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.bin.Instance;
  33 import jalview.datamodel.Alignment;
  34 import jalview.datamodel.AlignmentI;
  35 import jalview.datamodel.SequenceDummy;
  36 import jalview.datamodel.SequenceFeature;
  37 import jalview.datamodel.SequenceI;
  38 import jalview.datamodel.features.FeatureMatcher;
  39 import jalview.datamodel.features.FeatureMatcherI;
  40 import jalview.datamodel.features.FeatureMatcherSet;
  41 import jalview.datamodel.features.FeatureMatcherSetI;
  42 import jalview.datamodel.features.SequenceFeatures;
  43 import jalview.gui.AlignFrame;
  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(Instance.getDesktop());
  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 colum 9
 272     String gffData = "##gff-version 3\n"
 273             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
 274             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
 275             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
 276     FeaturesFile featuresFile = new FeaturesFile(gffData,
 277             DataSourceType.PASTE);
 278     assertTrue("Failed to parse features file",
 279             featuresFile.parse(al.getDataset(), colours, true));
 280
 281     // verify feature on FER_CAPAA
 282     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 283             .getSequenceFeatures();
 284     assertEquals(1, sfs.size());
 285     SequenceFeature sf = sfs.get(0);
 286     // description parsed from Note attribute
 287     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
 288     assertEquals(39, sf.begin);
 289     assertEquals(39, sf.end);
 290     assertEquals("uniprot", sf.featureGroup);
 291     assertEquals("METAL", sf.type);
 292     assertEquals(
 293             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
 294             sf.getValue("ATTRIBUTES"));
 295
 296     // verify feature on FER1_SOLLC1
 297     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 298     assertEquals(1, sfs.size());
 299     sf = sfs.get(0);
 300     // ID used for description if available
 301     assertEquals("$23", sf.description);
 302     assertEquals(55, sf.begin);
 303     assertEquals(130, sf.end);
 304     assertEquals("uniprot", sf.featureGroup);
 305     assertEquals("Pfam", sf.type);
 306     assertEquals(3f, sf.getScore(), 0.001f);
 307   }
 308
 309   /**
 310    * Test parsing a features file with Jalview format features (but no colour
 311    * descriptors or startgroup to give the hint not to parse as GFF)
 312    *
 313    * @throws Exception
 314    */
 315   @Test(groups = { "Functional" })
 316   public void testParse_jalviewFeaturesOnly() throws Exception
 317   {
 318     File f = new File("examples/uniref50.fa");
 319     AlignmentI al = readAlignmentFile(f);
 320     AlignFrame af = new AlignFrame(al, 500, 500);
 321     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 322             .getFeatureColours();
 323
 324     /*
 325      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
 326      */
 327     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 328             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
 329     FeaturesFile featuresFile = new FeaturesFile(featureData,
 330             DataSourceType.PASTE);
 331     assertTrue("Failed to parse features file",
 332             featuresFile.parse(al.getDataset(), colours, true));
 333
 334     // verify FER_CAPAA feature
 335     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
 336             .getSequenceFeatures();
 337     assertEquals(1, sfs.size());
 338     SequenceFeature sf = sfs.get(0);
 339     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
 340     assertEquals(39, sf.begin);
 341     assertEquals(39, sf.end);
 342     assertEquals("METAL", sf.type);
 343
 344     // verify FER1_SOLLC feature
 345     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
 346     assertEquals(1, sfs.size());
 347     sf = sfs.get(0);
 348     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
 349     assertEquals(86, sf.begin);
 350     assertEquals(87, sf.end);
 351     assertEquals("METALLIC", sf.type);
 352   }
 353
 354   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 355   {
 356     assertEquals("no sequences extracted from GFF3 file", 2,
 357             dataset.getHeight());
 358
 359     SequenceI seq1 = dataset.findName("seq1");
 360     SequenceI seq2 = dataset.findName("seq2");
 361     assertNotNull(seq1);
 362     assertNotNull(seq2);
 363     assertFalse(
 364             "Failed to replace dummy seq1 with real sequence",
 365             seq1 instanceof SequenceDummy
 366                     && ((SequenceDummy) seq1).isDummy());
 367     assertFalse(
 368             "Failed to replace dummy seq2 with real sequence",
 369             seq2 instanceof SequenceDummy
 370                     && ((SequenceDummy) seq2).isDummy());
 371     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 372     assertFalse("dummy replacement buggy for seq1",
 373             placeholderseq.equals(seq1.getSequenceAsString()));
 374     assertFalse("dummy replacement buggy for seq2",
 375             placeholderseq.equals(seq2.getSequenceAsString()));
 376     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
 377     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
 378             .size());
 379     assertTrue(seq2.getSequenceFeatures().isEmpty());
 380     assertEquals(
 381             "Wrong number of features",
 382             0,
 383             seq2.getSequenceFeatures() == null ? 0 : seq2
 384                     .getSequenceFeatures().size());
 385     assertTrue(
 386             "Expected at least one CDNA/Protein mapping for seq1",
 387             dataset.getCodonFrame(seq1) != null
 388                     && dataset.getCodonFrame(seq1).size() > 0);
 389
 390   }
 391
 392   @Test(groups = { "Functional" })
 393   public void readGff3File() throws IOException
 394   {
 395     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
 396             DataSourceType.FILE);
 397     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
 398     gffreader.addProperties(dataset);
 399     checkDatasetfromSimpleGff3(dataset);
 400   }
 401
 402   @Test(groups = { "Functional" })
 403   public void simpleGff3FileClass() throws IOException
 404   {
 405     AlignmentI dataset = new Alignment(new SequenceI[] {});
 406     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 407             DataSourceType.FILE);
 408
 409     boolean parseResult = ffile.parse(dataset, null, false, false);
 410     assertTrue("return result should be true", parseResult);
 411     checkDatasetfromSimpleGff3(dataset);
 412   }
 413
 414   @Test(groups = { "Functional" })
 415   public void simpleGff3FileLoader() throws IOException
 416   {
 417     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
 418             simpleGffFile, DataSourceType.FILE);
 419     assertTrue(
 420             "Didn't read the alignment into an alignframe from Gff3 File",
 421             af != null);
 422     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
 423   }
 424
 425   @Test(groups = { "Functional" })
 426   public void simpleGff3RelaxedIdMatching() throws IOException
 427   {
 428     AlignmentI dataset = new Alignment(new SequenceI[] {});
 429     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
 430             DataSourceType.FILE);
 431
 432     boolean parseResult = ffile.parse(dataset, null, false, true);
 433     assertTrue("return result (relaxedID matching) should be true",
 434             parseResult);
 435     checkDatasetfromSimpleGff3(dataset);
 436   }
 437
 438   @Test(groups = { "Functional" })
 439   public void testPrintJalviewFormat() throws Exception
 440   {
 441     File f = new File("examples/uniref50.fa");
 442     AlignmentI al = readAlignmentFile(f);
 443     AlignFrame af = new AlignFrame(al, 500, 500);
 444     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
 445             .getFeatureColours();
 446     String features = "METAL\tcc9900\n"
 447             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
 448             + "Pfam\tred\n"
 449             + "STARTGROUP\tuniprot\n"
 450             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
 451             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
 452             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
 453             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
 454             + "ENDGROUP\tuniprot\n";
 455     FeaturesFile featuresFile = new FeaturesFile(features,
 456             DataSourceType.PASTE);
 457     featuresFile.parse(al.getDataset(), colours, false);
 458
 459     /*
 460      * add positional and non-positional features with null and
 461      * empty feature group to check handled correctly
 462      */
 463     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
 464     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
 465             null));
 466     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
 467             Float.NaN, null));
 468     seq = al.getSequenceAt(2); // FER1_SOLLC
 469     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
 470             Float.NaN, ""));
 471     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
 472             -2.6f, ""));
 473
 474     /*
 475      * first with no features displayed, exclude non-positional features
 476      */
 477     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 478     String exported = featuresFile
 479             .printJalviewFormat(al.getSequencesArray(), fr, false);
 480     String expected = "No Features Visible";
 481     assertEquals(expected, exported);
 482
 483     /*
 484      * include non-positional features, but still no positional features
 485      */
 486     fr.setGroupVisibility("uniprot", true);
 487     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 488             true);
 489     expected = "\nSTARTGROUP\tuniprot\n"
 490             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 491             + "ENDGROUP\tuniprot\n\n"
 492             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
 493             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
 494     assertEquals(
 495             expected.replace("\n", System.getProperty("line.separator")),
 496             exported);
 497
 498     /*
 499      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 500      */
 501     fr.setVisible("METAL");
 502     fr.setVisible("GAMMA-TURN");
 503     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 504             false);
 505     expected = "METAL\tcc9900\n"
 506             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 507             + "\nSTARTGROUP\tuniprot\n"
 508             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 509             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 510             + "ENDGROUP\tuniprot\n";
 511     assertEquals(fixLineEnd(expected), exported);
 512
 513     /*
 514      * now set Pfam visible
 515      */
 516     fr.setVisible("Pfam");
 517     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 518             false);
 519     /*
 520      * features are output within group, ordered by sequence and type
 521      */
 522     expected = "METAL\tcc9900\n"
 523             + "Pfam\tff0000\n"
 524             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 525             + "\nSTARTGROUP\tuniprot\n"
 526             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
 527             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
 528             + "<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"
 529             + "ENDGROUP\tuniprot\n"
 530             // null / empty group features are output after named groups
 531             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 532             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 533     assertEquals(fixLineEnd(expected), exported);
 534
 535     /*
 536      * hide uniprot group
 537      */
 538     fr.setGroupVisibility("uniprot", false);
 539     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 540             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 541             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 542             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 543     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 544             false);
 545     assertEquals(fixLineEnd(expected), exported);
 546
 547     /*
 548      * include non-positional (overrides group not shown)
 549      */
 550     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 551             true);
 552     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
 553             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
 554             + "\nSTARTGROUP\tuniprot\n"
 555             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
 556             + "ENDGROUP\tuniprot\n"
 557             + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
 558             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
 559             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
 560             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
 561     assertEquals(fixLineEnd(expected), exported);
 562   }
 563
 564   @Test(groups = { "Functional" })
 565   public void testPrintGffFormat() throws Exception
 566   {
 567     File f = new File("examples/uniref50.fa");
 568     AlignmentI al = readAlignmentFile(f);
 569     AlignFrame af = new AlignFrame(al, 500, 500);
 570
 571     /*
 572      * no features
 573      */
 574     FeaturesFile featuresFile = new FeaturesFile();
 575     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
 576             .getFeatureRenderer();
 577     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 578             fr, false);
 579     String gffHeader = "##gff-version 2\n";
 580     assertEquals(
 581             fixLineEnd(gffHeader),
 582             exported);
 583     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 584             true);
 585     assertEquals(
 586             fixLineEnd(gffHeader),
 587             exported);
 588
 589     /*
 590      * add some features
 591      */
 592     al.getSequenceAt(0).addSequenceFeature(
 593             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
 594     al.getSequenceAt(0).addSequenceFeature(
 595             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
 596     al.getSequenceAt(1)
 597             .addSequenceFeature(
 598                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
 599                             "s3dm"));
 600     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
 601             "Uniprot");
 602     sf.setAttributes("x=y;black=white");
 603     sf.setStrand("+");
 604     sf.setPhase("2");
 605     al.getSequenceAt(1).addSequenceFeature(sf);
 606
 607     /*
 608      * 'discover' features then hide all feature types
 609      */
 610     fr.findAllFeatures(true);
 611     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 612     FeatureColourI fc = new FeatureColour(Color.PINK);
 613     data[0] = new FeatureSettingsBean("Domain", fc, null, false);
 614     data[1] = new FeatureSettingsBean("METAL", fc, null, false);
 615     data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
 616     data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
 617     fr.setFeaturePriority(data);
 618
 619     /*
 620      * with no features displayed, exclude non-positional features
 621      */
 622     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 623             false);
 624     assertEquals(
 625             fixLineEnd(gffHeader),
 626             exported);
 627
 628     /*
 629      * include non-positional features
 630      */
 631     fr.setGroupVisibility("Uniprot", true);
 632     fr.setGroupVisibility("s3dm", false);
 633     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 634             true);
 635     String expected = gffHeader
 636             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
 637     assertEquals(
 638             fixLineEnd(expected),
 639             exported);
 640
 641     /*
 642      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
 643      * only Uniprot group visible here...
 644      */
 645     fr.setVisible("METAL");
 646     fr.setVisible("GAMMA-TURN");
 647     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 648             false);
 649     // METAL feature has null group: description used for column 2
 650     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 651     assertEquals(
 652             expected.replace("\n", System.getProperty("line.separator")),
 653             exported);
 654
 655     /*
 656      * set s3dm group visible
 657      */
 658     fr.setGroupVisibility("s3dm", true);
 659     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 660             false);
 661     // METAL feature has null group: description used for column 2
 662     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 663             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
 664     assertEquals(
 665             expected.replace("\n", System.getProperty("line.separator")),
 666             exported);
 667
 668     /*
 669      * now set Pfam visible
 670      */
 671     fr.setVisible("Pfam");
 672     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 673             false);
 674     // Pfam feature columns include strand(+), phase(2), attributes
 675     expected = gffHeader
 676             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 677             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
 678             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
 679     assertEquals(
 680             expected.replace("\n", System.getProperty("line.separator")),
 681             exported);
 682   }
 683
 684   private String fixLineEnd(String s)
 685   {
 686     return s.replace("\n", System.getProperty("line.separator"));
 687   }
 688
 689   /**
 690    * Test for parsing of feature filters as represented in a Jalview features
 691    * file
 692    *
 693    * @throws Exception
 694    */
 695   @Test(groups = { "Functional" })
 696   public void testParseFilters() throws Exception
 697   {
 698     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
 699     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
 700             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
 701     FeaturesFile featuresFile = new FeaturesFile(text,
 702             DataSourceType.PASTE);
 703     featuresFile.parseFilters(filters);
 704     assertEquals(filters.size(), 2);
 705
 706     FeatureMatcherSetI fm = filters.get("sequence_variant");
 707     assertNotNull(fm);
 708     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
 709     FeatureMatcherI matcher = matchers.next();
 710     assertFalse(matchers.hasNext());
 711     String[] attributes = matcher.getAttribute();
 712     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
 713     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
 714     assertEquals(matcher.getMatcher().getPattern(), "damaging");
 715
 716     fm = filters.get("missense_variant");
 717     assertNotNull(fm);
 718     matchers = fm.getMatchers().iterator();
 719     matcher = matchers.next();
 720     assertTrue(matcher.isByLabel());
 721     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
 722     assertEquals(matcher.getMatcher().getPattern(), "foobar");
 723     matcher = matchers.next();
 724     assertTrue(matcher.isByScore());
 725     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
 726     assertEquals(matcher.getMatcher().getPattern(), "1.3");
 727     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
 728
 729     assertFalse(matchers.hasNext());
 730   }
 731
 732   @Test(groups = { "Functional" })
 733   public void testOutputFeatureFilters()
 734   {
 735     FeaturesFile ff = new FeaturesFile();
 736     StringBuilder sb = new StringBuilder();
 737     Map<String, FeatureColourI> visible = new HashMap<>();
 738     visible.put("pfam", new FeatureColour(Color.red));
 739     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 740
 741     // with no filters, nothing is output
 742     ff.outputFeatureFilters(sb, visible, featureFilters);
 743     assertEquals("", sb.toString());
 744
 745     // with filter for not visible features only, nothing is output
 746     FeatureMatcherSet filter = new FeatureMatcherSet();
 747     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
 748     featureFilters.put("foobar", filter);
 749     ff.outputFeatureFilters(sb, visible, featureFilters);
 750     assertEquals("", sb.toString());
 751
 752     // with filters for visible feature types
 753     FeatureMatcherSet filter2 = new FeatureMatcherSet();
 754     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
 755             "PolyPhen"));
 756     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
 757     featureFilters.put("pfam", filter2);
 758     visible.put("foobar", new FeatureColour(Color.blue));
 759     ff.outputFeatureFilters(sb, visible, featureFilters);
 760     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
 761     assertEquals(fixLineEnd(expected), sb.toString());
 762   }
 763
 764   /**
 765    * Output as GFF should not include features which are not visible due to
 766    * colour threshold or feature filter settings
 767    *
 768    * @throws Exception
 769    */
 770   @Test(groups = { "Functional" })
 771   public void testPrintGffFormat_withFilters() throws Exception
 772   {
 773     File f = new File("examples/uniref50.fa");
 774     AlignmentI al = readAlignmentFile(f);
 775     AlignFrame af = new AlignFrame(al, 500, 500);
 776     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 777             null);
 778     sf1.setValue("clin_sig", "Likely Pathogenic");
 779     sf1.setValue("AF", "24");
 780     al.getSequenceAt(0).addSequenceFeature(sf1);
 781     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 782             null);
 783     sf2.setValue("clin_sig", "Benign");
 784     sf2.setValue("AF", "46");
 785     al.getSequenceAt(0).addSequenceFeature(sf2);
 786
 787     FeaturesFile featuresFile = new FeaturesFile();
 788     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 789     final String gffHeader = "##gff-version 2\n";
 790
 791     fr.setVisible("METAL");
 792     fr.setColour("METAL", new FeatureColour(Color.PINK));
 793     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
 794             fr, false);
 795     String expected = gffHeader
 796             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 797             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 798     assertEquals(
 799             fixLineEnd(expected), exported);
 800
 801     /*
 802      * now threshold to Score > 1.1 - should exclude sf2
 803      */
 804     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 805             Color.white, 0f, 2f);
 806     fc.setAboveThreshold(true);
 807     fc.setThreshold(1.1f);
 808     fr.setColour("METAL", fc);
 809     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 810             false);
 811     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
 812     assertEquals(fixLineEnd(expected), exported);
 813
 814     /*
 815      * remove threshold and check sf2 is exported
 816      */
 817     fc.setAboveThreshold(false);
 818     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 819             false);
 820     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
 821             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 822     assertEquals(fixLineEnd(expected), exported);
 823
 824     /*
 825      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
 826      */
 827     FeatureMatcherSetI filter = new FeatureMatcherSet();
 828     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
 829             "clin_sig"));
 830     fr.setFeatureFilter("METAL", filter);
 831     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
 832             false);
 833     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
 834     assertEquals(fixLineEnd(expected), exported);
 835   }
 836
 837   /**
 838    * Output as Jalview should not include features which are not visible due to
 839    * colour threshold or feature filter settings
 840    *
 841    * @throws Exception
 842    */
 843   @Test(groups = { "Functional" })
 844   public void testPrintJalviewFormat_withFilters() throws Exception
 845   {
 846     File f = new File("examples/uniref50.fa");
 847     AlignmentI al = readAlignmentFile(f);
 848     AlignFrame af = new AlignFrame(al, 500, 500);
 849     SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
 850             "grp1");
 851     sf1.setValue("clin_sig", "Likely Pathogenic");
 852     sf1.setValue("AF", "24");
 853     al.getSequenceAt(0).addSequenceFeature(sf1);
 854     SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
 855             "grp2");
 856     sf2.setValue("clin_sig", "Benign");
 857     sf2.setValue("AF", "46");
 858     al.getSequenceAt(0).addSequenceFeature(sf2);
 859
 860     FeaturesFile featuresFile = new FeaturesFile();
 861     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
 862     fr.findAllFeatures(true);
 863
 864     fr.setVisible("METAL");
 865     fr.setColour("METAL", new FeatureColour(Color.PINK));
 866     String exported = featuresFile.printJalviewFormat(
 867             al.getSequencesArray(),
 868             fr, false);
 869     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
 870             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 871             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
 872             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
 873             + "ENDGROUP\tgrp2\n";
 874     assertEquals(
 875             fixLineEnd(expected),
 876             exported);
 877
 878     /*
 879      * now threshold to Score > 1.1 - should exclude sf2
 880      * (and there should be no empty STARTGROUP/ENDGROUP output)
 881      */
 882     FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
 883             Color.white, 0f, 2f);
 884     fc.setAboveThreshold(true);
 885     fc.setThreshold(1.1f);
 886     fr.setColour("METAL", fc);
 887     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
 888             false);
 889     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
 890             + "STARTGROUP\tgrp1\n"
 891             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
 892             + "ENDGROUP\tgrp1\n";
 893     assertEquals(
 894             expected.replace("\n", System.getProperty("line.separator")),
 895             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);
 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(fixLineEnd(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);
 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(fixLineEnd(expected), exported);
 927   }
 928 }