "Failed to replace dummy seq1 with real sequence",
 356             seq1 instanceof SequenceDummy
 357                     && ((SequenceDummy) seq1).isDummy());
 358     assertFalse(
 359             "Failed to replace dummy seq2 with real sequence",
 360             seq2 instanceof SequenceDummy
 361                     && ((SequenceDummy) seq2).isDummy());
 362     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 363     assertFalse("dummy replacement buggy for seq1",
 364             placeholderseq.equals(seq1.getSequenceAsString()));
 365     assertFalse("dummy replacement buggy for seq2",
 366             placeholderseq.equals(seq2.getSequenceAsString()));
 367     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 368     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 369             .size());
 370     assertTrue(seq2.getSequenceFeatures().isEmpty());
 371     assertEquals(
 372             "Wrong number of features",
 373             0,
 374             seq2.getSequenceFeatures() == null ? 0 : seq2
 375                     .getSequenceFeatures().size());
 376     assertTrue(
 377             "Expected at least one CDNA/Protein mapping for seq1",
 378             dataset.getCodonFrame(seq1) != null
 379                     && dataset.getCodonFrame(seq1).size() > 0);
 380
 381   }
 382
 383   @Test(groups = { "Functional" })
 384   public void readGff3File() throws IOException
 385   {
 386     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 387             DataSourceType.FILE);
 388     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 389     gffreader.addProperties(dataset);
 390     checkDatasetfromSimpleGff3(dataset);
 391   }
 392
 393   @Test(groups = { "Functional" })
 394   public void simpleGff3FileClass() throws IOException
 395   {
 396     AlignmentI dataset = new Alignment(new SequenceI[] {});
 397     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 398             DataSourceType.FILE);
 399
 400     boolean parseResult = ffile.parse(dataset, null, false, false);
 401     assertTrue("return result should be true", parseResult);
 402     checkDatasetfromSimpleGff3(dataset);
 403   }
 404
 405   @Test(groups = { "Functional" })
 406   public void simpleGff3FileLoader() throws IOException
 407   {
 408     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 409             simpleGffFile, DataSourceType.FILE);
 410     assertTrue(
 411             "Didn't read the alignment into an alignframe from Gff3 File",
 412             af != null);
 413     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 414   }
 415
 416   @Test(groups = { "Functional" })
 417   public void simpleGff3RelaxedIdMatching() throws IOException
 418   {
 419     AlignmentI dataset = new Alignment(new SequenceI[] {});
 420     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 421             DataSourceType.FILE);
 422
 423     boolean parseResult = ffile.parse(dataset, null, false, true);
 424     assertTrue("return result (relaxedID matching) should be true",
 425             parseResult);
 426     checkDatasetfromSimpleGff3(dataset);
 427   }
 428
 429   @Test(groups = { "Functional" })
 430   public void testPrintJalviewFormat() throws Exception
 431   {
 432     File f = new File("examples/uniref50.fa");
 433     AlignmentI al = readAlignmentFile(f);
 434     AlignFrame af = new AlignFrame(al, 500, 500);
 435     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 436             .getFeatureColours();
 437     String features = "METAL\tcc9900\n"
 438             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 439             + "Pfam\tred\n"
 440             + "STARTGROUP\tuniprot\n"
 441             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 442             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 443             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 444             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 445             + "ENDGROUP\tuniprot\n";
 446     FeaturesFile featuresFile = new FeaturesFile(features,
 447             DataSourceType.PASTE);
 448     featuresFile.parse(al.getDataset(), colours, false);
 449
 450     /*
 451      * add positional and non-positional features with null and
 452      * empty feature group to check handled correctly
 453      */
 454     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 455     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 456             null));
 457     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 458             Float.NaN, null));
 459     seq = al.getSequenceAt(2); // FER1_SOLLC
 460     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 461             Float.NaN, ""));
 462     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 463             -2.6f, ""));
 464
 465     /*
 466      * first with no features displayed, exclude non-positional features
 467      */
 468     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 469     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
 470     List<String> visibleGroups = new ArrayList<String>(
 471             Arrays.asList(new String[] {}));
 472     String exported = featuresFile.printJalviewFormat(
 473             al.getSequencesArray(), visible, visibleGroups, false);
 474     String expected = "No Features Visible";
 475     assertEquals(expected, exported);
 476
 477     /*
 478      * include non-positional features
 479      */
 480     visibleGroups.add("uniprot");
 481     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 482             visible, visibleGroups, true);
 483     expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 484             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 485             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
 486             + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
 487     assertEquals(expected, exported);
 488
 489     /*
 490      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 491      */
 492     fr.setVisible("METAL");
 493     fr.setVisible("GAMMA-TURN");
 494     visible = fr.getDisplayedFeatureCols();
 495     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 496             visible, visibleGroups, false);
 497     expected = "METAL\tcc9900\n"
 498             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 499             + "\nSTARTGROUP\tuniprot\n"
 500             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 501             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 502             + "ENDGROUP\tuniprot\n";
 503     assertEquals(expected, exported);
 504
 505     /*
 506      * now set Pfam visible
 507      */
 508     fr.setVisible("Pfam");
 509     visible = fr.getDisplayedFeatureCols();
 510     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
 511             visible, visibleGroups, false);
 512     /*
 513      * features are output within group, ordered by sequence and by type
 514      */
 515     expected = "METAL\tcc9900\n"
 516             + "Pfam\tff0000\n"
 517             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
 518             + "\nSTARTGROUP\tuniprot\n"
 519             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 520             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 521             + "<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"
 522             + "ENDGROUP\tuniprot\n"
 523             // null / empty group features output after features in named
 524             // groups:
 525             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 526             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 527     assertEquals(expected, exported);
 528   }
 529
 530   @Test(groups = { "Functional" })
 531   public void testPrintGffFormat() throws Exception
 532   {
 533     File f = new File("examples/uniref50.fa");
 534     AlignmentI al = readAlignmentFile(f);
 535     AlignFrame af = new AlignFrame(al, 500, 500);
 536
 537     /*
 538      * no features
 539      */
 540     FeaturesFile featuresFile = new FeaturesFile();
 541     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 542     Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
 543     List<String> visibleGroups = new ArrayList<String>(
 544             Arrays.asList(new String[] {}));
 545     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 546             visible, visibleGroups, false);
 547     String gffHeader = "##gff-version 2\n";
 548     assertEquals(gffHeader, exported);
 549     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 550             visibleGroups, true);
 551     assertEquals(gffHeader, exported);
 552
 553     /*
 554      * add some features
 555      */
 556     al.getSequenceAt(0).addSequenceFeature(
 557             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 558     al.getSequenceAt(0).addSequenceFeature(
 559             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 560     al.getSequenceAt(1)
 561             .addSequenceFeature(
 562                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 563                             "s3dm"));
 564     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 565             "Uniprot");
 566     sf.setAttributes("x=y;black=white");
 567     sf.setStrand("+");
 568     sf.setPhase("2");
 569     al.getSequenceAt(1).addSequenceFeature(sf);
 570
 571     /*
 572      * with no features displayed, exclude non-positional features
 573      */
 574     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 575             visibleGroups, false);
 576     assertEquals(gffHeader, exported);
 577
 578     /*
 579      * include non-positional features
 580      */
 581     visibleGroups.add("Uniprot");
 582     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 583             visibleGroups, true);
 584     String expected = gffHeader
 585             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 586     assertEquals(expected, exported);
 587
 588     /*
 589      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 590      * only Uniprot group visible here...
 591      */
 592     fr.setVisible("METAL");
 593     fr.setVisible("GAMMA-TURN");
 594     visible = fr.getDisplayedFeatureCols();
 595     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 596             visibleGroups, false);
 597     // METAL feature has null group: description used for column 2
 598     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 599     assertEquals(expected, exported);
 600
 601     /*
 602      * set s3dm group visible
 603      */
 604     visibleGroups.add("s3dm");
 605     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 606             visibleGroups, false);
 607     // METAL feature has null group: description used for column 2
 608     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 609             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 610     assertEquals(expected, exported);
 611
 612     /*
 613      * now set Pfam visible
 614      */
 615     fr.setVisible("Pfam");
 616     visible = fr.getDisplayedFeatureCols();
 617     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
 618             visibleGroups, false);
 619     // Pfam feature columns include strand(+), phase(2), attributes
 620     expected = gffHeader
 621             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 622             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
 623             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
 624     assertEquals(expected, exported);
 625   }
 626 }