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