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;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465\n"
 276             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 277     FeaturesFile featuresFile = new FeaturesFile(gffData,
 278             DataSourceType.PASTE);
 279     assertTrue("Failed to parse features file",
 280             featuresFile.parse(al.getDataset(), colours, true));
 281
 282     // verify feature on FER_CAPAA
 283     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 284             .getSequenceFeatures();
 285     assertEquals(1, sfs.size());
 286     SequenceFeature sf = sfs.get(0);
 287     // description parsed from Note attribute
 288     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 289     assertEquals(39, sf.begin);
 290     assertEquals(39, sf.end);
 291     assertEquals("uniprot", sf.featureGroup);
 292     assertEquals("METAL", sf.type);
 293     assertEquals(4, sf.otherDetails.size());
 294     assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465",
 295             sf.otherDetails.get("evidence"));
 296     assertEquals("Iron-sulfur (2Fe-2S),another note",
 297             sf.otherDetails.get("Note"));
 298     assertEquals(".", sf.otherDetails.get("STRAND"));
 299     assertEquals(".", sf.otherDetails.get("!Phase"));
 300
 301     // verify feature on FER1_SOLLC1
 302     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 303     assertEquals(1, sfs.size());
 304     sf = sfs.get(0);
 305     // ID used for description if available
 306     assertEquals("$23", sf.description);
 307     assertEquals(55, sf.begin);
 308     assertEquals(130, sf.end);
 309     assertEquals("uniprot", sf.featureGroup);
 310     assertEquals("Pfam", sf.type);
 311     assertEquals(3f, sf.getScore(), 0.001f);
 312   }
 313
 314   /**
 315    * Test parsing a features file with Jalview format features (but no colour
 316    * descriptors or startgroup to give the hint not to parse as GFF)
 317    *
 318    * @throws Exception
 319    */
 320   @Test(groups = { "Functional" })
 321   public void testParse_jalviewFeaturesOnly() throws Exception
 322   {
 323     File f = new File("examples/uniref50.fa");
 324     AlignmentI al = readAlignmentFile(f);
 325     AlignFrame af = new AlignFrame(al, 500, 500);
 326     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 327             .getFeatureColours();
 328
 329     /*
 330      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 331      */
 332     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 333             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 334     FeaturesFile featuresFile = new FeaturesFile(featureData,
 335             DataSourceType.PASTE);
 336     assertTrue("Failed to parse features file",
 337             featuresFile.parse(al.getDataset(), colours, true));
 338
 339     // verify FER_CAPAA feature
 340     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 341             .getSequenceFeatures();
 342     assertEquals(1, sfs.size());
 343     SequenceFeature sf = sfs.get(0);
 344     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 345     assertEquals(39, sf.begin);
 346     assertEquals(39, sf.end);
 347     assertEquals("METAL", sf.type);
 348
 349     // verify FER1_SOLLC feature
 350     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 351     assertEquals(1, sfs.size());
 352     sf = sfs.get(0);
 353     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 354     assertEquals(86, sf.begin);
 355     assertEquals(87, sf.end);
 356     assertEquals("METALLIC", sf.type);
 357   }
 358
 359   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 360   {
 361     assertEquals("no sequences extracted from GFF3 file", 2,
 362             dataset.getHeight());
 363
 364     SequenceI seq1 = dataset.findName("seq1");
 365     SequenceI seq2 = dataset.findName("seq2");
 366     assertNotNull(seq1);
 367     assertNotNull(seq2);
 368     assertFalse(
 369             "Failed to replace dummy seq1 with real sequence",
 370             seq1 instanceof SequenceDummy
 371                     && ((SequenceDummy) seq1).isDummy());
 372     assertFalse(
 373             "Failed to replace dummy seq2 with real sequence",
 374             seq2 instanceof SequenceDummy
 375                     && ((SequenceDummy) seq2).isDummy());
 376     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 377     assertFalse("dummy replacement buggy for seq1",
 378             placeholderseq.equals(seq1.getSequenceAsString()));
 379     assertFalse("dummy replacement buggy for seq2",
 380             placeholderseq.equals(seq2.getSequenceAsString()));
 381     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 382     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 383             .size());
 384     assertTrue(seq2.getSequenceFeatures().isEmpty());
 385     assertEquals(
 386             "Wrong number of features",
 387             0,
 388             seq2.getSequenceFeatures() == null ? 0 : seq2
 389                     .getSequenceFeatures().size());
 390     assertTrue(
 391             "Expected at least one CDNA/Protein mapping for seq1",
 392             dataset.getCodonFrame(seq1) != null
 393                     && dataset.getCodonFrame(seq1).size() > 0);
 394
 395   }
 396
 397   @Test(groups = { "Functional" })
 398   public void readGff3File() throws IOException
 399   {
 400     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 401             DataSourceType.FILE);
 402     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 403     gffreader.addProperties(dataset);
 404     checkDatasetfromSimpleGff3(dataset);
 405   }
 406
 407   @Test(groups = { "Functional" })
 408   public void simpleGff3FileClass() throws IOException
 409   {
 410     AlignmentI dataset = new Alignment(new SequenceI[] {});
 411     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 412             DataSourceType.FILE);
 413
 414     boolean parseResult = ffile.parse(dataset, null, false, false);
 415     assertTrue("return result should be true", parseResult);
 416     checkDatasetfromSimpleGff3(dataset);
 417   }
 418
 419   @Test(groups = { "Functional" })
 420   public void simpleGff3FileLoader() throws IOException
 421   {
 422     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 423             simpleGffFile, DataSourceType.FILE);
 424     assertTrue(
 425             "Didn't read the alignment into an alignframe from Gff3 File",
 426             af != null);
 427     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 428   }
 429
 430   @Test(groups = { "Functional" })
 431   public void simpleGff3RelaxedIdMatching() throws IOException
 432   {
 433     AlignmentI dataset = new Alignment(new SequenceI[] {});
 434     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 435             DataSourceType.FILE);
 436
 437     boolean parseResult = ffile.parse(dataset, null, false, true);
 438     assertTrue("return result (relaxedID matching) should be true",
 439             parseResult);
 440     checkDatasetfromSimpleGff3(dataset);
 441   }
 442
 443   @Test(groups = { "Functional" })
 444   public void testPrintJalviewFormat() throws Exception
 445   {
 446     File f = new File("examples/uniref50.fa");
 447     AlignmentI al = readAlignmentFile(f);
 448     AlignFrame af = new AlignFrame(al, 500, 500);
 449     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 450             .getFeatureColours();
 451     String features = "METAL\tcc9900\n"
 452             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 453             + "Pfam\tred\n"
 454             + "STARTGROUP\tuniprot\n"
 455             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 456             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 457             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 458             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 459             + "ENDGROUP\tuniprot\n";
 460     FeaturesFile featuresFile = new FeaturesFile(features,
 461             DataSourceType.PASTE);
 462     featuresFile.parse(al.getDataset(), colours, false);
 463
 464     /*
 465      * add positional and non-positional features with null and
 466      * empty feature group to check handled correctly
 467      */
 468     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 469     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 470             null));
 471     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 472             Float.NaN, null));
 473     seq = al.getSequenceAt(2); // FER1_SOLLC
 474     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 475             Float.NaN, ""));
 476     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 477             -2.6f, ""));
 478
 479     /*
 480      * first with no features displayed, exclude non-positional features
 481      */
 482     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 483     String exported = featuresFile
 484             .printJalviewFormat(al.getSequencesArray(), fr, false, false);
 485     String expected = "No Features Visible";
 486     assertEquals(expected, exported);
 487
 488     /*
 489      * include non-positional features, but still no positional features
 490      */
 491     fr.setGroupVisibility("uniprot", true);
 492     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 493             true, false);
 494     expected = "\nSTARTGROUP\tuniprot\n"
 495             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 496             + "ENDGROUP\tuniprot\n\n"
 497             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 498             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 499     assertEquals(expected, exported);
 500
 501     /*
 502      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 503      */
 504     fr.setVisible("METAL");
 505     fr.setVisible("GAMMA-TURN");
 506     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 507             false, false);
 508     expected = "METAL\tcc9900\n"
 509             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 510             + "\nSTARTGROUP\tuniprot\n"
 511             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 512             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 513             + "ENDGROUP\tuniprot\n";
 514     assertEquals(expected, exported);
 515
 516     /*
 517      * now set Pfam visible
 518      */
 519     fr.setVisible("Pfam");
 520     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 521             false, false);
 522     /*
 523      * features are output within group, ordered by sequence and type
 524      */
 525     expected = "METAL\tcc9900\n"
 526             + "Pfam\tff0000\n"
 527             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 528             + "\nSTARTGROUP\tuniprot\n"
 529             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 530             + "<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"
 531             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 532             + "ENDGROUP\tuniprot\n"
 533             // null / empty group features are output after named groups
 534             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 535             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 536     assertEquals(expected, exported);
 537
 538     /*
 539      * hide uniprot group
 540      */
 541     fr.setGroupVisibility("uniprot", false);
 542     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 543             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 544             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 545             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 546     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 547             false, false);
 548     assertEquals(expected, exported);
 549
 550     /*
 551      * include non-positional (overrides group not shown)
 552      */
 553     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 554             true, false);
 555     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 556             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 557             + "\nSTARTGROUP\tuniprot\n"
 558             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 559             + "ENDGROUP\tuniprot\n"
 560             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 561             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 562             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 563             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 564     assertEquals(expected, exported);
 565   }
 566
 567   @Test(groups = { "Functional" })
 568   public void testPrintGffFormat() throws Exception
 569   {
 570     File f = new File("examples/uniref50.fa");
 571     AlignmentI al = readAlignmentFile(f);
 572     AlignFrame af = new AlignFrame(al, 500, 500);
 573
 574     /*
 575      * no features
 576      */
 577     FeaturesFile featuresFile = new FeaturesFile();
 578     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 579             .getFeatureRenderer();
 580     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 581             fr, false, false);
 582     String gffHeader = "##gff-version 2\n";
 583     assertEquals(gffHeader, exported);
 584     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 585             true, false);
 586     assertEquals(gffHeader, exported);
 587
 588     /*
 589      * add some features
 590      */
 591     al.getSequenceAt(0).addSequenceFeature(
 592             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 593     al.getSequenceAt(0).addSequenceFeature(
 594             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 595     al.getSequenceAt(1)
 596             .addSequenceFeature(
 597                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 598                             "s3dm"));
 599     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 600             "Uniprot");
 601     sf.setStrand("+");
 602     sf.setPhase("2");
 603     sf.setValue("x", "y");
 604     sf.setValue("black", "white");
 605     al.getSequenceAt(1).addSequenceFeature(sf);
 606
 607     /*
 608      * 'discover' features then hide all feature types
 609      */
 610     fr.findAllFeatures(true);
 611     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 612     FeatureColourI fc = new FeatureColour(Color.PINK);
 613     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 614     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 615     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 616     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 617     fr.setFeaturePriority(data);
 618
 619     /*
 620      * with no features displayed, exclude non-positional features
 621      */
 622     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 623             false, false);
 624     assertEquals(gffHeader, exported);
 625
 626     /*
 627      * include non-positional features
 628      */
 629     fr.setGroupVisibility("Uniprot", true);
 630     fr.setGroupVisibility("s3dm", false);
 631     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 632             true, false);
 633     String expected = gffHeader
 634             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 635     assertEquals(expected, exported);
 636
 637     /*
 638      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 639      * only Uniprot group visible here...
 640      */
 641     fr.setVisible("METAL");
 642     fr.setVisible("GAMMA-TURN");
 643     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 644             false, false);
 645     // METAL feature has null group: description used for column 2
 646     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 647     assertEquals(expected, exported);
 648
 649     /*
 650      * set s3dm group visible
 651      */
 652     fr.setGroupVisibility("s3dm", true);
 653     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 654             false, false);
 655     // METAL feature has null group: description used for column 2
 656     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 657             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 658     assertEquals(expected, exported);
 659
 660     /*
 661      * now set Pfam visible
 662      */
 663     fr.setVisible("Pfam");
 664     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 665             false, false);
 666     // Pfam feature columns include strand(+), phase(2), attributes
 667     expected = gffHeader
 668             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 669             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
 670             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 671     assertEquals(expected, exported);
 672   }
 673
 674   /**
 675    * Test for parsing of feature filters as represented in a Jalview features
 676    * file
 677    *
 678    * @throws Exception
 679    */
 680   @Test(groups = { "Functional" })
 681   public void testParseFilters() throws Exception
 682   {
 683     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 684     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 685             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 686     FeaturesFile featuresFile = new FeaturesFile(text,
 687             DataSourceType.PASTE);
 688     featuresFile.parseFilters(filters);
 689     assertEquals(filters.size(), 2);
 690
 691     FeatureMatcherSetI fm = filters.get("sequence_variant");
 692     assertNotNull(fm);
 693     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 694     FeatureMatcherI matcher = matchers.next();
 695     assertFalse(matchers.hasNext());
 696     String[] attributes = matcher.getAttribute();
 697     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 698     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 699     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 700
 701     fm = filters.get("missense_variant");
 702     assertNotNull(fm);
 703     matchers = fm.getMatchers().iterator();
 704     matcher = matchers.next();
 705     assertTrue(matcher.isByLabel());
 706     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 707     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 708     matcher = matchers.next();
 709     assertTrue(matcher.isByScore());
 710     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 711     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 712     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 713
 714     assertFalse(matchers.hasNext());
 715   }
 716
 717   @Test(groups = { "Functional" })
 718   public void testOutputFeatureFilters()
 719   {
 720     FeaturesFile ff = new FeaturesFile();
 721     StringBuilder sb = new StringBuilder();
 722     Map<String, FeatureColourI> visible = new HashMap<>();
 723     visible.put("pfam", new FeatureColour(Color.red));
 724     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 725
 726     // with no filters, nothing is output
 727     ff.outputFeatureFilters(sb, visible, featureFilters);
 728     assertEquals("", sb.toString());
 729
 730     // with filter for not visible features only, nothing is output
 731     FeatureMatcherSet filter = new FeatureMatcherSet();
 732     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 733     featureFilters.put("foobar", filter);
 734     ff.outputFeatureFilters(sb, visible, featureFilters);
 735     assertEquals("", sb.toString());
 736
 737     // with filters for visible feature types
 738     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 739     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 740             "PolyPhen"));
 741     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 742     featureFilters.put("pfam", filter2);
 743     visible.put("foobar", new FeatureColour(Color.blue));
 744     ff.outputFeatureFilters(sb, visible, featureFilters);
 745     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 746     assertEquals(expected, sb.toString());
 747   }
 748
 749   /**
 750    * Output as GFF should not include features which are not visible due to
 751    * colour threshold or feature filter settings
 752    *
 753    * @throws Exception
 754    */
 755   @Test(groups = { "Functional" })
 756   public void testPrintGffFormat_withFilters() throws Exception
 757   {
 758     File f = new File("examples/uniref50.fa");
 759     AlignmentI al = readAlignmentFile(f);
 760     AlignFrame af = new AlignFrame(al, 500, 500);
 761     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 762             null);
 763     sf1.setValue("clin_sig", "Likely Pathogenic");
 764     sf1.setValue("AF", "24");
 765     al.getSequenceAt(0).addSequenceFeature(sf1);
 766     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 767             null);
 768     sf2.setValue("clin_sig", "Benign");
 769     sf2.setValue("AF", "46");
 770     al.getSequenceAt(0).addSequenceFeature(sf2);
 771
 772     FeaturesFile featuresFile = new FeaturesFile();
 773     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 774     final String gffHeader = "##gff-version 2\n";
 775
 776     fr.setVisible("METAL");
 777     fr.setColour("METAL", new FeatureColour(Color.PINK));
 778     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 779             fr, false, false);
 780     String expected = gffHeader
 781             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 782             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 783     assertEquals(expected, exported);
 784
 785     /*
 786      * now threshold to Score > 1.1 - should exclude sf2
 787      */
 788     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 789             Color.white, 0f, 2f);
 790     fc.setAboveThreshold(true);
 791     fc.setThreshold(1.1f);
 792     fr.setColour("METAL", fc);
 793     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 794             false, false);
 795     expected = gffHeader
 796             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
 797     assertEquals(expected, exported);
 798
 799     /*
 800      * remove threshold and check sf2 is exported
 801      */
 802     fc.setAboveThreshold(false);
 803     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 804             false, false);
 805     expected = gffHeader
 806             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 807             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 808     assertEquals(expected, exported);
 809
 810     /*
 811      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 812      */
 813     FeatureMatcherSetI filter = new FeatureMatcherSet();
 814     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 815             "clin_sig"));
 816     fr.setFeatureFilter("METAL", filter);
 817     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 818             false, false);
 819     expected = gffHeader
 820             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 821     assertEquals(expected, exported);
 822   }
 823
 824   /**
 825    * Output as Jalview should not include features which are not visible due to
 826    * colour threshold or feature filter settings
 827    *
 828    * @throws Exception
 829    */
 830   @Test(groups = { "Functional" })
 831   public void testPrintJalviewFormat_withFilters() throws Exception
 832   {
 833     File f = new File("examples/uniref50.fa");
 834     AlignmentI al = readAlignmentFile(f);
 835     AlignFrame af = new AlignFrame(al, 500, 500);
 836     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 837             "grp1");
 838     sf1.setValue("clin_sig", "Likely Pathogenic");
 839     sf1.setValue("AF", "24");
 840     al.getSequenceAt(0).addSequenceFeature(sf1);
 841     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 842             "grp2");
 843     sf2.setValue("clin_sig", "Benign");
 844     sf2.setValue("AF", "46");
 845     al.getSequenceAt(0).addSequenceFeature(sf2);
 846
 847     FeaturesFile featuresFile = new FeaturesFile();
 848     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 849     fr.findAllFeatures(true);
 850
 851     fr.setVisible("METAL");
 852     fr.setColour("METAL", new FeatureColour(Color.PINK));
 853     String exported = featuresFile.printJalviewFormat(
 854             al.getSequencesArray(),
 855             fr, false, false);
 856     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 857             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 858             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 859             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 860             + "ENDGROUP\tgrp2\n";
 861     assertEquals(expected, exported);
 862
 863     /*
 864      * now threshold to Score > 1.1 - should exclude sf2
 865      * (and there should be no empty STARTGROUP/ENDGROUP output)
 866      */
 867     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 868             Color.white, 0f, 2f);
 869     fc.setAboveThreshold(true);
 870     fc.setThreshold(1.1f);
 871     fr.setColour("METAL", fc);
 872     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 873             false, false);
 874     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 875             + "STARTGROUP\tgrp1\n"
 876             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 877             + "ENDGROUP\tgrp1\n";
 878     assertEquals(expected, exported);
 879
 880     /*
 881      * remove threshold and check sf2 is exported
 882      */
 883     fc.setAboveThreshold(false);
 884     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 885             false, false);
 886     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 887             + "STARTGROUP\tgrp1\n"
 888             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 889             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 890             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 891             + "ENDGROUP\tgrp2\n";
 892     assertEquals(expected, exported);
 893
 894     /*
 895      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 896      */
 897     FeatureMatcherSetI filter = new FeatureMatcherSet();
 898     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 899             "clin_sig"));
 900     fr.setFeatureFilter("METAL", filter);
 901     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 902             false, false);
 903     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 904     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 905             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 906             + "STARTGROUP\tgrp2\n"
 907             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 908             + "ENDGROUP\tgrp2\n";
 909     assertEquals(expected, exported);
 910   }
 911 }