test/jalview/io/FeaturesFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertNotNull;
  26 import static org.testng.AssertJUnit.assertSame;
  27 import static org.testng.AssertJUnit.assertTrue;
  28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
  29
  30 import jalview.api.FeatureColourI;
  31 import jalview.api.FeatureRenderer;
  32 import jalview.datamodel.Alignment;
  33 import jalview.datamodel.AlignmentI;
  34 import jalview.datamodel.SequenceDummy;
  35 import jalview.datamodel.SequenceFeature;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.datamodel.features.FeatureMatcher;
  38 import jalview.datamodel.features.FeatureMatcherI;
  39 import jalview.datamodel.features.FeatureMatcherSet;
  40 import jalview.datamodel.features.FeatureMatcherSetI;
  41 import jalview.datamodel.features.SequenceFeatures;
  42 import jalview.gui.AlignFrame;
  43 import jalview.gui.Desktop;
  44 import jalview.gui.JvOptionPane;
  45 import jalview.schemes.FeatureColour;
  46 import jalview.util.matcher.Condition;
  47 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  48 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  49
  50 import java.awt.Color;
  51 import java.io.File;
  52 import java.io.IOException;
  53 import java.util.HashMap;
  54 import java.util.Iterator;
  55 import java.util.List;
  56 import java.util.Map;
  57
  58 import org.testng.annotations.AfterClass;
  59 import org.testng.annotations.BeforeClass;
  60 import org.testng.annotations.Test;
  61
  62 public class FeaturesFileTest
  63 {
  64   private static final String LINE_SEPARATOR = System.getProperty("line.separator");
  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     Desktop.getStructureSelectionManager().resetAll();
  74   }
  75
  76   @BeforeClass(alwaysRun = true)
  77   public void setUpJvOptionPane()
  78   {
  79     JvOptionPane.setInteractiveMode(false);
  80     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  81   }
  82
  83   @Test(groups = { "Functional" })
  84   public void testParse() throws Exception
  85   {
  86     File f = new File("examples/uniref50.fa");
  87     AlignmentI al = readAlignmentFile(f);
  88     AlignFrame af = new AlignFrame(al, 500, 500);
  89     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
  90             .getFeatureColours();
  91     FeaturesFile featuresFile = new FeaturesFile(
  92             "examples/exampleFeatures.txt", DataSourceType.FILE);
  93     assertTrue("Test " + "Features file test"
  94             + "\nFailed to parse features file.",
  95             featuresFile.parse(al.getDataset(), colours, true));
  96
  97     /*
  98      * Refetch the colour map from the FeatureRenderer (to confirm it has been
  99      * updated - JAL-1904), and verify (some) feature group colours
 100      */
 101     colours = af.getFeatureRenderer().getFeatureColours();
 102     assertEquals("27 feature group colours not found", 27, colours.size());
 103     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
 104     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
 105     FeatureColourI kdColour = colours.get("kdHydrophobicity");
 106     assertTrue(kdColour.isGraduatedColour());
 107     assertTrue(kdColour.isAboveThreshold());
 108     assertEquals(-2f, kdColour.getThreshold());
 109
 110     /*
 111      * verify (some) features on sequences
 112      */
 113     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 114             .getSequenceFeatures(); // FER_CAPAA
 115     SequenceFeatures.sortFeatures(sfs, true);
 116     assertEquals(8, sfs.size());
 117
 118     /*
 119      * verify (in ascending start position order)
 120      */
 121     SequenceFeature sf = sfs.get(0);
 122     assertEquals("Pfam family%LINK%", sf.description);
 123     assertEquals(0, sf.begin);
 124     assertEquals(0, sf.end);
 125     assertEquals("uniprot", sf.featureGroup);
 126     assertEquals("Pfam", sf.type);
 127     assertEquals(1, sf.links.size());
 128     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
 129             sf.links.get(0));
 130
 131     sf = sfs.get(1);
 132     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
 133     assertEquals(3, sf.begin);
 134     assertEquals(93, sf.end);
 135     assertEquals("uniprot", sf.featureGroup);
 136     assertEquals("Cath", sf.type);
 137
 138     sf = sfs.get(2);
 139     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
 140             sf.description);
 141     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
 142             sf.links.get(0));
 143     assertEquals(8, sf.begin);
 144     assertEquals(83, sf.end);
 145     assertEquals("uniprot", sf.featureGroup);
 146     assertEquals("Pfam", sf.type);
 147
 148     sf = sfs.get(3);
 149     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 150     assertEquals(39, sf.begin);
 151     assertEquals(39, sf.end);
 152     assertEquals("uniprot", sf.featureGroup);
 153     assertEquals("METAL", sf.type);
 154
 155     sf = sfs.get(4);
 156     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 157     assertEquals(44, sf.begin);
 158     assertEquals(44, sf.end);
 159     assertEquals("uniprot", sf.featureGroup);
 160     assertEquals("METAL", sf.type);
 161
 162     sf = sfs.get(5);
 163     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 164     assertEquals(47, sf.begin);
 165     assertEquals(47, sf.end);
 166     assertEquals("uniprot", sf.featureGroup);
 167     assertEquals("METAL", sf.type);
 168
 169     sf = sfs.get(6);
 170     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 171     assertEquals(77, sf.begin);
 172     assertEquals(77, sf.end);
 173     assertEquals("uniprot", sf.featureGroup);
 174     assertEquals("METAL", sf.type);
 175
 176     sf = sfs.get(7);
 177     assertEquals(
 178             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
 179             sf.description);
 180     assertEquals(
 181             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
 182             sf.links.get(0));
 183     assertEquals(89, sf.begin);
 184     assertEquals(89, sf.end);
 185     assertEquals("netphos", sf.featureGroup);
 186     assertEquals("PHOSPHORYLATION (T)", sf.type);
 187   }
 188
 189   /**
 190    * Test parsing a features file with a mix of Jalview and GFF formatted
 191    * content
 192    *
 193    * @throws Exception
 194    */
 195   @Test(groups = { "Functional" })
 196   public void testParse_mixedJalviewGff() throws Exception
 197   {
 198     File f = new File("examples/uniref50.fa");
 199     AlignmentI al = readAlignmentFile(f);
 200     AlignFrame af = new AlignFrame(al, 500, 500);
 201     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 202             .getFeatureColours();
 203     // GFF2 uses space as name/value separator in column 9
 204     String gffData = "METAL\tcc9900\n"
 205             + "GFF\n"
 206             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
 207             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
 208     FeaturesFile featuresFile = new FeaturesFile(gffData,
 209             DataSourceType.PASTE);
 210     assertTrue("Failed to parse features file",
 211             featuresFile.parse(al.getDataset(), colours, true));
 212
 213     // verify colours read or synthesized
 214     colours = af.getFeatureRenderer().getFeatureColours();
 215     assertEquals("1 feature group colours not found", 1, colours.size());
 216     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 217
 218     // verify feature on FER_CAPAA
 219     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 220             .getSequenceFeatures();
 221     assertEquals(1, sfs.size());
 222     SequenceFeature sf = sfs.get(0);
 223     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
 224     assertEquals(44, sf.begin);
 225     assertEquals(45, sf.end);
 226     assertEquals("uniprot", sf.featureGroup);
 227     assertEquals("METAL", sf.type);
 228     assertEquals(4f, sf.getScore(), 0.001f);
 229
 230     // verify feature on FER1_SOLLC
 231     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 232     assertEquals(1, sfs.size());
 233     sf = sfs.get(0);
 234     assertEquals("uniprot", sf.description);
 235     assertEquals(55, sf.begin);
 236     assertEquals(130, sf.end);
 237     assertEquals("uniprot", sf.featureGroup);
 238     assertEquals("Pfam", sf.type);
 239     assertEquals(2f, sf.getScore(), 0.001f);
 240   }
 241
 242   public static AlignmentI readAlignmentFile(File f) throws IOException
 243   {
 244     System.out.println("Reading file: " + f);
 245     String ff = f.getPath();
 246     FormatAdapter rf = new FormatAdapter();
 247
 248     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
 249             new IdentifyFile().identify(ff, DataSourceType.FILE));
 250
 251     al.setDataset(null); // creates dataset sequences
 252     assertNotNull("Couldn't read supplied alignment data.", al);
 253     return al;
 254   }
 255
 256   /**
 257    * Test parsing a features file with GFF formatted content only
 258    *
 259    * @throws Exception
 260    */
 261   @Test(groups = { "Functional" })
 262   public void testParse_pureGff3() throws Exception
 263   {
 264     File f = new File("examples/uniref50.fa");
 265     AlignmentI al = readAlignmentFile(f);
 266     AlignFrame af = new AlignFrame(al, 500, 500);
 267     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 268             .getFeatureColours();
 269     // GFF3 uses '=' separator for name/value pairs in colum 9
 270     String gffData = "##gff-version 3\n"
 271             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 272             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 273             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 274     FeaturesFile featuresFile = new FeaturesFile(gffData,
 275             DataSourceType.PASTE);
 276     assertTrue("Failed to parse features file",
 277             featuresFile.parse(al.getDataset(), colours, true));
 278
 279     // verify feature on FER_CAPAA
 280     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 281             .getSequenceFeatures();
 282     assertEquals(1, sfs.size());
 283     SequenceFeature sf = sfs.get(0);
 284     // description parsed from Note attribute
 285     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 286     assertEquals(39, sf.begin);
 287     assertEquals(39, sf.end);
 288     assertEquals("uniprot", sf.featureGroup);
 289     assertEquals("METAL", sf.type);
 290     assertEquals(
 291             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 292             sf.getValue("ATTRIBUTES"));
 293
 294     // verify feature on FER1_SOLLC1
 295     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 296     assertEquals(1, sfs.size());
 297     sf = sfs.get(0);
 298     // ID used for description if available
 299     assertEquals("$23", sf.description);
 300     assertEquals(55, sf.begin);
 301     assertEquals(130, sf.end);
 302     assertEquals("uniprot", sf.featureGroup);
 303     assertEquals("Pfam", sf.type);
 304     assertEquals(3f, sf.getScore(), 0.001f);
 305   }
 306
 307   /**
 308    * Test parsing a features file with Jalview format features (but no colour
 309    * descriptors or startgroup to give the hint not to parse as GFF)
 310    *
 311    * @throws Exception
 312    */
 313   @Test(groups = { "Functional" })
 314   public void testParse_jalviewFeaturesOnly() throws Exception
 315   {
 316     File f = new File("examples/uniref50.fa");
 317     AlignmentI al = readAlignmentFile(f);
 318     AlignFrame af = new AlignFrame(al, 500, 500);
 319     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 320             .getFeatureColours();
 321
 322     /*
 323      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 324      */
 325     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 326             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 327     FeaturesFile featuresFile = new FeaturesFile(featureData,
 328             DataSourceType.PASTE);
 329     assertTrue("Failed to parse features file",
 330             featuresFile.parse(al.getDataset(), colours, true));
 331
 332     // verify FER_CAPAA feature
 333     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 334             .getSequenceFeatures();
 335     assertEquals(1, sfs.size());
 336     SequenceFeature sf = sfs.get(0);
 337     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 338     assertEquals(39, sf.begin);
 339     assertEquals(39, sf.end);
 340     assertEquals("METAL", sf.type);
 341
 342     // verify FER1_SOLLC feature
 343     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 344     assertEquals(1, sfs.size());
 345     sf = sfs.get(0);
 346     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 347     assertEquals(86, sf.begin);
 348     assertEquals(87, sf.end);
 349     assertEquals("METALLIC", sf.type);
 350   }
 351
 352   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 353   {
 354     assertEquals("no sequences extracted from GFF3 file", 2,
 355             dataset.getHeight());
 356
 357     SequenceI seq1 = dataset.findName("seq1");
 358     SequenceI seq2 = dataset.findName("seq2");
 359     assertNotNull(seq1);
 360     assertNotNull(seq2);
 361     assertFalse(
 362             "Failed to replace dummy seq1 with real sequence",
 363             seq1 instanceof SequenceDummy
 364                     && ((SequenceDummy) seq1).isDummy());
 365     assertFalse(
 366             "Failed to replace dummy seq2 with real sequence",
 367             seq2 instanceof SequenceDummy
 368                     && ((SequenceDummy) seq2).isDummy());
 369     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 370     assertFalse("dummy replacement buggy for seq1",
 371             placeholderseq.equals(seq1.getSequenceAsString()));
 372     assertFalse("dummy replacement buggy for seq2",
 373             placeholderseq.equals(seq2.getSequenceAsString()));
 374     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 375     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 376             .size());
 377     assertTrue(seq2.getSequenceFeatures().isEmpty());
 378     assertEquals(
 379             "Wrong number of features",
 380             0,
 381             seq2.getSequenceFeatures() == null ? 0 : seq2
 382                     .getSequenceFeatures().size());
 383     assertTrue(
 384             "Expected at least one CDNA/Protein mapping for seq1",
 385             dataset.getCodonFrame(seq1) != null
 386                     && dataset.getCodonFrame(seq1).size() > 0);
 387
 388   }
 389
 390   @Test(groups = { "Functional" })
 391   public void readGff3File() throws IOException
 392   {
 393     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 394             DataSourceType.FILE);
 395     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 396     gffreader.addProperties(dataset);
 397     checkDatasetfromSimpleGff3(dataset);
 398   }
 399
 400   @Test(groups = { "Functional" })
 401   public void simpleGff3FileClass() throws IOException
 402   {
 403     AlignmentI dataset = new Alignment(new SequenceI[] {});
 404     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 405             DataSourceType.FILE);
 406
 407     boolean parseResult = ffile.parse(dataset, null, false, false);
 408     assertTrue("return result should be true", parseResult);
 409     checkDatasetfromSimpleGff3(dataset);
 410   }
 411
 412   @Test(groups = { "Functional" })
 413   public void simpleGff3FileLoader() throws IOException
 414   {
 415     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 416             simpleGffFile, DataSourceType.FILE);
 417     assertTrue(
 418             "Didn't read the alignment into an alignframe from Gff3 File",
 419             af != null);
 420     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 421   }
 422
 423   @Test(groups = { "Functional" })
 424   public void simpleGff3RelaxedIdMatching() throws IOException
 425   {
 426     AlignmentI dataset = new Alignment(new SequenceI[] {});
 427     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 428             DataSourceType.FILE);
 429
 430     boolean parseResult = ffile.parse(dataset, null, false, true);
 431     assertTrue("return result (relaxedID matching) should be true",
 432             parseResult);
 433     checkDatasetfromSimpleGff3(dataset);
 434   }
 435
 436   @Test(groups = { "Functional" })
 437   public void testPrintJalviewFormat() throws Exception
 438   {
 439     File f = new File("examples/uniref50.fa");
 440     AlignmentI al = readAlignmentFile(f);
 441     AlignFrame af = new AlignFrame(al, 500, 500);
 442     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 443             .getFeatureColours();
 444     String features = "METAL\tcc9900\n"
 445             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 446             + "Pfam\tred\n"
 447             + "STARTGROUP\tuniprot\n"
 448             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 449             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 450             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 451             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 452             + "ENDGROUP\tuniprot\n";
 453     FeaturesFile featuresFile = new FeaturesFile(features,
 454             DataSourceType.PASTE);
 455     featuresFile.parse(al.getDataset(), colours, false);
 456
 457     /*
 458      * add positional and non-positional features with null and
 459      * empty feature group to check handled correctly
 460      */
 461     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 462     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 463             null));
 464     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 465             Float.NaN, null));
 466     seq = al.getSequenceAt(2); // FER1_SOLLC
 467     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 468             Float.NaN, ""));
 469     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 470             -2.6f, ""));
 471
 472     /*
 473      * first with no features displayed, exclude non-positional features
 474      */
 475     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 476     String exported = featuresFile
 477             .printJalviewFormat(al.getSequencesArray(), fr, false);
 478     String expected = "No Features Visible";
 479     assertEquals(expected, exported);
 480
 481     /*
 482      * include non-positional features, but still no positional features
 483      */
 484     fr.setGroupVisibility("uniprot", true);
 485     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 486             true);
 487     expected = "\nSTARTGROUP\tuniprot\n"
 488             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 489             + "ENDGROUP\tuniprot\n\n"
 490             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 491             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 492     assertEquals(
 493             expected.replace("\n", LINE_SEPARATOR),
 494             exported);
 495
 496     /*
 497      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 498      */
 499     fr.setVisible("METAL");
 500     fr.setVisible("GAMMA-TURN");
 501     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 502             false);
 503     expected = "METAL\tcc9900\n"
 504             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 505             + "\nSTARTGROUP\tuniprot\n"
 506             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 507             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 508             + "ENDGROUP\tuniprot\n";
 509     assertEquals(fixLineEnd(expected), exported);
 510
 511     /*
 512      * now set Pfam visible
 513      */
 514     fr.setVisible("Pfam");
 515     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 516             false);
 517     /*
 518      * features are output within group, ordered by sequence and type
 519      */
 520     expected = "METAL\tcc9900\n"
 521             + "Pfam\tff0000\n"
 522             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 523             + "\nSTARTGROUP\tuniprot\n"
 524             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 525             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 526             + "<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"
 527             + "ENDGROUP\tuniprot\n"
 528             // null / empty group features are output after named groups
 529             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 530             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 531     assertEquals(fixLineEnd(expected), exported);
 532
 533     /*
 534      * hide uniprot group
 535      */
 536     fr.setGroupVisibility("uniprot", false);
 537     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 538             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 539             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 540             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 541     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 542             false);
 543     assertEquals(fixLineEnd(expected), exported);
 544
 545     /*
 546      * include non-positional (overrides group not shown)
 547      */
 548     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 549             true);
 550     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 551             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 552             + "\nSTARTGROUP\tuniprot\n"
 553             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 554             + "ENDGROUP\tuniprot\n"
 555             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 556             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 557             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 558             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 559     assertEquals(fixLineEnd(expected), exported);
 560   }
 561
 562   @Test(groups = { "Functional" })
 563   public void testPrintGffFormat() throws Exception
 564   {
 565     File f = new File("examples/uniref50.fa");
 566     AlignmentI al = readAlignmentFile(f);
 567     AlignFrame af = new AlignFrame(al, 500, 500);
 568
 569     /*
 570      * no features
 571      */
 572     FeaturesFile featuresFile = new FeaturesFile();
 573     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 574             .getFeatureRenderer();
 575     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 576             fr, false);
 577     String gffHeader = "##gff-version 2\n";
 578     assertEquals(
 579             fixLineEnd(gffHeader),
 580             exported);
 581     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 582             true);
 583     assertEquals(
 584             fixLineEnd(gffHeader),
 585             exported);
 586
 587     /*
 588      * add some features
 589      */
 590     al.getSequenceAt(0).addSequenceFeature(
 591             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 592     al.getSequenceAt(0).addSequenceFeature(
 593             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 594     al.getSequenceAt(1)
 595             .addSequenceFeature(
 596                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 597                             "s3dm"));
 598     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 599             "Uniprot");
 600     sf.setAttributes("x=y;black=white");
 601     sf.setStrand("+");
 602     sf.setPhase("2");
 603     al.getSequenceAt(1).addSequenceFeature(sf);
 604
 605     /*
 606      * 'discover' features then hide all feature types
 607      */
 608     fr.findAllFeatures(true);
 609     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 610     FeatureColourI fc = new FeatureColour(Color.PINK);
 611     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 612     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 613     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 614     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 615     fr.setFeaturePriority(data);
 616
 617     /*
 618      * with no features displayed, exclude non-positional features
 619      */
 620     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 621             false);
 622     assertEquals(
 623             fixLineEnd(gffHeader),
 624             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);
 633     String expected = gffHeader
 634             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 635     assertEquals(
 636             fixLineEnd(expected),
 637             exported);
 638
 639     /*
 640      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 641      * only Uniprot group visible here...
 642      */
 643     fr.setVisible("METAL");
 644     fr.setVisible("GAMMA-TURN");
 645     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 646             false);
 647     // METAL feature has null group: description used for column 2
 648     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 649     assertEquals(
 650             expected.replace("\n", LINE_SEPARATOR),
 651             exported);
 652
 653     /*
 654      * set s3dm group visible
 655      */
 656     fr.setGroupVisibility("s3dm", true);
 657     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 658             false);
 659     // METAL feature has null group: description used for column 2
 660     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 661             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 662     assertEquals(
 663             expected.replace("\n", LINE_SEPARATOR),
 664             exported);
 665
 666     /*
 667      * now set Pfam visible
 668      */
 669     fr.setVisible("Pfam");
 670     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 671             false);
 672     // Pfam feature columns include strand(+), phase(2), attributes
 673     expected = gffHeader
 674             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 675             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
 676             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
 677     assertEquals(fixLineEnd(expected), exported);
 678   }
 679
 680   private String fixLineEnd(String s)
 681   {
 682     return s.replace("\n", LINE_SEPARATOR);
 683   }
 684
 685   /**
 686    * Test for parsing of feature filters as represented in a Jalview features
 687    * file
 688    *
 689    * @throws Exception
 690    */
 691   @Test(groups = { "Functional" })
 692   public void testParseFilters() throws Exception
 693   {
 694     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 695     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 696             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 697     FeaturesFile featuresFile = new FeaturesFile(text,
 698             DataSourceType.PASTE);
 699     featuresFile.parseFilters(filters);
 700     assertEquals(filters.size(), 2);
 701
 702     FeatureMatcherSetI fm = filters.get("sequence_variant");
 703     assertNotNull(fm);
 704     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 705     FeatureMatcherI matcher = matchers.next();
 706     assertFalse(matchers.hasNext());
 707     String[] attributes = matcher.getAttribute();
 708     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 709     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 710     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 711
 712     fm = filters.get("missense_variant");
 713     assertNotNull(fm);
 714     matchers = fm.getMatchers().iterator();
 715     matcher = matchers.next();
 716     assertTrue(matcher.isByLabel());
 717     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 718     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 719     matcher = matchers.next();
 720     assertTrue(matcher.isByScore());
 721     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 722     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 723     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 724
 725     assertFalse(matchers.hasNext());
 726   }
 727
 728   @Test(groups = { "Functional" })
 729   public void testOutputFeatureFilters()
 730   {
 731     FeaturesFile ff = new FeaturesFile();
 732     StringBuilder sb = new StringBuilder();
 733     Map<String, FeatureColourI> visible = new HashMap<>();
 734     visible.put("pfam", new FeatureColour(Color.red));
 735     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 736
 737     // with no filters, nothing is output
 738     ff.outputFeatureFilters(sb, visible, featureFilters);
 739     assertEquals("", sb.toString());
 740
 741     // with filter for not visible features only, nothing is output
 742     FeatureMatcherSet filter = new FeatureMatcherSet();
 743     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 744     featureFilters.put("foobar", filter);
 745     ff.outputFeatureFilters(sb, visible, featureFilters);
 746     assertEquals("", sb.toString());
 747
 748     // with filters for visible feature types
 749     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 750     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 751             "PolyPhen"));
 752     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 753     featureFilters.put("pfam", filter2);
 754     visible.put("foobar", new FeatureColour(Color.blue));
 755     ff.outputFeatureFilters(sb, visible, featureFilters);
 756     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 757     assertEquals(fixLineEnd(expected), sb.toString());
 758   }
 759
 760   /**
 761    * Output as GFF should not include features which are not visible due to
 762    * colour threshold or feature filter settings
 763    *
 764    * @throws Exception
 765    */
 766   @Test(groups = { "Functional" })
 767   public void testPrintGffFormat_withFilters() throws Exception
 768   {
 769     File f = new File("examples/uniref50.fa");
 770     AlignmentI al = readAlignmentFile(f);
 771     AlignFrame af = new AlignFrame(al, 500, 500);
 772     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 773             null);
 774     sf1.setValue("clin_sig", "Likely Pathogenic");
 775     sf1.setValue("AF", "24");
 776     al.getSequenceAt(0).addSequenceFeature(sf1);
 777     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 778             null);
 779     sf2.setValue("clin_sig", "Benign");
 780     sf2.setValue("AF", "46");
 781     al.getSequenceAt(0).addSequenceFeature(sf2);
 782
 783     FeaturesFile featuresFile = new FeaturesFile();
 784     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 785     final String gffHeader = "##gff-version 2\n";
 786
 787     fr.setVisible("METAL");
 788     fr.setColour("METAL", new FeatureColour(Color.PINK));
 789     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 790             fr, false);
 791     String expected = gffHeader
 792             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 793             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 794     assertEquals(
 795             fixLineEnd(expected), exported);
 796
 797     /*
 798      * now threshold to Score > 1.1 - should exclude sf2
 799      */
 800     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 801             Color.white, 0f, 2f);
 802     fc.setAboveThreshold(true);
 803     fc.setThreshold(1.1f);
 804     fr.setColour("METAL", fc);
 805     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 806             false);
 807     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 808     assertEquals(fixLineEnd(expected), exported);
 809
 810     /*
 811      * remove threshold and check sf2 is exported
 812      */
 813     fc.setAboveThreshold(false);
 814     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 815             false);
 816     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 817             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 818     assertEquals(fixLineEnd(expected), exported);
 819
 820     /*
 821      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 822      */
 823     FeatureMatcherSetI filter = new FeatureMatcherSet();
 824     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 825             "clin_sig"));
 826     fr.setFeatureFilter("METAL", filter);
 827     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 828             false);
 829     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 830     assertEquals(fixLineEnd(expected), exported);
 831   }
 832
 833   /**
 834    * Output as Jalview should not include features which are not visible due to
 835    * colour threshold or feature filter settings
 836    *
 837    * @throws Exception
 838    */
 839   @Test(groups = { "Functional" })
 840   public void testPrintJalviewFormat_withFilters() throws Exception
 841   {
 842     File f = new File("examples/uniref50.fa");
 843     AlignmentI al = readAlignmentFile(f);
 844     AlignFrame af = new AlignFrame(al, 500, 500);
 845     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 846             "grp1");
 847     sf1.setValue("clin_sig", "Likely Pathogenic");
 848     sf1.setValue("AF", "24");
 849     al.getSequenceAt(0).addSequenceFeature(sf1);
 850     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 851             "grp2");
 852     sf2.setValue("clin_sig", "Benign");
 853     sf2.setValue("AF", "46");
 854     al.getSequenceAt(0).addSequenceFeature(sf2);
 855
 856     FeaturesFile featuresFile = new FeaturesFile();
 857     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 858     fr.findAllFeatures(true);
 859
 860     fr.setVisible("METAL");
 861     fr.setColour("METAL", new FeatureColour(Color.PINK));
 862     String exported = featuresFile.printJalviewFormat(
 863             al.getSequencesArray(),
 864             fr, false);
 865     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 866             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 867             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 868             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 869             + "ENDGROUP\tgrp2\n";
 870     assertEquals(
 871             fixLineEnd(expected),
 872             exported);
 873
 874     /*
 875      * now threshold to Score > 1.1 - should exclude sf2
 876      * (and there should be no empty STARTGROUP/ENDGROUP output)
 877      */
 878     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 879             Color.white, 0f, 2f);
 880     fc.setAboveThreshold(true);
 881     fc.setThreshold(1.1f);
 882     fr.setColour("METAL", fc);
 883     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 884             false);
 885     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 886             + "STARTGROUP\tgrp1\n"
 887             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 888             + "ENDGROUP\tgrp1\n";
 889     assertEquals(
 890             expected.replace("\n", LINE_SEPARATOR),
 891             exported);
 892
 893     /*
 894      * remove threshold and check sf2 is exported
 895      */
 896     fc.setAboveThreshold(false);
 897     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 898             false);
 899     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 900             + "STARTGROUP\tgrp1\n"
 901             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 902             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 903             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 904             + "ENDGROUP\tgrp2\n";
 905     assertEquals(fixLineEnd(expected), exported);
 906
 907     /*
 908      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 909      */
 910     FeatureMatcherSetI filter = new FeatureMatcherSet();
 911     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 912             "clin_sig"));
 913     fr.setFeatureFilter("METAL", filter);
 914     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 915             false);
 916     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 917     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
 918             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
 919             + "STARTGROUP\tgrp2\n"
 920             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 921             + "ENDGROUP\tgrp2\n";
 922     assertEquals(fixLineEnd(expected), exported);
 923   }
 924 }