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.assertSame;
  27 import static org.testng.AssertJUnit.assertTrue;
  28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
  29
  30 import jalview.api.FeatureColourI;
  31 import jalview.api.FeatureRenderer;
  32 import jalview.datamodel.Alignment;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.SequenceDummy;
  35 import jalview.datamodel.SequenceFeature;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.datamodel.features.FeatureMatcher;
  38 import jalview.datamodel.features.FeatureMatcherI;
  39 import jalview.datamodel.features.FeatureMatcherSet;
  40 import jalview.datamodel.features.FeatureMatcherSetI;
  41 import jalview.datamodel.features.SequenceFeatures;
  42 import jalview.gui.AlignFrame;
  43 import jalview.gui.Desktop;
  44 import jalview.gui.JvOptionPane;
  45 import jalview.schemes.FeatureColour;
  46 import jalview.util.matcher.Condition;
  47 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  48 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  49
  50 import java.awt.Color;
  51 import java.io.File;
  52 import java.io.IOException;
  53 import java.util.HashMap;
  54 import java.util.Iterator;
  55 import java.util.List;
  56 import java.util.Map;
  57
  58 import org.testng.annotations.AfterClass;
  59 import org.testng.annotations.BeforeClass;
  60 import org.testng.annotations.Test;
  61
  62 public class FeaturesFileTest
  63 {
  64   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  65
  66   @AfterClass(alwaysRun = true)
  67   public void tearDownAfterClass()
  68   {
  69     /*
  70      * remove any sequence mappings created so they don't pollute other tests
  71      */
  72     Desktop.getInstance().getStructureSelectionManager().resetAll();
  73   }
  74
  75   @BeforeClass(alwaysRun = true)
  76   public void setUpJvOptionPane()
  77   {
  78     JvOptionPane.setInteractiveMode(false);
  79     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  80   }
  81
  82   @Test(groups = { "Functional" })
  83   public void testParse() throws Exception
  84   {
  85     File f = new File("examples/uniref50.fa");
  86     AlignmentI al = readAlignmentFile(f);
  87     AlignFrame af = new AlignFrame(al, 500, 500);
  88     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  89             .getFeatureColours();
  90     FeaturesFile featuresFile = new FeaturesFile(
  91             "examples/exampleFeatures.txt", DataSourceType.FILE);
  92     assertTrue("Test " + "Features file test"
  93             + "\nFailed to parse features file.",
  94             featuresFile.parse(al.getDataset(), colours, true));
  95
  96     /*
  97      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  98      * updated - JAL-1904), and verify (some) feature group colours
  99      */
 100     colours = af.getFeatureRenderer().getFeatureColours();
 101     assertEquals("27 feature group colours not found", 27, colours.size());
 102     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
 103     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
 104     FeatureColourI kdColour = colours.get("kdHydrophobicity");
 105     assertTrue(kdColour.isGraduatedColour());
 106     assertTrue(kdColour.isAboveThreshold());
 107     assertEquals(-2f, kdColour.getThreshold());
 108
 109     /*
 110      * verify (some) features on sequences
 111      */
 112     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 113             .getSequenceFeatures(); // FER_CAPAA
 114     SequenceFeatures.sortFeatures(sfs, true);
 115     assertEquals(8, sfs.size());
 116
 117     /*
 118      * verify (in ascending start position order)
 119      */
 120     SequenceFeature sf = sfs.get(0);
 121     assertEquals("Pfam family%LINK%", sf.description);
 122     assertEquals(0, sf.begin);
 123     assertEquals(0, sf.end);
 124     assertEquals("uniprot", sf.featureGroup);
 125     assertEquals("Pfam", sf.type);
 126     assertEquals(1, sf.links.size());
 127     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 128             sf.links.get(0));
 129
 130     sf = sfs.get(1);
 131     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 132     assertEquals(3, sf.begin);
 133     assertEquals(93, sf.end);
 134     assertEquals("uniprot", sf.featureGroup);
 135     assertEquals("Cath", sf.type);
 136
 137     sf = sfs.get(2);
 138     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 139             sf.description);
 140     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 141             sf.links.get(0));
 142     assertEquals(8, sf.begin);
 143     assertEquals(83, sf.end);
 144     assertEquals("uniprot", sf.featureGroup);
 145     assertEquals("Pfam", sf.type);
 146
 147     sf = sfs.get(3);
 148     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 149     assertEquals(39, sf.begin);
 150     assertEquals(39, sf.end);
 151     assertEquals("uniprot", sf.featureGroup);
 152     assertEquals("METAL", sf.type);
 153
 154     sf = sfs.get(4);
 155     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 156     assertEquals(44, sf.begin);
 157     assertEquals(44, sf.end);
 158     assertEquals("uniprot", sf.featureGroup);
 159     assertEquals("METAL", sf.type);
 160
 161     sf = sfs.get(5);
 162     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 163     assertEquals(47, sf.begin);
 164     assertEquals(47, sf.end);
 165     assertEquals("uniprot", sf.featureGroup);
 166     assertEquals("METAL", sf.type);
 167
 168     sf = sfs.get(6);
 169     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 170     assertEquals(77, sf.begin);
 171     assertEquals(77, sf.end);
 172     assertEquals("uniprot", sf.featureGroup);
 173     assertEquals("METAL", sf.type);
 174
 175     sf = sfs.get(7);
 176     assertEquals(
 177             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 178             sf.description);
 179     assertEquals(
 180             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 181             sf.links.get(0));
 182     assertEquals(89, sf.begin);
 183     assertEquals(89, sf.end);
 184     assertEquals("netphos", sf.featureGroup);
 185     assertEquals("PHOSPHORYLATION (T)", sf.type);
 186   }
 187
 188   /**
 189    * Test parsing a features file with a mix of Jalview and GFF formatted
 190    * content
 191    *
 192    * @throws Exception
 193    */
 194   @Test(groups = { "Functional" })
 195   public void testParse_mixedJalviewGff() throws Exception
 196   {
 197     File f = new File("examples/uniref50.fa");
 198     AlignmentI al = readAlignmentFile(f);
 199     AlignFrame af = new AlignFrame(al, 500, 500);
 200     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 201             .getFeatureColours();
 202     // GFF2 uses space as name/value separator in column 9
 203     String gffData = "METAL\tcc9900\n"
 204             + "GFF\n"
 205             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 206             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 207     FeaturesFile featuresFile = new FeaturesFile(gffData,
 208             DataSourceType.PASTE);
 209     assertTrue("Failed to parse features file",
 210             featuresFile.parse(al.getDataset(), colours, true));
 211
 212     // verify colours read or synthesized
 213     colours = af.getFeatureRenderer().getFeatureColours();
 214     assertEquals("1 feature group colours not found", 1, colours.size());
 215     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 216
 217     // verify feature on FER_CAPAA
 218     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 219             .getSequenceFeatures();
 220     assertEquals(1, sfs.size());
 221     SequenceFeature sf = sfs.get(0);
 222     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 223     assertEquals(44, sf.begin);
 224     assertEquals(45, sf.end);
 225     assertEquals("uniprot", sf.featureGroup);
 226     assertEquals("METAL", sf.type);
 227     assertEquals(4f, sf.getScore(), 0.001f);
 228
 229     // verify feature on FER1_SOLLC
 230     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 231     assertEquals(1, sfs.size());
 232     sf = sfs.get(0);
 233     assertEquals("uniprot", sf.description);
 234     assertEquals(55, sf.begin);
 235     assertEquals(130, sf.end);
 236     assertEquals("uniprot", sf.featureGroup);
 237     assertEquals("Pfam", sf.type);
 238     assertEquals(2f, sf.getScore(), 0.001f);
 239   }
 240
 241   public static AlignmentI readAlignmentFile(File f) throws IOException
 242   {
 243     System.out.println("Reading file: " + f);
 244     String ff = f.getPath();
 245     FormatAdapter rf = new FormatAdapter();
 246
 247     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 248             new IdentifyFile().identify(ff, DataSourceType.FILE));
 249
 250     al.setDataset(null); // creates dataset sequences
 251     assertNotNull("Couldn't read supplied alignment data.", al);
 252     return al;
 253   }
 254
 255   /**
 256    * Test parsing a features file with GFF formatted content only
 257    *
 258    * @throws Exception
 259    */
 260   @Test(groups = { "Functional" })
 261   public void testParse_pureGff3() throws Exception
 262   {
 263     File f = new File("examples/uniref50.fa");
 264     AlignmentI al = readAlignmentFile(f);
 265     AlignFrame af = new AlignFrame(al, 500, 500);
 266     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 267             .getFeatureColours();
 268     // GFF3 uses '=' separator for name/value pairs in colum 9
 269     String gffData = "##gff-version 3\n"
 270             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 271             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 272             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 273     FeaturesFile featuresFile = new FeaturesFile(gffData,
 274             DataSourceType.PASTE);
 275     assertTrue("Failed to parse features file",
 276             featuresFile.parse(al.getDataset(), colours, true));
 277
 278     // verify feature on FER_CAPAA
 279     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 280             .getSequenceFeatures();
 281     assertEquals(1, sfs.size());
 282     SequenceFeature sf = sfs.get(0);
 283     // description parsed from Note attribute
 284     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 285     assertEquals(39, sf.begin);
 286     assertEquals(39, sf.end);
 287     assertEquals("uniprot", sf.featureGroup);
 288     assertEquals("METAL", sf.type);
 289     assertEquals(
 290             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 291             sf.getValue("ATTRIBUTES"));
 292
 293     // verify feature on FER1_SOLLC1
 294     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 295     assertEquals(1, sfs.size());
 296     sf = sfs.get(0);
 297     // ID used for description if available
 298     assertEquals("$23", sf.description);
 299     assertEquals(55, sf.begin);
 300     assertEquals(130, sf.end);
 301     assertEquals("uniprot", sf.featureGroup);
 302     assertEquals("Pfam", sf.type);
 303     assertEquals(3f, sf.getScore(), 0.001f);
 304   }
 305
 306   /**
 307    * Test parsing a features file with Jalview format features (but no colour
 308    * descriptors or startgroup to give the hint not to parse as GFF)
 309    *
 310    * @throws Exception
 311    */
 312   @Test(groups = { "Functional" })
 313   public void testParse_jalviewFeaturesOnly() throws Exception
 314   {
 315     File f = new File("examples/uniref50.fa");
 316     AlignmentI al = readAlignmentFile(f);
 317     AlignFrame af = new AlignFrame(al, 500, 500);
 318     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 319             .getFeatureColours();
 320
 321     /*
 322      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 323      */
 324     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 325             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 326     FeaturesFile featuresFile = new FeaturesFile(featureData,
 327             DataSourceType.PASTE);
 328     assertTrue("Failed to parse features file",
 329             featuresFile.parse(al.getDataset(), colours, true));
 330
 331     // verify FER_CAPAA feature
 332     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 333             .getSequenceFeatures();
 334     assertEquals(1, sfs.size());
 335     SequenceFeature sf = sfs.get(0);
 336     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 337     assertEquals(39, sf.begin);
 338     assertEquals(39, sf.end);
 339     assertEquals("METAL", sf.type);
 340
 341     // verify FER1_SOLLC feature
 342     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 343     assertEquals(1, sfs.size());
 344     sf = sfs.get(0);
 345     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 346     assertEquals(86, sf.begin);
 347     assertEquals(87, sf.end);
 348     assertEquals("METALLIC", sf.type);
 349   }
 350
 351   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 352   {
 353     assertEquals("no sequences extracted from GFF3 file", 2,
 354             dataset.getHeight());
 355
 356     SequenceI seq1 = dataset.findName("seq1");
 357     SequenceI seq2 = dataset.findName("seq2");
 358     assertNotNull(seq1);
 359     assertNotNull(seq2);
 360     assertFalse(
 361             "Failed to replace dummy seq1 with real sequence",
 362             seq1 instanceof SequenceDummy
 363                     && ((SequenceDummy) seq1).isDummy());
 364     assertFalse(
 365             "Failed to replace dummy seq2 with real sequence",
 366             seq2 instanceof SequenceDummy
 367                     && ((SequenceDummy) seq2).isDummy());
 368     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 369     assertFalse("dummy replacement buggy for seq1",
 370             placeholderseq.equals(seq1.getSequenceAsString()));
 371     assertFalse("dummy replacement buggy for seq2",
 372             placeholderseq.equals(seq2.getSequenceAsString()));
 373     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 374     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 375             .size());
 376     assertTrue(seq2.getSequenceFeatures().isEmpty());
 377     assertEquals(
 378             "Wrong number of features",
 379             0,
 380             seq2.getSequenceFeatures() == null ? 0 : seq2
 381                     .getSequenceFeatures().size());
 382     assertTrue(
 383             "Expected at least one CDNA/Protein mapping for seq1",
 384             dataset.getCodonFrame(seq1) != null
 385                     && dataset.getCodonFrame(seq1).size() > 0);
 386
 387   }
 388
 389   @Test(groups = { "Functional" })
 390   public void readGff3File() throws IOException
 391   {
 392     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 393             DataSourceType.FILE);
 394     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 395     gffreader.addProperties(dataset);
 396     checkDatasetfromSimpleGff3(dataset);
 397   }
 398
 399   @Test(groups = { "Functional" })
 400   public void simpleGff3FileClass() throws IOException
 401   {
 402     AlignmentI dataset = new Alignment(new SequenceI[] {});
 403     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 404             DataSourceType.FILE);
 405
 406     boolean parseResult = ffile.parse(dataset, null, false, false);
 407     assertTrue("return result should be true", parseResult);
 408     checkDatasetfromSimpleGff3(dataset);
 409   }
 410
 411   @Test(groups = { "Functional" })
 412   public void simpleGff3FileLoader() throws IOException
 413   {
 414     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 415             simpleGffFile, DataSourceType.FILE);
 416     assertTrue(
 417             "Didn't read the alignment into an alignframe from Gff3 File",
 418             af != null);
 419     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 420   }
 421
 422   @Test(groups = { "Functional" })
 423   public void simpleGff3RelaxedIdMatching() throws IOException
 424   {
 425     AlignmentI dataset = new Alignment(new SequenceI[] {});
 426     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 427             DataSourceType.FILE);
 428
 429     boolean parseResult = ffile.parse(dataset, null, false, true);
 430     assertTrue("return result (relaxedID matching) should be true",
 431             parseResult);
 432     checkDatasetfromSimpleGff3(dataset);
 433   }
 434
 435   @Test(groups = { "Functional" })
 436   public void testPrintJalviewFormat() throws Exception
 437   {
 438     File f = new File("examples/uniref50.fa");
 439     AlignmentI al = readAlignmentFile(f);
 440     AlignFrame af = new AlignFrame(al, 500, 500);
 441     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 442             .getFeatureColours();
 443     String features = "METAL\tcc9900\n"
 444             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 445             + "Pfam\tred\n"
 446             + "STARTGROUP\tuniprot\n"
 447             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 448             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 449             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 450             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 451             + "ENDGROUP\tuniprot\n";
 452     FeaturesFile featuresFile = new FeaturesFile(features,
 453             DataSourceType.PASTE);
 454     featuresFile.parse(al.getDataset(), colours, false);
 455
 456     /*
 457      * add positional and non-positional features with null and
 458      * empty feature group to check handled correctly
 459      */
 460     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 461     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 462             null));
 463     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 464             Float.NaN, null));
 465     seq = al.getSequenceAt(2); // FER1_SOLLC
 466     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 467             Float.NaN, ""));
 468     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 469             -2.6f, ""));
 470
 471     /*
 472      * first with no features displayed, exclude non-positional features
 473      */
 474     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 475     String exported = featuresFile
 476             .printJalviewFormat(al.getSequencesArray(), fr, false);
 477     String expected = "No Features Visible";
 478     assertEquals(expected, exported);
 479
 480     /*
 481      * include non-positional features, but still no positional features
 482      */
 483     fr.setGroupVisibility("uniprot", true);
 484     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 485             true);
 486     expected = "\nSTARTGROUP\tuniprot\n"
 487             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 488             + "ENDGROUP\tuniprot\n\n"
 489             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 490             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 491     assertEquals(
 492             expected.replace("\n", System.getProperty("line.separator")),
 493             exported);
 494
 495     /*
 496      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 497      */
 498     fr.setVisible("METAL");
 499     fr.setVisible("GAMMA-TURN");
 500     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 501             false);
 502     expected = "METAL\tcc9900\n"
 503             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 504             + "\nSTARTGROUP\tuniprot\n"
 505             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 506             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 507             + "ENDGROUP\tuniprot\n";
 508     assertEquals(fixLineEnd(expected), exported);
 509
 510     /*
 511      * now set Pfam visible
 512      */
 513     fr.setVisible("Pfam");
 514     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 515             false);
 516     /*
 517      * features are output within group, ordered by sequence and type
 518      */
 519     expected = "METAL\tcc9900\n"
 520             + "Pfam\tff0000\n"
 521             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 522             + "\nSTARTGROUP\tuniprot\n"
 523             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 524             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 525             + "<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"
 526             + "ENDGROUP\tuniprot\n"
 527             // null / empty group features are output after named groups
 528             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 529             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 530     assertEquals(fixLineEnd(expected), exported);
 531
 532     /*
 533      * hide uniprot group
 534      */
 535     fr.setGroupVisibility("uniprot", false);
 536     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 537             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 538             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 539             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 540     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 541             false);
 542     assertEquals(fixLineEnd(expected), exported);
 543
 544     /*
 545      * include non-positional (overrides group not shown)
 546      */
 547     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 548             true);
 549     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 550             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 551             + "\nSTARTGROUP\tuniprot\n"
 552             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 553             + "ENDGROUP\tuniprot\n"
 554             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 555             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 556             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 557             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 558     assertEquals(fixLineEnd(expected), exported);
 559   }
 560
 561   @Test(groups = { "Functional" })
 562   public void testPrintGffFormat() throws Exception
 563   {
 564     File f = new File("examples/uniref50.fa");
 565     AlignmentI al = readAlignmentFile(f);
 566     AlignFrame af = new AlignFrame(al, 500, 500);
 567
 568     /*
 569      * no features
 570      */
 571     FeaturesFile featuresFile = new FeaturesFile();
 572     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 573             .getFeatureRenderer();
 574     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 575             fr, false);
 576     String gffHeader = "##gff-version 2\n";
 577     assertEquals(
 578             fixLineEnd(gffHeader),
 579             exported);
 580     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 581             true);
 582     assertEquals(
 583             fixLineEnd(gffHeader),
 584             exported);
 585
 586     /*
 587      * add some features
 588      */
 589     al.getSequenceAt(0).addSequenceFeature(
 590             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 591     al.getSequenceAt(0).addSequenceFeature(
 592             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 593     al.getSequenceAt(1)
 594             .addSequenceFeature(
 595                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 596                             "s3dm"));
 597     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 598             "Uniprot");
 599     sf.setAttributes("x=y;black=white");
 600     sf.setStrand("+");
 601     sf.setPhase("2");
 602     al.getSequenceAt(1).addSequenceFeature(sf);
 603
 604     /*
 605      * 'discover' features then hide all feature types
 606      */
 607     fr.findAllFeatures(true);
 608     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 609     FeatureColourI fc = new FeatureColour(Color.PINK);
 610     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 611     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 612     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 613     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 614     fr.setFeaturePriority(data);
 615
 616     /*
 617      * with no features displayed, exclude non-positional features
 618      */
 619     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 620             false);
 621     assertEquals(
 622             fixLineEnd(gffHeader),
 623             exported);
 624
 625     /*
 626      * include non-positional features
 627      */
 628     fr.setGroupVisibility("Uniprot", true);
 629     fr.setGroupVisibility("s3dm", false);
 630     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 631             true);
 632     String expected = gffHeader
 633             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 634     assertEquals(
 635             fixLineEnd(expected),
 636             exported);
 637
 638     /*
 639      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 640      * only Uniprot group visible here...
 641      */
 642     fr.setVisible("METAL");
 643     fr.setVisible("GAMMA-TURN");
 644     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 645             false);
 646     // METAL feature has null group: description used for column 2
 647     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 648     assertEquals(
 649             expected.replace("\n", System.getProperty("line.separator")),
 650             exported);
 651
 652     /*
 653      * set s3dm group visible
 654      */
 655     fr.setGroupVisibility("s3dm", true);
 656     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 657             false);
 658     // METAL feature has null group: description used for column 2
 659     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 660             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 661     assertEquals(
 662             expected.replace("\n", System.getProperty("line.separator")),
 663             exported);
 664
 665     /*
 666      * now set Pfam visible
 667      */
 668     fr.setVisible("Pfam");
 669     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 670             false);
 671     // Pfam feature columns include strand(+), phase(2), attributes
 672     expected = gffHeader
 673             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 674             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
 675             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
 676     assertEquals(
 677             expected.replace("\n", System.getProperty("line.separator")),
 678             exported);
 679   }
 680
 681   private String fixLineEnd(String s)
 682   {
 683     return s.replace("\n", System.getProperty("line.separator"));
 684   }
 685
 686   /**
 687    * Test for parsing of feature filters as represented in a Jalview features
 688    * file
 689    *
 690    * @throws Exception
 691    */
 692   @Test(groups = { "Functional" })
 693   public void testParseFilters() throws Exception
 694   {
 695     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 696     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 697             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 698     FeaturesFile featuresFile = new FeaturesFile(text,
 699             DataSourceType.PASTE);
 700     featuresFile.parseFilters(filters);
 701     assertEquals(filters.size(), 2);
 702
 703     FeatureMatcherSetI fm = filters.get("sequence_variant");
 704     assertNotNull(fm);
 705     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 706     FeatureMatcherI matcher = matchers.next();
 707     assertFalse(matchers.hasNext());
 708     String[] attributes = matcher.getAttribute();
 709     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 710     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 711     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 712
 713     fm = filters.get("missense_variant");
 714     assertNotNull(fm);
 715     matchers = fm.getMatchers().iterator();
 716     matcher = matchers.next();
 717     assertTrue(matcher.isByLabel());
 718     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 719     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 720     matcher = matchers.next();
 721     assertTrue(matcher.isByScore());
 722     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 723     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 724     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 725
 726     assertFalse(matchers.hasNext());
 727   }
 728
 729   @Test(groups = { "Functional" })
 730   public void testOutputFeatureFilters()
 731   {
 732     FeaturesFile ff = new FeaturesFile();
 733     StringBuilder sb = new StringBuilder();
 734     Map<String, FeatureColourI> visible = new HashMap<>();
 735     visible.put("pfam", new FeatureColour(Color.red));
 736     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 737
 738     // with no filters, nothing is output
 739     ff.outputFeatureFilters(sb, visible, featureFilters);
 740     assertEquals("", sb.toString());
 741
 742     // with filter for not visible features only, nothing is output
 743     FeatureMatcherSet filter = new FeatureMatcherSet();
 744     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 745     featureFilters.put("foobar", filter);
 746     ff.outputFeatureFilters(sb, visible, featureFilters);
 747     assertEquals("", sb.toString());
 748
 749     // with filters for visible feature types
 750     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 751     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 752             "PolyPhen"));
 753     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 754     featureFilters.put("pfam", filter2);
 755     visible.put("foobar", new FeatureColour(Color.blue));
 756     ff.outputFeatureFilters(sb, visible, featureFilters);
 757     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 758     assertEquals(fixLineEnd(expected), sb.toString());
 759   }
 760
 761   /**
 762    * Output as GFF should not include features which are not visible due to
 763    * colour threshold or feature filter settings
 764    *
 765    * @throws Exception
 766    */
 767   @Test(groups = { "Functional" })
 768   public void testPrintGffFormat_withFilters() throws Exception
 769   {
 770     File f = new File("examples/uniref50.fa");
 771     AlignmentI al = readAlignmentFile(f);
 772     AlignFrame af = new AlignFrame(al, 500, 500);
 773     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 774             null);
 775     sf1.setValue("clin_sig", "Likely Pathogenic");
 776     sf1.setValue("AF", "24");
 777     al.getSequenceAt(0).addSequenceFeature(sf1);
 778     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 779             null);
 780     sf2.setValue("clin_sig", "Benign");
 781     sf2.setValue("AF", "46");
 782     al.getSequenceAt(0).addSequenceFeature(sf2);
 783
 784     FeaturesFile featuresFile = new FeaturesFile();
 785     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 786     final String gffHeader = "##gff-version 2\n";
 787
 788     fr.setVisible("METAL");
 789     fr.setColour("METAL", new FeatureColour(Color.PINK));
 790     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 791             fr, false);
 792     String expected = gffHeader
 793             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 794             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 795     assertEquals(
 796             fixLineEnd(expected), exported);
 797
 798     /*
 799      * now threshold to Score > 1.1 - should exclude sf2
 800      */
 801     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 802             Color.white, 0f, 2f);
 803     fc.setAboveThreshold(true);
 804     fc.setThreshold(1.1f);
 805     fr.setColour("METAL", fc);
 806     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 807             false);
 808     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 809     assertEquals(fixLineEnd(expected), exported);
 810
 811     /*
 812      * remove threshold and check sf2 is exported
 813      */
 814     fc.setAboveThreshold(false);
 815     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 816             false);
 817     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 818             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 819     assertEquals(fixLineEnd(expected), exported);
 820
 821     /*
 822      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 823      */
 824     FeatureMatcherSetI filter = new FeatureMatcherSet();
 825     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 826             "clin_sig"));
 827     fr.setFeatureFilter("METAL", filter);
 828     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 829             false);
 830     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 831     assertEquals(fixLineEnd(expected), exported);
 832   }
 833
 834   /**
 835    * Output as Jalview should not include features which are not visible due to
 836    * colour threshold or feature filter settings
 837    *
 838    * @throws Exception
 839    */
 840   @Test(groups = { "Functional" })
 841   public void testPrintJalviewFormat_withFilters() throws Exception
 842   {
 843     File f = new File("examples/uniref50.fa");
 844     AlignmentI al = readAlignmentFile(f);
 845     AlignFrame af = new AlignFrame(al, 500, 500);
 846     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 847             "grp1");
 848     sf1.setValue("clin_sig", "Likely Pathogenic");
 849     sf1.setValue("AF", "24");
 850     al.getSequenceAt(0).addSequenceFeature(sf1);
 851     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 852             "grp2");
 853     sf2.setValue("clin_sig", "Benign");
 854     sf2.setValue("AF", "46");
 855     al.getSequenceAt(0).addSequenceFeature(sf2);
 856
 857     FeaturesFile featuresFile = new FeaturesFile();
 858     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 859     fr.findAllFeatures(true);
 860
 861     fr.setVisible("METAL");
 862     fr.setColour("METAL", new FeatureColour(Color.PINK));
 863     String exported = featuresFile.printJalviewFormat(
 864             al.getSequencesArray(),
 865             fr, false);
 866     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 867             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 868             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 869             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 870             + "ENDGROUP\tgrp2\n";
 871     assertEquals(
 872             fixLineEnd(expected),
 873             exported);
 874
 875     /*
 876      * now threshold to Score > 1.1 - should exclude sf2
 877      * (and there should be no empty STARTGROUP/ENDGROUP output)
 878      */
 879     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 880             Color.white, 0f, 2f);
 881     fc.setAboveThreshold(true);
 882     fc.setThreshold(1.1f);
 883     fr.setColour("METAL", fc);
 884     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 885             false);
 886     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 887             + "STARTGROUP\tgrp1\n"
 888             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 889             + "ENDGROUP\tgrp1\n";
 890     assertEquals(
 891             expected.replace("\n", System.getProperty("line.separator")),
 892             exported);
 893
 894     /*
 895      * remove threshold and check sf2 is exported
 896      */
 897     fc.setAboveThreshold(false);
 898     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 899             false);
 900     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 901             + "STARTGROUP\tgrp1\n"
 902             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 903             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 904             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 905             + "ENDGROUP\tgrp2\n";
 906     assertEquals(fixLineEnd(expected), exported);
 907
 908     /*
 909      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 910      */
 911     FeatureMatcherSetI filter = new FeatureMatcherSet();
 912     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 913             "clin_sig"));
 914     fr.setFeatureFilter("METAL", filter);
 915     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 916             false);
 917     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 918     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 919             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 920             + "STARTGROUP\tgrp2\n"
 921             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 922             + "ENDGROUP\tgrp2\n";
 923     assertEquals(fixLineEnd(expected), exported);
 924   }
 925 }