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 java.awt.Color;
  31 import java.io.File;
  32 import java.io.IOException;
  33 import java.util.HashMap;
  34 import java.util.Iterator;
  35 import java.util.List;
  36 import java.util.Map;
  37
  38 import org.testng.annotations.AfterClass;
  39 import org.testng.annotations.BeforeClass;
  40 import org.testng.annotations.Test;
  41
  42 import jalview.api.FeatureColourI;
  43 import jalview.api.FeatureRenderer;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentI;
  46 import jalview.datamodel.SequenceDummy;
  47 import jalview.datamodel.SequenceFeature;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.datamodel.features.FeatureMatcher;
  50 import jalview.datamodel.features.FeatureMatcherI;
  51 import jalview.datamodel.features.FeatureMatcherSet;
  52 import jalview.datamodel.features.FeatureMatcherSetI;
  53 import jalview.datamodel.features.SequenceFeatures;
  54 import jalview.gui.AlignFrame;
  55 import jalview.gui.Desktop;
  56 import jalview.gui.JvOptionPane;
  57 import jalview.schemes.FeatureColour;
  58 import jalview.structure.StructureSelectionManager;
  59 import jalview.util.matcher.Condition;
  60 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  61 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  62 import junit.extensions.PA;
  63
  64 public class FeaturesFileTest
  65 {
  66   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
  67
  68   @AfterClass(alwaysRun = true)
  69   public void tearDownAfterClass()
  70   {
  71     /*
  72      * remove any sequence mappings created so they don't pollute other tests
  73      */
  74     StructureSelectionManager ssm = StructureSelectionManager
  75             .getStructureSelectionManager(Desktop.instance);
  76     ssm.resetAll();
  77   }
  78
  79   @BeforeClass(alwaysRun = true)
  80   public void setUpJvOptionPane()
  81   {
  82     JvOptionPane.setInteractiveMode(false);
  83     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  84   }
  85
  86   @Test(groups = { "Functional" })
  87   public void testParse() throws Exception
  88   {
  89     File f = new File("examples/uniref50.fa");
  90     AlignmentI al = readAlignmentFile(f);
  91     AlignFrame af = new AlignFrame(al, 500, 500);
  92     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  93             .getFeatureColours();
  94     FeaturesFile featuresFile = new FeaturesFile(
  95             "examples/exampleFeatures.txt", DataSourceType.FILE);
  96     assertTrue("Test " + "Features file test"
  97             + "\nFailed to parse features file.",
  98             featuresFile.parse(al.getDataset(), colours, true));
  99
 100     /*
 101      * Refetch the colour map from the FeatureRenderer (to confirm it has been
 102      * updated - JAL-1904), and verify (some) feature group colours
 103      */
 104     colours = af.getFeatureRenderer().getFeatureColours();
 105     assertEquals("27 feature group colours not found", 27, colours.size());
 106     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
 107     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
 108     FeatureColourI kdColour = colours.get("kdHydrophobicity");
 109     assertTrue(kdColour.isGraduatedColour());
 110     assertTrue(kdColour.isAboveThreshold());
 111     assertEquals(-2f, kdColour.getThreshold());
 112
 113     /*
 114      * verify (some) features on sequences
 115      */
 116     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 117             .getSequenceFeatures(); // FER_CAPAA
 118     SequenceFeatures.sortFeatures(sfs, true);
 119     assertEquals(8, sfs.size());
 120
 121     /*
 122      * verify (in ascending start position order)
 123      */
 124     SequenceFeature sf = sfs.get(0);
 125     assertEquals("Pfam family%LINK%", sf.description);
 126     assertEquals(0, sf.begin);
 127     assertEquals(0, sf.end);
 128     assertEquals("uniprot", sf.featureGroup);
 129     assertEquals("Pfam", sf.type);
 130     assertEquals(1, sf.links.size());
 131     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 132             sf.links.get(0));
 133
 134     sf = sfs.get(1);
 135     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 136     assertEquals(3, sf.begin);
 137     assertEquals(93, sf.end);
 138     assertEquals("uniprot", sf.featureGroup);
 139     assertEquals("Cath", sf.type);
 140
 141     sf = sfs.get(2);
 142     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 143             sf.description);
 144     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 145             sf.links.get(0));
 146     assertEquals(8, sf.begin);
 147     assertEquals(83, sf.end);
 148     assertEquals("uniprot", sf.featureGroup);
 149     assertEquals("Pfam", sf.type);
 150
 151     sf = sfs.get(3);
 152     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 153     assertEquals(39, sf.begin);
 154     assertEquals(39, sf.end);
 155     assertEquals("uniprot", sf.featureGroup);
 156     assertEquals("METAL", sf.type);
 157
 158     sf = sfs.get(4);
 159     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 160     assertEquals(44, sf.begin);
 161     assertEquals(44, sf.end);
 162     assertEquals("uniprot", sf.featureGroup);
 163     assertEquals("METAL", sf.type);
 164
 165     sf = sfs.get(5);
 166     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 167     assertEquals(47, sf.begin);
 168     assertEquals(47, sf.end);
 169     assertEquals("uniprot", sf.featureGroup);
 170     assertEquals("METAL", sf.type);
 171
 172     sf = sfs.get(6);
 173     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 174     assertEquals(77, sf.begin);
 175     assertEquals(77, sf.end);
 176     assertEquals("uniprot", sf.featureGroup);
 177     assertEquals("METAL", sf.type);
 178
 179     sf = sfs.get(7);
 180     assertEquals(
 181             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 182             sf.description);
 183     assertEquals(
 184             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 185             sf.links.get(0));
 186     assertEquals(89, sf.begin);
 187     assertEquals(89, sf.end);
 188     assertEquals("netphos", sf.featureGroup);
 189     assertEquals("PHOSPHORYLATION (T)", sf.type);
 190   }
 191
 192   /**
 193    * Test parsing a features file with a mix of Jalview and GFF formatted
 194    * content
 195    *
 196    * @throws Exception
 197    */
 198   @Test(groups = { "Functional" })
 199   public void testParse_mixedJalviewGff() throws Exception
 200   {
 201     File f = new File("examples/uniref50.fa");
 202     AlignmentI al = readAlignmentFile(f);
 203     AlignFrame af = new AlignFrame(al, 500, 500);
 204     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 205             .getFeatureColours();
 206     // GFF2 uses space as name/value separator in column 9
 207     String gffData = "METAL\tcc9900\n"
 208             + "GFF\n"
 209             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 210             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 211     FeaturesFile featuresFile = new FeaturesFile(gffData,
 212             DataSourceType.PASTE);
 213     assertTrue("Failed to parse features file",
 214             featuresFile.parse(al.getDataset(), colours, true));
 215
 216     // verify colours read or synthesized
 217     colours = af.getFeatureRenderer().getFeatureColours();
 218     assertEquals("1 feature group colours not found", 1, colours.size());
 219     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 220
 221     // verify feature on FER_CAPAA
 222     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 223             .getSequenceFeatures();
 224     assertEquals(1, sfs.size());
 225     SequenceFeature sf = sfs.get(0);
 226     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 227     assertEquals(44, sf.begin);
 228     assertEquals(45, sf.end);
 229     assertEquals("uniprot", sf.featureGroup);
 230     assertEquals("METAL", sf.type);
 231     assertEquals(4f, sf.getScore(), 0.001f);
 232
 233     // verify feature on FER1_SOLLC
 234     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 235     assertEquals(1, sfs.size());
 236     sf = sfs.get(0);
 237     assertEquals("uniprot", sf.description);
 238     assertEquals(55, sf.begin);
 239     assertEquals(130, sf.end);
 240     assertEquals("uniprot", sf.featureGroup);
 241     assertEquals("Pfam", sf.type);
 242     assertEquals(2f, sf.getScore(), 0.001f);
 243   }
 244
 245   public static AlignmentI readAlignmentFile(File f) throws IOException
 246   {
 247     System.out.println("Reading file: " + f);
 248     String ff = f.getPath();
 249     FormatAdapter rf = new FormatAdapter();
 250
 251     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 252             new IdentifyFile().identify(ff, DataSourceType.FILE));
 253
 254     al.setDataset(null); // creates dataset sequences
 255     assertNotNull("Couldn't read supplied alignment data.", al);
 256     return al;
 257   }
 258
 259   /**
 260    * Test parsing a features file with GFF formatted content only
 261    *
 262    * @throws Exception
 263    */
 264   @Test(groups = { "Functional" })
 265   public void testParse_pureGff3() throws Exception
 266   {
 267     File f = new File("examples/uniref50.fa");
 268     AlignmentI al = readAlignmentFile(f);
 269     AlignFrame af = new AlignFrame(al, 500, 500);
 270     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 271             .getFeatureColours();
 272     // GFF3 uses '=' separator for name/value pairs in column 9
 273     // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
 274     String gffData = "##gff-version 3\n"
 275             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 276             + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
 277             + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
 278             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 279     FeaturesFile featuresFile = new FeaturesFile(gffData,
 280             DataSourceType.PASTE);
 281     assertTrue("Failed to parse features file",
 282             featuresFile.parse(al.getDataset(), colours, true));
 283
 284     // verify feature on FER_CAPAA
 285     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 286             .getSequenceFeatures();
 287     assertEquals(1, sfs.size());
 288     SequenceFeature sf = sfs.get(0);
 289     // description parsed from Note attribute
 290     assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
 291             sf.description);
 292     assertEquals(39, sf.begin);
 293     assertEquals(39, sf.end);
 294     assertEquals("uniprot", sf.featureGroup);
 295     assertEquals("METAL", sf.type);
 296     assertEquals(5, sf.otherDetails.size());
 297     assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
 298             sf.getValue("evidence"));
 299     assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
 300             sf.getValue("Note"));
 301     assertEquals("21", sf.getValueAsString("CSQ", "AF"));
 302     assertEquals("benign,possibly_damaging",
 303             sf.getValueAsString("CSQ", "POLYPHEN"));
 304     assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
 305     // todo change STRAND and !Phase into fields of SequenceFeature instead
 306     assertEquals(".", sf.otherDetails.get("STRAND"));
 307     assertEquals(0, sf.getStrand());
 308     assertEquals(".", sf.getPhase());
 309
 310     // verify feature on FER1_SOLLC1
 311     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 312     assertEquals(1, sfs.size());
 313     sf = sfs.get(0);
 314     // ID used for description if available
 315     assertEquals("$23", sf.description);
 316     assertEquals(55, sf.begin);
 317     assertEquals(130, sf.end);
 318     assertEquals("uniprot", sf.featureGroup);
 319     assertEquals("Pfam", sf.type);
 320     assertEquals(3f, sf.getScore(), 0.001f);
 321   }
 322
 323   /**
 324    * Test parsing a features file with Jalview format features (but no colour
 325    * descriptors or startgroup to give the hint not to parse as GFF)
 326    *
 327    * @throws Exception
 328    */
 329   @Test(groups = { "Functional" })
 330   public void testParse_jalviewFeaturesOnly() throws Exception
 331   {
 332     File f = new File("examples/uniref50.fa");
 333     AlignmentI al = readAlignmentFile(f);
 334     AlignFrame af = new AlignFrame(al, 500, 500);
 335     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 336             .getFeatureColours();
 337
 338     /*
 339      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 340      */
 341     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 342             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 343     FeaturesFile featuresFile = new FeaturesFile(featureData,
 344             DataSourceType.PASTE);
 345     assertTrue("Failed to parse features file",
 346             featuresFile.parse(al.getDataset(), colours, true));
 347
 348     // verify FER_CAPAA feature
 349     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 350             .getSequenceFeatures();
 351     assertEquals(1, sfs.size());
 352     SequenceFeature sf = sfs.get(0);
 353     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 354     assertEquals(39, sf.begin);
 355     assertEquals(39, sf.end);
 356     assertEquals("METAL", sf.type);
 357
 358     // verify FER1_SOLLC feature
 359     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 360     assertEquals(1, sfs.size());
 361     sf = sfs.get(0);
 362     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 363     assertEquals(86, sf.begin);
 364     assertEquals(87, sf.end);
 365     assertEquals("METALLIC", sf.type);
 366   }
 367
 368   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 369   {
 370     assertEquals("no sequences extracted from GFF3 file", 2,
 371             dataset.getHeight());
 372
 373     SequenceI seq1 = dataset.findName("seq1");
 374     SequenceI seq2 = dataset.findName("seq2");
 375     assertNotNull(seq1);
 376     assertNotNull(seq2);
 377     assertFalse(
 378             "Failed to replace dummy seq1 with real sequence",
 379             seq1 instanceof SequenceDummy
 380                     && ((SequenceDummy) seq1).isDummy());
 381     assertFalse(
 382             "Failed to replace dummy seq2 with real sequence",
 383             seq2 instanceof SequenceDummy
 384                     && ((SequenceDummy) seq2).isDummy());
 385     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 386     assertFalse("dummy replacement buggy for seq1",
 387             placeholderseq.equals(seq1.getSequenceAsString()));
 388     assertFalse("dummy replacement buggy for seq2",
 389             placeholderseq.equals(seq2.getSequenceAsString()));
 390     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 391     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 392             .size());
 393     assertTrue(seq2.getSequenceFeatures().isEmpty());
 394     assertEquals(
 395             "Wrong number of features",
 396             0,
 397             seq2.getSequenceFeatures() == null ? 0 : seq2
 398                     .getSequenceFeatures().size());
 399     assertTrue(
 400             "Expected at least one CDNA/Protein mapping for seq1",
 401             dataset.getCodonFrame(seq1) != null
 402                     && dataset.getCodonFrame(seq1).size() > 0);
 403
 404   }
 405
 406   @Test(groups = { "Functional" })
 407   public void readGff3File() throws IOException
 408   {
 409     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 410             DataSourceType.FILE);
 411     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 412     gffreader.addProperties(dataset);
 413     checkDatasetfromSimpleGff3(dataset);
 414   }
 415
 416   @Test(groups = { "Functional" })
 417   public void simpleGff3FileClass() throws IOException
 418   {
 419     AlignmentI dataset = new Alignment(new SequenceI[] {});
 420     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 421             DataSourceType.FILE);
 422
 423     boolean parseResult = ffile.parse(dataset, null, false, false);
 424     assertTrue("return result should be true", parseResult);
 425     checkDatasetfromSimpleGff3(dataset);
 426   }
 427
 428   @Test(groups = { "Functional" })
 429   public void simpleGff3FileLoader() throws IOException
 430   {
 431     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 432             simpleGffFile, DataSourceType.FILE);
 433     assertTrue(
 434             "Didn't read the alignment into an alignframe from Gff3 File",
 435             af != null);
 436     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 437   }
 438
 439   @Test(groups = { "Functional" })
 440   public void simpleGff3RelaxedIdMatching() throws IOException
 441   {
 442     AlignmentI dataset = new Alignment(new SequenceI[] {});
 443     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 444             DataSourceType.FILE);
 445
 446     boolean parseResult = ffile.parse(dataset, null, false, true);
 447     assertTrue("return result (relaxedID matching) should be true",
 448             parseResult);
 449     checkDatasetfromSimpleGff3(dataset);
 450   }
 451
 452   @Test(groups = { "Functional" })
 453   public void testPrintJalviewFormat() throws Exception
 454   {
 455     File f = new File("examples/uniref50.fa");
 456     AlignmentI al = readAlignmentFile(f);
 457     AlignFrame af = new AlignFrame(al, 500, 500);
 458     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 459             .getFeatureColours();
 460     String features = "METAL\tcc9900\n"
 461             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 462             + "Pfam\tred\n"
 463             + "STARTGROUP\tuniprot\n"
 464             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 465             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 466             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 467             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 468             + "ENDGROUP\tuniprot\n";
 469     FeaturesFile featuresFile = new FeaturesFile(features,
 470             DataSourceType.PASTE);
 471     featuresFile.parse(al.getDataset(), colours, false);
 472
 473     /*
 474      * add positional and non-positional features with null and
 475      * empty feature group to check handled correctly
 476      */
 477     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 478     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 479             null));
 480     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 481             Float.NaN, null));
 482     seq = al.getSequenceAt(2); // FER1_SOLLC
 483     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 484             Float.NaN, ""));
 485     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 486             -2.6f, ""));
 487
 488     /*
 489      * first with no features displayed, exclude non-positional features
 490      */
 491     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 492     String exported = featuresFile
 493             .printJalviewFormat(al.getSequencesArray(), fr, false, false);
 494     String expected = "No Features Visible";
 495     assertEquals(expected, exported);
 496
 497     /*
 498      * include non-positional features, but still no positional features
 499      */
 500     fr.setGroupVisibility("uniprot", true);
 501     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 502             true, false);
 503     expected = "\nSTARTGROUP\tuniprot\n"
 504             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 505             + "ENDGROUP\tuniprot\n\n"
 506             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 507             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 508     assertEquals(expected, exported);
 509
 510     /*
 511      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 512      */
 513     fr.setVisible("METAL");
 514     fr.setVisible("GAMMA-TURN");
 515     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 516             false, false);
 517     expected = "METAL\tcc9900\n"
 518             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 519             + "\nSTARTGROUP\tuniprot\n"
 520             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 521             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 522             + "ENDGROUP\tuniprot\n";
 523     assertEquals(expected, exported);
 524
 525     /*
 526      * now set Pfam visible
 527      */
 528     fr.setVisible("Pfam");
 529     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 530             false, false);
 531     /*
 532      * features are output within group, ordered by sequence and type
 533      */
 534     expected = "METAL\tcc9900\n"
 535             + "Pfam\tff0000\n"
 536             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 537             + "\nSTARTGROUP\tuniprot\n"
 538             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 539             + "<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"
 540             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 541             + "ENDGROUP\tuniprot\n"
 542             // null / empty group features are output after named groups
 543             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 544             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 545     assertEquals(expected, exported);
 546
 547     /*
 548      * hide uniprot group
 549      */
 550     fr.setGroupVisibility("uniprot", false);
 551     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 552             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 553             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 554             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 555     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 556             false, false);
 557     assertEquals(expected, exported);
 558
 559     /*
 560      * include non-positional (overrides group not shown)
 561      */
 562     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 563             true, false);
 564     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 565             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 566             + "\nSTARTGROUP\tuniprot\n"
 567             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 568             + "ENDGROUP\tuniprot\n"
 569             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 570             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 571             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 572             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 573     assertEquals(expected, exported);
 574   }
 575
 576   @Test(groups = { "Functional" })
 577   public void testPrintGffFormat() throws Exception
 578   {
 579     File f = new File("examples/uniref50.fa");
 580     AlignmentI al = readAlignmentFile(f);
 581     AlignFrame af = new AlignFrame(al, 500, 500);
 582
 583     /*
 584      * no features
 585      */
 586     FeaturesFile featuresFile = new FeaturesFile();
 587     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 588             .getFeatureRenderer();
 589     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 590             fr, false, false);
 591     String gffHeader = "##gff-version 2\n";
 592     assertEquals(gffHeader, exported);
 593     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 594             true, false);
 595     assertEquals(gffHeader, exported);
 596
 597     /*
 598      * add some features
 599      */
 600     al.getSequenceAt(0).addSequenceFeature(
 601             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 602     al.getSequenceAt(0).addSequenceFeature(
 603             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 604     al.getSequenceAt(1)
 605             .addSequenceFeature(
 606                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 607                             "s3dm"));
 608     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 609             "Uniprot");
 610     sf.setStrand("+");
 611     sf.setPhase("2");
 612     sf.setValue("x", "y");
 613     sf.setValue("black", "white");
 614     Map<String, String> csq = new HashMap<>();
 615     csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
 616     csq.put("consequence", "missense_variant");
 617     sf.setValue("CSQ", csq);
 618     al.getSequenceAt(1).addSequenceFeature(sf);
 619
 620     /*
 621      * 'discover' features then hide all feature types
 622      */
 623     fr.findAllFeatures(true);
 624     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 625     FeatureColourI fc = new FeatureColour(Color.PINK);
 626     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 627     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 628     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 629     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 630     fr.setFeaturePriority(data);
 631
 632     /*
 633      * with no features displayed, exclude non-positional features
 634      */
 635     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 636             false, false);
 637     assertEquals(gffHeader, exported);
 638
 639     /*
 640      * include non-positional features
 641      */
 642     fr.setGroupVisibility("Uniprot", true);
 643     fr.setGroupVisibility("s3dm", false);
 644     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 645             true, false);
 646     String expected = gffHeader
 647             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 648     assertEquals(expected, exported);
 649
 650     /*
 651      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 652      * only Uniprot group visible here...
 653      */
 654     fr.setVisible("METAL");
 655     fr.setVisible("GAMMA-TURN");
 656     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 657             false, 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     assertEquals(expected, exported);
 661
 662     /*
 663      * set s3dm group visible
 664      */
 665     fr.setGroupVisibility("s3dm", true);
 666     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 667             false, false);
 668     // METAL feature has null group: description used for column 2
 669     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 670             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 671     assertEquals(expected, exported);
 672
 673     /*
 674      * now set Pfam visible
 675      */
 676     fr.setVisible("Pfam");
 677     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 678             false, false);
 679     // Pfam feature columns include strand(+), phase(2), attributes
 680     expected = gffHeader
 681             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 682             // CSQ output as CSQ=att1=value1,att2=value2
 683             // note all commas are encoded here which is wrong - it should be
 684             // SIFT=benign,mostly benign,cloudy%2C with meatballs
 685             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
 686             + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
 687             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 688     assertEquals(expected, exported);
 689   }
 690
 691   /**
 692    * Test for parsing of feature filters as represented in a Jalview features
 693    * file
 694    *
 695    * @throws Exception
 696    */
 697   @Test(groups = { "Functional" })
 698   public void testParseFilters() throws Exception
 699   {
 700     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 701     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 702             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 703     FeaturesFile featuresFile = new FeaturesFile(text,
 704             DataSourceType.PASTE);
 705     featuresFile.parseFilters(filters);
 706     assertEquals(filters.size(), 2);
 707
 708     FeatureMatcherSetI fm = filters.get("sequence_variant");
 709     assertNotNull(fm);
 710     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 711     FeatureMatcherI matcher = matchers.next();
 712     assertFalse(matchers.hasNext());
 713     String[] attributes = matcher.getAttribute();
 714     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 715     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 716     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 717
 718     fm = filters.get("missense_variant");
 719     assertNotNull(fm);
 720     matchers = fm.getMatchers().iterator();
 721     matcher = matchers.next();
 722     assertTrue(matcher.isByLabel());
 723     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 724     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 725     matcher = matchers.next();
 726     assertTrue(matcher.isByScore());
 727     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 728     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 729     assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f);
 730
 731     assertFalse(matchers.hasNext());
 732   }
 733
 734   @Test(groups = { "Functional" })
 735   public void testOutputFeatureFilters()
 736   {
 737     FeaturesFile ff = new FeaturesFile();
 738     StringBuilder sb = new StringBuilder();
 739     Map<String, FeatureColourI> visible = new HashMap<>();
 740     visible.put("pfam", new FeatureColour(Color.red));
 741     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 742
 743     // with no filters, nothing is output
 744     ff.outputFeatureFilters(sb, visible, featureFilters);
 745     assertEquals("", sb.toString());
 746
 747     // with filter for not visible features only, nothing is output
 748     FeatureMatcherSet filter = new FeatureMatcherSet();
 749     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 750     featureFilters.put("foobar", filter);
 751     ff.outputFeatureFilters(sb, visible, featureFilters);
 752     assertEquals("", sb.toString());
 753
 754     // with filters for visible feature types
 755     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 756     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 757             "PolyPhen"));
 758     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 759     featureFilters.put("pfam", filter2);
 760     visible.put("foobar", new FeatureColour(Color.blue));
 761     ff.outputFeatureFilters(sb, visible, featureFilters);
 762     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 763     assertEquals(expected, sb.toString());
 764   }
 765
 766   /**
 767    * Output as GFF should not include features which are not visible due to
 768    * colour threshold or feature filter settings
 769    *
 770    * @throws Exception
 771    */
 772   @Test(groups = { "Functional" })
 773   public void testPrintGffFormat_withFilters() throws Exception
 774   {
 775     File f = new File("examples/uniref50.fa");
 776     AlignmentI al = readAlignmentFile(f);
 777     AlignFrame af = new AlignFrame(al, 500, 500);
 778     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 779             null);
 780     sf1.setValue("clin_sig", "Likely Pathogenic");
 781     sf1.setValue("AF", "24");
 782     al.getSequenceAt(0).addSequenceFeature(sf1);
 783     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 784             null);
 785     sf2.setValue("clin_sig", "Benign");
 786     sf2.setValue("AF", "46");
 787     al.getSequenceAt(0).addSequenceFeature(sf2);
 788
 789     FeaturesFile featuresFile = new FeaturesFile();
 790     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 791     final String gffHeader = "##gff-version 2\n";
 792
 793     fr.setVisible("METAL");
 794     fr.setColour("METAL", new FeatureColour(Color.PINK));
 795     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 796             fr, false, false);
 797     String expected = gffHeader
 798             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 799             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 800     assertEquals(expected, exported);
 801
 802     /*
 803      * now threshold to Score > 1.1 - should exclude sf2
 804      */
 805     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 806             Color.white, 0f, 2f);
 807     fc.setAboveThreshold(true);
 808     fc.setThreshold(1.1f);
 809     fr.setColour("METAL", fc);
 810     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 811             false, false);
 812     expected = gffHeader
 813             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
 814     assertEquals(expected, exported);
 815
 816     /*
 817      * remove threshold and check sf2 is exported
 818      */
 819     fc.setAboveThreshold(false);
 820     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 821             false, false);
 822     expected = gffHeader
 823             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 824             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 825     assertEquals(expected, exported);
 826
 827     /*
 828      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 829      */
 830     FeatureMatcherSetI filter = new FeatureMatcherSet();
 831     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 832             "clin_sig"));
 833     fr.setFeatureFilter("METAL", filter);
 834     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 835             false, false);
 836     expected = gffHeader
 837             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 838     assertEquals(expected, exported);
 839   }
 840
 841   /**
 842    * Output as Jalview should not include features which are not visible due to
 843    * colour threshold or feature filter settings
 844    *
 845    * @throws Exception
 846    */
 847   @Test(groups = { "Functional" })
 848   public void testPrintJalviewFormat_withFilters() throws Exception
 849   {
 850     File f = new File("examples/uniref50.fa");
 851     AlignmentI al = readAlignmentFile(f);
 852     AlignFrame af = new AlignFrame(al, 500, 500);
 853     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 854             "grp1");
 855     sf1.setValue("clin_sig", "Likely Pathogenic");
 856     sf1.setValue("AF", "24");
 857     al.getSequenceAt(0).addSequenceFeature(sf1);
 858     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 859             "grp2");
 860     sf2.setValue("clin_sig", "Benign");
 861     sf2.setValue("AF", "46");
 862     al.getSequenceAt(0).addSequenceFeature(sf2);
 863
 864     FeaturesFile featuresFile = new FeaturesFile();
 865     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 866     fr.findAllFeatures(true);
 867
 868     fr.setVisible("METAL");
 869     fr.setColour("METAL", new FeatureColour(Color.PINK));
 870     String exported = featuresFile.printJalviewFormat(
 871             al.getSequencesArray(),
 872             fr, false, false);
 873     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 874             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 875             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 876             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 877             + "ENDGROUP\tgrp2\n";
 878     assertEquals(expected, exported);
 879
 880     /*
 881      * now threshold to Score > 1.1 - should exclude sf2
 882      * (and there should be no empty STARTGROUP/ENDGROUP output)
 883      */
 884     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 885             Color.white, 0f, 2f);
 886     fc.setAboveThreshold(true);
 887     fc.setThreshold(1.1f);
 888     fr.setColour("METAL", fc);
 889     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 890             false, false);
 891     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 892             + "STARTGROUP\tgrp1\n"
 893             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 894             + "ENDGROUP\tgrp1\n";
 895     assertEquals(expected, exported);
 896
 897     /*
 898      * remove threshold and check sf2 is exported
 899      */
 900     fc.setAboveThreshold(false);
 901     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 902             false, false);
 903     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 904             + "STARTGROUP\tgrp1\n"
 905             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 906             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 907             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 908             + "ENDGROUP\tgrp2\n";
 909     assertEquals(expected, exported);
 910
 911     /*
 912      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 913      */
 914     FeatureMatcherSetI filter = new FeatureMatcherSet();
 915     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 916             "clin_sig"));
 917     fr.setFeatureFilter("METAL", filter);
 918     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 919             false, false);
 920     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 921     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 922             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 923             + "STARTGROUP\tgrp2\n"
 924             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 925             + "ENDGROUP\tgrp2\n";
 926     assertEquals(expected, exported);
 927   }
 928 }