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;"
 276             + "jvmap_CSQ={AF=21,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", sf.description);
 290     assertEquals(39, sf.begin);
 291     assertEquals(39, sf.end);
 292     assertEquals("uniprot", sf.featureGroup);
 293     assertEquals("METAL", sf.type);
 294     assertEquals(5, sf.otherDetails.size());
 295     assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
 296             sf.getValue("evidence"));
 297     assertEquals("Iron-sulfur (2Fe-2S),another note",
 298             sf.getValue("Note"));
 299     assertEquals("21", sf.getValueAsString("CSQ", "AF"));
 300     assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
 301     // todo change STRAND and !Phase into fields of SequenceFeature instead
 302     assertEquals(".", sf.otherDetails.get("STRAND"));
 303     assertEquals(0, sf.getStrand());
 304     assertEquals(".", sf.getPhase());
 305
 306     // verify feature on FER1_SOLLC1
 307     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 308     assertEquals(1, sfs.size());
 309     sf = sfs.get(0);
 310     // ID used for description if available
 311     assertEquals("$23", sf.description);
 312     assertEquals(55, sf.begin);
 313     assertEquals(130, sf.end);
 314     assertEquals("uniprot", sf.featureGroup);
 315     assertEquals("Pfam", sf.type);
 316     assertEquals(3f, sf.getScore(), 0.001f);
 317   }
 318
 319   /**
 320    * Test parsing a features file with Jalview format features (but no colour
 321    * descriptors or startgroup to give the hint not to parse as GFF)
 322    *
 323    * @throws Exception
 324    */
 325   @Test(groups = { "Functional" })
 326   public void testParse_jalviewFeaturesOnly() throws Exception
 327   {
 328     File f = new File("examples/uniref50.fa");
 329     AlignmentI al = readAlignmentFile(f);
 330     AlignFrame af = new AlignFrame(al, 500, 500);
 331     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 332             .getFeatureColours();
 333
 334     /*
 335      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 336      */
 337     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 338             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 339     FeaturesFile featuresFile = new FeaturesFile(featureData,
 340             DataSourceType.PASTE);
 341     assertTrue("Failed to parse features file",
 342             featuresFile.parse(al.getDataset(), colours, true));
 343
 344     // verify FER_CAPAA feature
 345     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 346             .getSequenceFeatures();
 347     assertEquals(1, sfs.size());
 348     SequenceFeature sf = sfs.get(0);
 349     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 350     assertEquals(39, sf.begin);
 351     assertEquals(39, sf.end);
 352     assertEquals("METAL", sf.type);
 353
 354     // verify FER1_SOLLC feature
 355     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 356     assertEquals(1, sfs.size());
 357     sf = sfs.get(0);
 358     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 359     assertEquals(86, sf.begin);
 360     assertEquals(87, sf.end);
 361     assertEquals("METALLIC", sf.type);
 362   }
 363
 364   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 365   {
 366     assertEquals("no sequences extracted from GFF3 file", 2,
 367             dataset.getHeight());
 368
 369     SequenceI seq1 = dataset.findName("seq1");
 370     SequenceI seq2 = dataset.findName("seq2");
 371     assertNotNull(seq1);
 372     assertNotNull(seq2);
 373     assertFalse(
 374             "Failed to replace dummy seq1 with real sequence",
 375             seq1 instanceof SequenceDummy
 376                     && ((SequenceDummy) seq1).isDummy());
 377     assertFalse(
 378             "Failed to replace dummy seq2 with real sequence",
 379             seq2 instanceof SequenceDummy
 380                     && ((SequenceDummy) seq2).isDummy());
 381     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 382     assertFalse("dummy replacement buggy for seq1",
 383             placeholderseq.equals(seq1.getSequenceAsString()));
 384     assertFalse("dummy replacement buggy for seq2",
 385             placeholderseq.equals(seq2.getSequenceAsString()));
 386     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 387     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 388             .size());
 389     assertTrue(seq2.getSequenceFeatures().isEmpty());
 390     assertEquals(
 391             "Wrong number of features",
 392             0,
 393             seq2.getSequenceFeatures() == null ? 0 : seq2
 394                     .getSequenceFeatures().size());
 395     assertTrue(
 396             "Expected at least one CDNA/Protein mapping for seq1",
 397             dataset.getCodonFrame(seq1) != null
 398                     && dataset.getCodonFrame(seq1).size() > 0);
 399
 400   }
 401
 402   @Test(groups = { "Functional" })
 403   public void readGff3File() throws IOException
 404   {
 405     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 406             DataSourceType.FILE);
 407     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 408     gffreader.addProperties(dataset);
 409     checkDatasetfromSimpleGff3(dataset);
 410   }
 411
 412   @Test(groups = { "Functional" })
 413   public void simpleGff3FileClass() throws IOException
 414   {
 415     AlignmentI dataset = new Alignment(new SequenceI[] {});
 416     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 417             DataSourceType.FILE);
 418
 419     boolean parseResult = ffile.parse(dataset, null, false, false);
 420     assertTrue("return result should be true", parseResult);
 421     checkDatasetfromSimpleGff3(dataset);
 422   }
 423
 424   @Test(groups = { "Functional" })
 425   public void simpleGff3FileLoader() throws IOException
 426   {
 427     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 428             simpleGffFile, DataSourceType.FILE);
 429     assertTrue(
 430             "Didn't read the alignment into an alignframe from Gff3 File",
 431             af != null);
 432     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 433   }
 434
 435   @Test(groups = { "Functional" })
 436   public void simpleGff3RelaxedIdMatching() throws IOException
 437   {
 438     AlignmentI dataset = new Alignment(new SequenceI[] {});
 439     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 440             DataSourceType.FILE);
 441
 442     boolean parseResult = ffile.parse(dataset, null, false, true);
 443     assertTrue("return result (relaxedID matching) should be true",
 444             parseResult);
 445     checkDatasetfromSimpleGff3(dataset);
 446   }
 447
 448   @Test(groups = { "Functional" })
 449   public void testPrintJalviewFormat() throws Exception
 450   {
 451     File f = new File("examples/uniref50.fa");
 452     AlignmentI al = readAlignmentFile(f);
 453     AlignFrame af = new AlignFrame(al, 500, 500);
 454     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 455             .getFeatureColours();
 456     String features = "METAL\tcc9900\n"
 457             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 458             + "Pfam\tred\n"
 459             + "STARTGROUP\tuniprot\n"
 460             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 461             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 462             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 463             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 464             + "ENDGROUP\tuniprot\n";
 465     FeaturesFile featuresFile = new FeaturesFile(features,
 466             DataSourceType.PASTE);
 467     featuresFile.parse(al.getDataset(), colours, false);
 468
 469     /*
 470      * add positional and non-positional features with null and
 471      * empty feature group to check handled correctly
 472      */
 473     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 474     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 475             null));
 476     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 477             Float.NaN, null));
 478     seq = al.getSequenceAt(2); // FER1_SOLLC
 479     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 480             Float.NaN, ""));
 481     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 482             -2.6f, ""));
 483
 484     /*
 485      * first with no features displayed, exclude non-positional features
 486      */
 487     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 488     String exported = featuresFile
 489             .printJalviewFormat(al.getSequencesArray(), fr, false, false);
 490     String expected = "No Features Visible";
 491     assertEquals(expected, exported);
 492
 493     /*
 494      * include non-positional features, but still no positional features
 495      */
 496     fr.setGroupVisibility("uniprot", true);
 497     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 498             true, false);
 499     expected = "\nSTARTGROUP\tuniprot\n"
 500             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 501             + "ENDGROUP\tuniprot\n\n"
 502             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 503             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 504     assertEquals(expected, exported);
 505
 506     /*
 507      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 508      */
 509     fr.setVisible("METAL");
 510     fr.setVisible("GAMMA-TURN");
 511     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 512             false, false);
 513     expected = "METAL\tcc9900\n"
 514             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 515             + "\nSTARTGROUP\tuniprot\n"
 516             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 517             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 518             + "ENDGROUP\tuniprot\n";
 519     assertEquals(expected, exported);
 520
 521     /*
 522      * now set Pfam visible
 523      */
 524     fr.setVisible("Pfam");
 525     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 526             false, false);
 527     /*
 528      * features are output within group, ordered by sequence and type
 529      */
 530     expected = "METAL\tcc9900\n"
 531             + "Pfam\tff0000\n"
 532             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 533             + "\nSTARTGROUP\tuniprot\n"
 534             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 535             + "<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"
 536             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 537             + "ENDGROUP\tuniprot\n"
 538             // null / empty group features are output after named groups
 539             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 540             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 541     assertEquals(expected, exported);
 542
 543     /*
 544      * hide uniprot group
 545      */
 546     fr.setGroupVisibility("uniprot", false);
 547     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 548             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 549             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 550             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 551     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 552             false, false);
 553     assertEquals(expected, exported);
 554
 555     /*
 556      * include non-positional (overrides group not shown)
 557      */
 558     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 559             true, false);
 560     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 561             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 562             + "\nSTARTGROUP\tuniprot\n"
 563             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 564             + "ENDGROUP\tuniprot\n"
 565             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 566             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 567             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 568             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 569     assertEquals(expected, exported);
 570   }
 571
 572   @Test(groups = { "Functional" })
 573   public void testPrintGffFormat() throws Exception
 574   {
 575     File f = new File("examples/uniref50.fa");
 576     AlignmentI al = readAlignmentFile(f);
 577     AlignFrame af = new AlignFrame(al, 500, 500);
 578
 579     /*
 580      * no features
 581      */
 582     FeaturesFile featuresFile = new FeaturesFile();
 583     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 584             .getFeatureRenderer();
 585     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 586             fr, false, false);
 587     String gffHeader = "##gff-version 2\n";
 588     assertEquals(gffHeader, exported);
 589     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 590             true, false);
 591     assertEquals(gffHeader, exported);
 592
 593     /*
 594      * add some features
 595      */
 596     al.getSequenceAt(0).addSequenceFeature(
 597             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 598     al.getSequenceAt(0).addSequenceFeature(
 599             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 600     al.getSequenceAt(1)
 601             .addSequenceFeature(
 602                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 603                             "s3dm"));
 604     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 605             "Uniprot");
 606     sf.setStrand("+");
 607     sf.setPhase("2");
 608     sf.setValue("x", "y");
 609     sf.setValue("black", "white");
 610     al.getSequenceAt(1).addSequenceFeature(sf);
 611
 612     /*
 613      * 'discover' features then hide all feature types
 614      */
 615     fr.findAllFeatures(true);
 616     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 617     FeatureColourI fc = new FeatureColour(Color.PINK);
 618     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 619     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 620     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 621     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 622     fr.setFeaturePriority(data);
 623
 624     /*
 625      * with no features displayed, exclude non-positional features
 626      */
 627     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 628             false, false);
 629     assertEquals(gffHeader, exported);
 630
 631     /*
 632      * include non-positional features
 633      */
 634     fr.setGroupVisibility("Uniprot", true);
 635     fr.setGroupVisibility("s3dm", false);
 636     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 637             true, false);
 638     String expected = gffHeader
 639             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 640     assertEquals(expected, exported);
 641
 642     /*
 643      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 644      * only Uniprot group visible here...
 645      */
 646     fr.setVisible("METAL");
 647     fr.setVisible("GAMMA-TURN");
 648     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 649             false, false);
 650     // METAL feature has null group: description used for column 2
 651     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 652     assertEquals(expected, exported);
 653
 654     /*
 655      * set s3dm group visible
 656      */
 657     fr.setGroupVisibility("s3dm", true);
 658     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 659             false, false);
 660     // METAL feature has null group: description used for column 2
 661     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 662             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 663     assertEquals(expected, exported);
 664
 665     /*
 666      * now set Pfam visible
 667      */
 668     fr.setVisible("Pfam");
 669     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 670             false, false);
 671     // Pfam feature columns include strand(+), phase(2), attributes
 672     expected = gffHeader
 673             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 674             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
 675             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 676     assertEquals(expected, exported);
 677   }
 678
 679   /**
 680    * Test for parsing of feature filters as represented in a Jalview features
 681    * file
 682    *
 683    * @throws Exception
 684    */
 685   @Test(groups = { "Functional" })
 686   public void testParseFilters() throws Exception
 687   {
 688     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 689     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 690             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 691     FeaturesFile featuresFile = new FeaturesFile(text,
 692             DataSourceType.PASTE);
 693     featuresFile.parseFilters(filters);
 694     assertEquals(filters.size(), 2);
 695
 696     FeatureMatcherSetI fm = filters.get("sequence_variant");
 697     assertNotNull(fm);
 698     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 699     FeatureMatcherI matcher = matchers.next();
 700     assertFalse(matchers.hasNext());
 701     String[] attributes = matcher.getAttribute();
 702     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 703     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 704     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 705
 706     fm = filters.get("missense_variant");
 707     assertNotNull(fm);
 708     matchers = fm.getMatchers().iterator();
 709     matcher = matchers.next();
 710     assertTrue(matcher.isByLabel());
 711     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 712     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 713     matcher = matchers.next();
 714     assertTrue(matcher.isByScore());
 715     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 716     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 717     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 718
 719     assertFalse(matchers.hasNext());
 720   }
 721
 722   @Test(groups = { "Functional" })
 723   public void testOutputFeatureFilters()
 724   {
 725     FeaturesFile ff = new FeaturesFile();
 726     StringBuilder sb = new StringBuilder();
 727     Map<String, FeatureColourI> visible = new HashMap<>();
 728     visible.put("pfam", new FeatureColour(Color.red));
 729     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 730
 731     // with no filters, nothing is output
 732     ff.outputFeatureFilters(sb, visible, featureFilters);
 733     assertEquals("", sb.toString());
 734
 735     // with filter for not visible features only, nothing is output
 736     FeatureMatcherSet filter = new FeatureMatcherSet();
 737     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 738     featureFilters.put("foobar", filter);
 739     ff.outputFeatureFilters(sb, visible, featureFilters);
 740     assertEquals("", sb.toString());
 741
 742     // with filters for visible feature types
 743     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 744     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 745             "PolyPhen"));
 746     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 747     featureFilters.put("pfam", filter2);
 748     visible.put("foobar", new FeatureColour(Color.blue));
 749     ff.outputFeatureFilters(sb, visible, featureFilters);
 750     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 751     assertEquals(expected, sb.toString());
 752   }
 753
 754   /**
 755    * Output as GFF should not include features which are not visible due to
 756    * colour threshold or feature filter settings
 757    *
 758    * @throws Exception
 759    */
 760   @Test(groups = { "Functional" })
 761   public void testPrintGffFormat_withFilters() throws Exception
 762   {
 763     File f = new File("examples/uniref50.fa");
 764     AlignmentI al = readAlignmentFile(f);
 765     AlignFrame af = new AlignFrame(al, 500, 500);
 766     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 767             null);
 768     sf1.setValue("clin_sig", "Likely Pathogenic");
 769     sf1.setValue("AF", "24");
 770     al.getSequenceAt(0).addSequenceFeature(sf1);
 771     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 772             null);
 773     sf2.setValue("clin_sig", "Benign");
 774     sf2.setValue("AF", "46");
 775     al.getSequenceAt(0).addSequenceFeature(sf2);
 776
 777     FeaturesFile featuresFile = new FeaturesFile();
 778     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 779     final String gffHeader = "##gff-version 2\n";
 780
 781     fr.setVisible("METAL");
 782     fr.setColour("METAL", new FeatureColour(Color.PINK));
 783     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 784             fr, false, false);
 785     String expected = gffHeader
 786             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 787             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 788     assertEquals(expected, exported);
 789
 790     /*
 791      * now threshold to Score > 1.1 - should exclude sf2
 792      */
 793     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 794             Color.white, 0f, 2f);
 795     fc.setAboveThreshold(true);
 796     fc.setThreshold(1.1f);
 797     fr.setColour("METAL", fc);
 798     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 799             false, false);
 800     expected = gffHeader
 801             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
 802     assertEquals(expected, exported);
 803
 804     /*
 805      * remove threshold and check sf2 is exported
 806      */
 807     fc.setAboveThreshold(false);
 808     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 809             false, false);
 810     expected = gffHeader
 811             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
 812             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 813     assertEquals(expected, exported);
 814
 815     /*
 816      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 817      */
 818     FeatureMatcherSetI filter = new FeatureMatcherSet();
 819     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 820             "clin_sig"));
 821     fr.setFeatureFilter("METAL", filter);
 822     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 823             false, false);
 824     expected = gffHeader
 825             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
 826     assertEquals(expected, exported);
 827   }
 828
 829   /**
 830    * Output as Jalview should not include features which are not visible due to
 831    * colour threshold or feature filter settings
 832    *
 833    * @throws Exception
 834    */
 835   @Test(groups = { "Functional" })
 836   public void testPrintJalviewFormat_withFilters() throws Exception
 837   {
 838     File f = new File("examples/uniref50.fa");
 839     AlignmentI al = readAlignmentFile(f);
 840     AlignFrame af = new AlignFrame(al, 500, 500);
 841     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 842             "grp1");
 843     sf1.setValue("clin_sig", "Likely Pathogenic");
 844     sf1.setValue("AF", "24");
 845     al.getSequenceAt(0).addSequenceFeature(sf1);
 846     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 847             "grp2");
 848     sf2.setValue("clin_sig", "Benign");
 849     sf2.setValue("AF", "46");
 850     al.getSequenceAt(0).addSequenceFeature(sf2);
 851
 852     FeaturesFile featuresFile = new FeaturesFile();
 853     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 854     fr.findAllFeatures(true);
 855
 856     fr.setVisible("METAL");
 857     fr.setColour("METAL", new FeatureColour(Color.PINK));
 858     String exported = featuresFile.printJalviewFormat(
 859             al.getSequencesArray(),
 860             fr, false, false);
 861     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 862             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 863             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 864             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 865             + "ENDGROUP\tgrp2\n";
 866     assertEquals(expected, exported);
 867
 868     /*
 869      * now threshold to Score > 1.1 - should exclude sf2
 870      * (and there should be no empty STARTGROUP/ENDGROUP output)
 871      */
 872     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 873             Color.white, 0f, 2f);
 874     fc.setAboveThreshold(true);
 875     fc.setThreshold(1.1f);
 876     fr.setColour("METAL", fc);
 877     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 878             false, false);
 879     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 880             + "STARTGROUP\tgrp1\n"
 881             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 882             + "ENDGROUP\tgrp1\n";
 883     assertEquals(expected, exported);
 884
 885     /*
 886      * remove threshold and check sf2 is exported
 887      */
 888     fc.setAboveThreshold(false);
 889     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 890             false, false);
 891     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 892             + "STARTGROUP\tgrp1\n"
 893             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 894             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 895             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 896             + "ENDGROUP\tgrp2\n";
 897     assertEquals(expected, exported);
 898
 899     /*
 900      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 901      */
 902     FeatureMatcherSetI filter = new FeatureMatcherSet();
 903     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 904             "clin_sig"));
 905     fr.setFeatureFilter("METAL", filter);
 906     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 907             false, false);
 908     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 909     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 910             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 911             + "STARTGROUP\tgrp2\n"
 912             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 913             + "ENDGROUP\tgrp2\n";
 914     assertEquals(expected, exported);
 915   }
 916 }