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.structure.StructureSelectionManager;
  47 import jalview.util.matcher.Condition;
  48 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  49 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  50
  51 import java.awt.Color;
  52 import java.io.File;
  53 import java.io.IOException;
  54 import java.util.HashMap;
  55 import java.util.Iterator;
  56 import java.util.List;
  57 import java.util.Map;
  58
  59 import org.testng.annotations.AfterClass;
  60 import org.testng.annotations.BeforeClass;
  61 import org.testng.annotations.Test;
  62
  63 public class FeaturesFileTest
  64 {
  65   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  66
  67   @AfterClass(alwaysRun = true)
  68   public void tearDownAfterClass()
  69   {
  70     /*
  71      * remove any sequence mappings created so they don't pollute other tests
  72      */
  73     StructureSelectionManager ssm = StructureSelectionManager
  74             .getStructureSelectionManager(Desktop.instance);
  75     ssm.resetAll();
  76   }
  77
  78   @BeforeClass(alwaysRun = true)
  79   public void setUpJvOptionPane()
  80   {
  81     JvOptionPane.setInteractiveMode(false);
  82     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  83   }
  84
  85   @Test(groups = { "Functional" })
  86   public void testParse() throws Exception
  87   {
  88     File f = new File("examples/uniref50.fa");
  89     AlignmentI al = readAlignmentFile(f);
  90     AlignFrame af = new AlignFrame(al, 500, 500);
  91     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  92             .getFeatureColours();
  93     FeaturesFile featuresFile = new FeaturesFile(
  94             "examples/exampleFeatures.txt", DataSourceType.FILE);
  95     assertTrue("Test " + "Features file test"
  96             + "\nFailed to parse features file.",
  97             featuresFile.parse(al.getDataset(), colours, true));
  98
  99     /*
 100      * Refetch the colour map from the FeatureRenderer (to confirm it has been
 101      * updated - JAL-1904), and verify (some) feature group colours
 102      */
 103     colours = af.getFeatureRenderer().getFeatureColours();
 104     assertEquals("27 feature group colours not found", 27, colours.size());
 105     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
 106     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
 107     FeatureColourI kdColour = colours.get("kdHydrophobicity");
 108     assertTrue(kdColour.isGraduatedColour());
 109     assertTrue(kdColour.isAboveThreshold());
 110     assertEquals(-2f, kdColour.getThreshold());
 111
 112     /*
 113      * verify (some) features on sequences
 114      */
 115     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 116             .getSequenceFeatures(); // FER_CAPAA
 117     SequenceFeatures.sortFeatures(sfs, true);
 118     assertEquals(8, sfs.size());
 119
 120     /*
 121      * verify (in ascending start position order)
 122      */
 123     SequenceFeature sf = sfs.get(0);
 124     assertEquals("Pfam family%LINK%", sf.description);
 125     assertEquals(0, sf.begin);
 126     assertEquals(0, sf.end);
 127     assertEquals("uniprot", sf.featureGroup);
 128     assertEquals("Pfam", sf.type);
 129     assertEquals(1, sf.links.size());
 130     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 131             sf.links.get(0));
 132
 133     sf = sfs.get(1);
 134     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 135     assertEquals(3, sf.begin);
 136     assertEquals(93, sf.end);
 137     assertEquals("uniprot", sf.featureGroup);
 138     assertEquals("Cath", sf.type);
 139
 140     sf = sfs.get(2);
 141     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 142             sf.description);
 143     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 144             sf.links.get(0));
 145     assertEquals(8, sf.begin);
 146     assertEquals(83, sf.end);
 147     assertEquals("uniprot", sf.featureGroup);
 148     assertEquals("Pfam", sf.type);
 149
 150     sf = sfs.get(3);
 151     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 152     assertEquals(39, sf.begin);
 153     assertEquals(39, sf.end);
 154     assertEquals("uniprot", sf.featureGroup);
 155     assertEquals("METAL", sf.type);
 156
 157     sf = sfs.get(4);
 158     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 159     assertEquals(44, sf.begin);
 160     assertEquals(44, sf.end);
 161     assertEquals("uniprot", sf.featureGroup);
 162     assertEquals("METAL", sf.type);
 163
 164     sf = sfs.get(5);
 165     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 166     assertEquals(47, sf.begin);
 167     assertEquals(47, sf.end);
 168     assertEquals("uniprot", sf.featureGroup);
 169     assertEquals("METAL", sf.type);
 170
 171     sf = sfs.get(6);
 172     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 173     assertEquals(77, sf.begin);
 174     assertEquals(77, sf.end);
 175     assertEquals("uniprot", sf.featureGroup);
 176     assertEquals("METAL", sf.type);
 177
 178     sf = sfs.get(7);
 179     assertEquals(
 180             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 181             sf.description);
 182     assertEquals(
 183             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 184             sf.links.get(0));
 185     assertEquals(89, sf.begin);
 186     assertEquals(89, sf.end);
 187     assertEquals("netphos", sf.featureGroup);
 188     assertEquals("PHOSPHORYLATION (T)", sf.type);
 189   }
 190
 191   /**
 192    * Test parsing a features file with a mix of Jalview and GFF formatted
 193    * content
 194    *
 195    * @throws Exception
 196    */
 197   @Test(groups = { "Functional" })
 198   public void testParse_mixedJalviewGff() throws Exception
 199   {
 200     File f = new File("examples/uniref50.fa");
 201     AlignmentI al = readAlignmentFile(f);
 202     AlignFrame af = new AlignFrame(al, 500, 500);
 203     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 204             .getFeatureColours();
 205     // GFF2 uses space as name/value separator in column 9
 206     String gffData = "METAL\tcc9900\n"
 207             + "GFF\n"
 208             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 209             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 210     FeaturesFile featuresFile = new FeaturesFile(gffData,
 211             DataSourceType.PASTE);
 212     assertTrue("Failed to parse features file",
 213             featuresFile.parse(al.getDataset(), colours, true));
 214
 215     // verify colours read or synthesized
 216     colours = af.getFeatureRenderer().getFeatureColours();
 217     assertEquals("1 feature group colours not found", 1, colours.size());
 218     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 219
 220     // verify feature on FER_CAPAA
 221     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 222             .getSequenceFeatures();
 223     assertEquals(1, sfs.size());
 224     SequenceFeature sf = sfs.get(0);
 225     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 226     assertEquals(44, sf.begin);
 227     assertEquals(45, sf.end);
 228     assertEquals("uniprot", sf.featureGroup);
 229     assertEquals("METAL", sf.type);
 230     assertEquals(4f, sf.getScore(), 0.001f);
 231
 232     // verify feature on FER1_SOLLC
 233     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 234     assertEquals(1, sfs.size());
 235     sf = sfs.get(0);
 236     assertEquals("uniprot", sf.description);
 237     assertEquals(55, sf.begin);
 238     assertEquals(130, sf.end);
 239     assertEquals("uniprot", sf.featureGroup);
 240     assertEquals("Pfam", sf.type);
 241     assertEquals(2f, sf.getScore(), 0.001f);
 242   }
 243
 244   public static AlignmentI readAlignmentFile(File f) throws IOException
 245   {
 246     System.out.println("Reading file: " + f);
 247     String ff = f.getPath();
 248     FormatAdapter rf = new FormatAdapter();
 249
 250     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 251             new IdentifyFile().identify(ff, DataSourceType.FILE));
 252
 253     al.setDataset(null); // creates dataset sequences
 254     assertNotNull("Couldn't read supplied alignment data.", al);
 255     return al;
 256   }
 257
 258   /**
 259    * Test parsing a features file with GFF formatted content only
 260    *
 261    * @throws Exception
 262    */
 263   @Test(groups = { "Functional" })
 264   public void testParse_pureGff3() throws Exception
 265   {
 266     File f = new File("examples/uniref50.fa");
 267     AlignmentI al = readAlignmentFile(f);
 268     AlignFrame af = new AlignFrame(al, 500, 500);
 269     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 270             .getFeatureColours();
 271     // GFF3 uses '=' separator for name/value pairs in column 9
 272     // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
 273     String gffData = "##gff-version 3\n"
 274             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 275             + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
 276             + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
 277             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 278     FeaturesFile featuresFile = new FeaturesFile(gffData,
 279             DataSourceType.PASTE);
 280     assertTrue("Failed to parse features file",
 281             featuresFile.parse(al.getDataset(), colours, true));
 282
 283     // verify feature on FER_CAPAA
 284     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 285             .getSequenceFeatures();
 286     assertEquals(1, sfs.size());
 287     SequenceFeature sf = sfs.get(0);
 288     // description parsed from Note attribute
 289     assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
 290             sf.description);
 291     assertEquals(39, sf.begin);
 292     assertEquals(39, sf.end);
 293     assertEquals("uniprot", sf.featureGroup);
 294     assertEquals("METAL", sf.type);
 295     assertEquals(5, sf.otherDetails.size());
 296     assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
 297             sf.getValue("evidence"));
 298     assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
 299             sf.getValue("Note"));
 300     assertEquals("21", sf.getValueAsString("CSQ", "AF"));
 301     assertEquals("benign,possibly_damaging",
 302             sf.getValueAsString("CSQ", "POLYPHEN"));
 303     assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
 304     // todo change STRAND and !Phase into fields of SequenceFeature instead
 305     assertEquals(".", sf.otherDetails.get("STRAND"));
 306     assertEquals(0, sf.getStrand());
 307     assertEquals(".", sf.getPhase());
 308
 309     // verify feature on FER1_SOLLC1
 310     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 311     assertEquals(1, sfs.size());
 312     sf = sfs.get(0);
 313     // ID used for description if available
 314     assertEquals("$23", sf.description);
 315     assertEquals(55, sf.begin);
 316     assertEquals(130, sf.end);
 317     assertEquals("uniprot", sf.featureGroup);
 318     assertEquals("Pfam", sf.type);
 319     assertEquals(3f, sf.getScore(), 0.001f);
 320   }
 321
 322   /**
 323    * Test parsing a features file with Jalview format features (but no colour
 324    * descriptors or startgroup to give the hint not to parse as GFF)
 325    *
 326    * @throws Exception
 327    */
 328   @Test(groups = { "Functional" })
 329   public void testParse_jalviewFeaturesOnly() throws Exception
 330   {
 331     File f = new File("examples/uniref50.fa");
 332     AlignmentI al = readAlignmentFile(f);
 333     AlignFrame af = new AlignFrame(al, 500, 500);
 334     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 335             .getFeatureColours();
 336
 337     /*
 338      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 339      */
 340     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 341             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 342     FeaturesFile featuresFile = new FeaturesFile(featureData,
 343             DataSourceType.PASTE);
 344     assertTrue("Failed to parse features file",
 345             featuresFile.parse(al.getDataset(), colours, true));
 346
 347     // verify FER_CAPAA feature
 348     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 349             .getSequenceFeatures();
 350     assertEquals(1, sfs.size());
 351     SequenceFeature sf = sfs.get(0);
 352     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 353     assertEquals(39, sf.begin);
 354     assertEquals(39, sf.end);
 355     assertEquals("METAL", sf.type);
 356
 357     // verify FER1_SOLLC feature
 358     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 359     assertEquals(1, sfs.size());
 360     sf = sfs.get(0);
 361     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 362     assertEquals(86, sf.begin);
 363     assertEquals(87, sf.end);
 364     assertEquals("METALLIC", sf.type);
 365   }
 366
 367   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 368   {
 369     assertEquals("no sequences extracted from GFF3 file", 2,
 370             dataset.getHeight());
 371
 372     SequenceI seq1 = dataset.findName("seq1");
 373     SequenceI seq2 = dataset.findName("seq2");
 374     assertNotNull(seq1);
 375     assertNotNull(seq2);
 376     assertFalse(
 377             "Failed to replace dummy seq1 with real sequence",
 378             seq1 instanceof SequenceDummy
 379                     && ((SequenceDummy) seq1).isDummy());
 380     assertFalse(
 381             "Failed to replace dummy seq2 with real sequence",
 382             seq2 instanceof SequenceDummy
 383                     && ((SequenceDummy) seq2).isDummy());
 384     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 385     assertFalse("dummy replacement buggy for seq1",
 386             placeholderseq.equals(seq1.getSequenceAsString()));
 387     assertFalse("dummy replacement buggy for seq2",
 388             placeholderseq.equals(seq2.getSequenceAsString()));
 389     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 390     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 391             .size());
 392     assertTrue(seq2.getSequenceFeatures().isEmpty());
 393     assertEquals(
 394             "Wrong number of features",
 395             0,
 396             seq2.getSequenceFeatures() == null ? 0 : seq2
 397                     .getSequenceFeatures().size());
 398     assertTrue(
 399             "Expected at least one CDNA/Protein mapping for seq1",
 400             dataset.getCodonFrame(seq1) != null
 401                     && dataset.getCodonFrame(seq1).size() > 0);
 402
 403   }
 404
 405   @Test(groups = { "Functional" })
 406   public void readGff3File() throws IOException
 407   {
 408     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 409             DataSourceType.FILE);
 410     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 411     gffreader.addProperties(dataset);
 412     checkDatasetfromSimpleGff3(dataset);
 413   }
 414
 415   @Test(groups = { "Functional" })
 416   public void simpleGff3FileClass() throws IOException
 417   {
 418     AlignmentI dataset = new Alignment(new SequenceI[] {});
 419     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 420             DataSourceType.FILE);
 421
 422     boolean parseResult = ffile.parse(dataset, null, false, false);
 423     assertTrue("return result should be true", parseResult);
 424     checkDatasetfromSimpleGff3(dataset);
 425   }
 426
 427   @Test(groups = { "Functional" })
 428   public void simpleGff3FileLoader() throws IOException
 429   {
 430     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 431             simpleGffFile, DataSourceType.FILE);
 432     assertTrue(
 433             "Didn't read the alignment into an alignframe from Gff3 File",
 434             af != null);
 435     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 436   }
 437
 438   @Test(groups = { "Functional" })
 439   public void simpleGff3RelaxedIdMatching() throws IOException
 440   {
 441     AlignmentI dataset = new Alignment(new SequenceI[] {});
 442     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 443             DataSourceType.FILE);
 444
 445     boolean parseResult = ffile.parse(dataset, null, false, true);
 446     assertTrue("return result (relaxedID matching) should be true",
 447             parseResult);
 448     checkDatasetfromSimpleGff3(dataset);
 449   }
 450
 451   @Test(groups = { "Functional" })
 452   public void testPrintJalviewFormat() throws Exception
 453   {
 454     File f = new File("examples/uniref50.fa");
 455     AlignmentI al = readAlignmentFile(f);
 456     AlignFrame af = new AlignFrame(al, 500, 500);
 457     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 458             .getFeatureColours();
 459     String features = "METAL\tcc9900\n"
 460             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 461             + "Pfam\tred\n"
 462             + "STARTGROUP\tuniprot\n"
 463             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 464             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 465             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 466             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 467             + "ENDGROUP\tuniprot\n";
 468     FeaturesFile featuresFile = new FeaturesFile(features,
 469             DataSourceType.PASTE);
 470     featuresFile.parse(al.getDataset(), colours, false);
 471
 472     /*
 473      * add positional and non-positional features with null and
 474      * empty feature group to check handled correctly
 475      */
 476     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 477     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 478             null));
 479     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 480             Float.NaN, null));
 481     seq = al.getSequenceAt(2); // FER1_SOLLC
 482     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 483             Float.NaN, ""));
 484     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 485             -2.6f, ""));
 486
 487     /*
 488      * first with no features displayed, exclude non-positional features
 489      */
 490     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 491     String exported = featuresFile
 492             .printJalviewFormat(al.getSequencesArray(), fr, false, false);
 493     String expected = "No Features Visible";
 494     assertEquals(expected, exported);
 495
 496     /*
 497      * include non-positional features, but still no positional features
 498      */
 499     fr.setGroupVisibility("uniprot", true);
 500     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 501             true, false);
 502     expected = "\nSTARTGROUP\tuniprot\n"
 503             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 504             + "ENDGROUP\tuniprot\n\n"
 505             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 506             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 507     assertEquals(expected, exported);
 508
 509     /*
 510      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 511      */
 512     fr.setVisible("METAL");
 513     fr.setVisible("GAMMA-TURN");
 514     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 515             false, false);
 516     expected = "METAL\tcc9900\n"
 517             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 518             + "\nSTARTGROUP\tuniprot\n"
 519             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 520             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 521             + "ENDGROUP\tuniprot\n";
 522     assertEquals(expected, exported);
 523
 524     /*
 525      * now set Pfam visible
 526      */
 527     fr.setVisible("Pfam");
 528     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 529             false, false);
 530     /*
 531      * features are output within group, ordered by sequence and type
 532      */
 533     expected = "METAL\tcc9900\n"
 534             + "Pfam\tff0000\n"
 535             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 536             + "\nSTARTGROUP\tuniprot\n"
 537             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 538             + "<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"
 539             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 540             + "ENDGROUP\tuniprot\n"
 541             // null / empty group features are output after named groups
 542             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 543             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 544     assertEquals(expected, exported);
 545
 546     /*
 547      * hide uniprot group
 548      */
 549     fr.setGroupVisibility("uniprot", false);
 550     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 551             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 552             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 553             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 554     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 555             false, false);
 556     assertEquals(expected, exported);
 557
 558     /*
 559      * include non-positional (overrides group not shown)
 560      */
 561     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 562             true, false);
 563     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 564             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 565             + "\nSTARTGROUP\tuniprot\n"
 566             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 567             + "ENDGROUP\tuniprot\n"
 568             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 569             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 570             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 571             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 572     assertEquals(expected, exported);
 573   }
 574
 575   @Test(groups = { "Functional" })
 576   public void testPrintGffFormat() throws Exception
 577   {
 578     File f = new File("examples/uniref50.fa");
 579     AlignmentI al = readAlignmentFile(f);
 580     AlignFrame af = new AlignFrame(al, 500, 500);
 581
 582     /*
 583      * no features
 584      */
 585     FeaturesFile featuresFile = new FeaturesFile();
 586     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 587             .getFeatureRenderer();
 588     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 589             fr, false, false);
 590     String gffHeader = "##gff-version 2\n";
 591     assertEquals(gffHeader, exported);
 592     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 593             true, false);
 594     assertEquals(gffHeader, exported);
 595
 596     /*
 597      * add some features
 598      */
 599     al.getSequenceAt(0).addSequenceFeature(
 600             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 601     al.getSequenceAt(0).addSequenceFeature(
 602             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 603     al.getSequenceAt(1)
 604             .addSequenceFeature(
 605                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 606                             "s3dm"));
 607     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 608             "Uniprot");
 609     sf.setStrand("+");
 610     sf.setPhase("2");
 611     sf.setValue("x", "y");
 612     sf.setValue("black", "white");
 613     Map<String, String> csq = new HashMap<>();
 614     csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
 615     csq.put("consequence", "missense_variant");
 616     sf.setValue("CSQ", csq);
 617     al.getSequenceAt(1).addSequenceFeature(sf);
 618
 619     /*
 620      * 'discover' features then hide all feature types
 621      */
 622     fr.findAllFeatures(true);
 623     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 624     FeatureColourI fc = new FeatureColour(Color.PINK);
 625     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 626     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 627     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 628     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 629     fr.setFeaturePriority(data);
 630
 631     /*
 632      * with no features displayed, exclude non-positional features
 633      */
 634     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 635             false, false);
 636     assertEquals(gffHeader, exported);
 637
 638     /*
 639      * include non-positional features
 640      */
 641     fr.setGroupVisibility("Uniprot", true);
 642     fr.setGroupVisibility("s3dm", false);
 643     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 644             true, false);
 645     String expected = gffHeader
 646             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 647     assertEquals(expected, exported);
 648
 649     /*
 650      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 651      * only Uniprot group visible here...
 652      */
 653     fr.setVisible("METAL");
 654     fr.setVisible("GAMMA-TURN");
 655     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 656             false, false);
 657     // METAL feature has null group: description used for column 2
 658     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 659     assertEquals(expected, exported);
 660
 661     /*
 662      * set s3dm group visible
 663      */
 664     fr.setGroupVisibility("s3dm", true);
 665     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 666             false, false);
 667     // METAL feature has null group: description used for column 2
 668     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 669             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 670     assertEquals(expected, exported);
 671
 672     /*
 673      * now set Pfam visible
 674      */
 675     fr.setVisible("Pfam");
 676     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 677             false, false);
 678     // Pfam feature columns include strand(+), phase(2), attributes
 679     expected = gffHeader
 680             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 681             // CSQ output as CSQ=att1=value1,att2=value2
 682             // note all commas are encoded here which is wrong - it should be
 683             // SIFT=benign,mostly benign,cloudy%2C with meatballs
 684             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
 685             + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
 686             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 687     assertEquals(expected, exported);
 688   }
 689
 690   /**
 691    * Test for parsing of feature filters as represented in a Jalview features
 692    * file
 693    *
 694    * @throws Exception
 695    */
 696   @Test(groups = { "Functional" })
 697   public void testParseFilters() throws Exception
 698   {
 699     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 700     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 701             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 702     FeaturesFile featuresFile = new FeaturesFile(text,
 703             DataSourceType.PASTE);
 704     featuresFile.parseFilters(filters);
 705     assertEquals(filters.size(), 2);
 706
 707     FeatureMatcherSetI fm = filters.get("sequence_variant");
 708     assertNotNull(fm);
 709     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 710     FeatureMatcherI matcher = matchers.next();
 711     assertFalse(matchers.hasNext());
 712     String[] attributes = matcher.getAttribute();
 713     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 714     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 715     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 716
 717     fm = filters.get("missense_variant");
 718     assertNotNull(fm);
 719     matchers = fm.getMatchers().iterator();
 720     matcher = matchers.next();
 721     assertTrue(matcher.isByLabel());
 722     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 723     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 724     matcher = matchers.next();
 725     assertTrue(matcher.isByScore());
 726     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 727     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 728     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 729
 730     assertFalse(matchers.hasNext());
 731   }
 732
 733   @Test(groups = { "Functional" })
 734   public void testOutputFeatureFilters()
 735   {
 736     FeaturesFile ff = new FeaturesFile();
 737     StringBuilder sb = new StringBuilder();
 738     Map<String, FeatureColourI> visible = new HashMap<>();
 739     visible.put("pfam", new FeatureColour(Color.red));
 740     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 741
 742     // with no filters, nothing is output
 743     ff.outputFeatureFilters(sb, visible, featureFilters);
 744     assertEquals("", sb.toString());
 745
 746     // with filter for not visible features only, nothing is output
 747     FeatureMatcherSet filter = new FeatureMatcherSet();
 748     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 749     featureFilters.put("foobar", filter);
 750     ff.outputFeatureFilters(sb, visible, featureFilters);
 751     assertEquals("", sb.toString());
 752
 753     // with filters for visible feature types
 754     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 755     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 756             "PolyPhen"));
 757     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 758     featureFilters.put("pfam", filter2);
 759     visible.put("foobar", new FeatureColour(Color.blue));
 760     ff.outputFeatureFilters(sb, visible, featureFilters);
 761     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 762     assertEquals(expected, sb.toString());
 763   }
 764
 765   /**
 766    * Output as GFF should not include features which are not visible due to
 767    * colour threshold or feature filter settings
 768    *
 769    * @throws Exception
 770    */
 771   @Test(groups = { "Functional" })
 772   public void testPrintGffFormat_withFilters() throws Exception
 773   {
 774     File f = new File("examples/uniref50.fa");
 775     AlignmentI al = readAlignmentFile(f);
 776     AlignFrame af = new AlignFrame(al, 500, 500);
 777     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 778             null);
 779     sf1.setValue("clin_sig", "Likely Pathogenic");
 780     sf1.setValue("AF", "24");
 781     al.getSequenceAt(0).addSequenceFeature(sf1);
 782     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 783             null);
 784     sf2.setValue("clin_sig", "Benign");
 785     sf2.setValue("AF", "46");
 786     al.getSequenceAt(0).addSequenceFeature(sf2);
 787
 788     FeaturesFile featuresFile = new FeaturesFile();
 789     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 790     final String gffHeader = "##gff-version 2\n";
 791
 792     fr.setVisible("METAL");
 793     fr.setColour("METAL", new FeatureColour(Color.PINK));
 794     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 795             fr, false, false);
 796     String expected = gffHeader
 797             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 798             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 799     assertEquals(expected, exported);
 800
 801     /*
 802      * now threshold to Score > 1.1 - should exclude sf2
 803      */
 804     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 805             Color.white, 0f, 2f);
 806     fc.setAboveThreshold(true);
 807     fc.setThreshold(1.1f);
 808     fr.setColour("METAL", fc);
 809     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 810             false, false);
 811     expected = gffHeader
 812             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
 813     assertEquals(expected, exported);
 814
 815     /*
 816      * remove threshold and check sf2 is exported
 817      */
 818     fc.setAboveThreshold(false);
 819     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 820             false, false);
 821     expected = gffHeader
 822             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 823             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 824     assertEquals(expected, exported);
 825
 826     /*
 827      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 828      */
 829     FeatureMatcherSetI filter = new FeatureMatcherSet();
 830     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 831             "clin_sig"));
 832     fr.setFeatureFilter("METAL", filter);
 833     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 834             false, false);
 835     expected = gffHeader
 836             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 837     assertEquals(expected, exported);
 838   }
 839
 840   /**
 841    * Output as Jalview should not include features which are not visible due to
 842    * colour threshold or feature filter settings
 843    *
 844    * @throws Exception
 845    */
 846   @Test(groups = { "Functional" })
 847   public void testPrintJalviewFormat_withFilters() throws Exception
 848   {
 849     File f = new File("examples/uniref50.fa");
 850     AlignmentI al = readAlignmentFile(f);
 851     AlignFrame af = new AlignFrame(al, 500, 500);
 852     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 853             "grp1");
 854     sf1.setValue("clin_sig", "Likely Pathogenic");
 855     sf1.setValue("AF", "24");
 856     al.getSequenceAt(0).addSequenceFeature(sf1);
 857     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 858             "grp2");
 859     sf2.setValue("clin_sig", "Benign");
 860     sf2.setValue("AF", "46");
 861     al.getSequenceAt(0).addSequenceFeature(sf2);
 862
 863     FeaturesFile featuresFile = new FeaturesFile();
 864     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 865     fr.findAllFeatures(true);
 866
 867     fr.setVisible("METAL");
 868     fr.setColour("METAL", new FeatureColour(Color.PINK));
 869     String exported = featuresFile.printJalviewFormat(
 870             al.getSequencesArray(),
 871             fr, false, false);
 872     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 873             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 874             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 875             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 876             + "ENDGROUP\tgrp2\n";
 877     assertEquals(expected, exported);
 878
 879     /*
 880      * now threshold to Score > 1.1 - should exclude sf2
 881      * (and there should be no empty STARTGROUP/ENDGROUP output)
 882      */
 883     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 884             Color.white, 0f, 2f);
 885     fc.setAboveThreshold(true);
 886     fc.setThreshold(1.1f);
 887     fr.setColour("METAL", fc);
 888     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 889             false, false);
 890     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 891             + "STARTGROUP\tgrp1\n"
 892             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 893             + "ENDGROUP\tgrp1\n";
 894     assertEquals(expected, exported);
 895
 896     /*
 897      * remove threshold and check sf2 is exported
 898      */
 899     fc.setAboveThreshold(false);
 900     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 901             false, false);
 902     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 903             + "STARTGROUP\tgrp1\n"
 904             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 905             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 906             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 907             + "ENDGROUP\tgrp2\n";
 908     assertEquals(expected, exported);
 909
 910     /*
 911      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 912      */
 913     FeatureMatcherSetI filter = new FeatureMatcherSet();
 914     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 915             "clin_sig"));
 916     fr.setFeatureFilter("METAL", filter);
 917     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 918             false, false);
 919     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 920     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 921             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 922             + "STARTGROUP\tgrp2\n"
 923             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 924             + "ENDGROUP\tgrp2\n";
 925     assertEquals(expected, exported);
 926   }
 927 }