test/jalview/io/Jalview2xmlTests.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.Assert.assertEquals;
  24 import static org.testng.Assert.assertFalse;
  25 import static org.testng.Assert.assertNotNull;
  26 import static org.testng.Assert.assertNull;
  27 import static org.testng.Assert.assertSame;
  28 import static org.testng.Assert.assertTrue;
  29
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.AlignmentViewPanel;
  32 import jalview.api.FeatureColourI;
  33 import jalview.api.ViewStyleI;
  34 import jalview.datamodel.AlignmentAnnotation;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.HiddenSequences;
  37 import jalview.datamodel.PDBEntry;
  38 import jalview.datamodel.PDBEntry.Type;
  39 import jalview.datamodel.SequenceCollectionI;
  40 import jalview.datamodel.SequenceFeature;
  41 import jalview.datamodel.SequenceGroup;
  42 import jalview.datamodel.SequenceI;
  43 import jalview.datamodel.features.FeatureMatcher;
  44 import jalview.datamodel.features.FeatureMatcherSet;
  45 import jalview.datamodel.features.FeatureMatcherSetI;
  46 import jalview.gui.AlignFrame;
  47 import jalview.gui.AlignmentPanel;
  48 import jalview.gui.Desktop;
  49 import jalview.gui.FeatureRenderer;
  50 import jalview.gui.Jalview2XML;
  51 import jalview.gui.JvOptionPane;
  52 import jalview.gui.PopupMenu;
  53 import jalview.gui.SliderPanel;
  54 import jalview.renderer.ResidueShaderI;
  55 import jalview.schemes.AnnotationColourGradient;
  56 import jalview.schemes.BuriedColourScheme;
  57 import jalview.schemes.ColourSchemeI;
  58 import jalview.schemes.ColourSchemeProperty;
  59 import jalview.schemes.FeatureColour;
  60 import jalview.schemes.JalviewColourScheme;
  61 import jalview.schemes.RNAHelicesColour;
  62 import jalview.schemes.StrandColourScheme;
  63 import jalview.schemes.TCoffeeColourScheme;
  64 import jalview.structure.StructureImportSettings;
  65 import jalview.util.matcher.Condition;
  66 import jalview.viewmodel.AlignmentViewport;
  67
  68 import java.awt.Color;
  69 import java.io.File;
  70 import java.io.IOException;
  71 import java.util.ArrayList;
  72 import java.util.HashMap;
  73 import java.util.List;
  74 import java.util.Map;
  75
  76 import org.testng.Assert;
  77 import org.testng.AssertJUnit;
  78 import org.testng.annotations.BeforeClass;
  79 import org.testng.annotations.Test;
  80
  81 @Test(singleThreaded = true)
  82 public class Jalview2xmlTests extends Jalview2xmlBase
  83 {
  84
  85   @Override
  86   @BeforeClass(alwaysRun = true)
  87   public void setUpJvOptionPane()
  88   {
  89     JvOptionPane.setInteractiveMode(false);
  90     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  91   }
  92
  93   @Test(groups = { "Functional" })
  94   public void testRNAStructureRecovery() throws Exception
  95   {
  96     String inFile = "examples/RF00031_folded.stk";
  97     String tfile = File.createTempFile("JalviewTest", ".jvp")
  98             .getAbsolutePath();
  99     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 100             DataSourceType.FILE);
 101     assertNotNull(af, "Didn't read input file " + inFile);
 102     int olddsann = countDsAnn(af.getViewport());
 103     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 104     af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
 105             .toString());
 106     assertTrue(
 107             af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 108             "Couldn't apply RNA helices colourscheme");
 109     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 110             "Failed to store as a project.");
 111     af.closeMenuItem_actionPerformed(true);
 112     af = null;
 113     af = new FileLoader()
 114             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 115     assertNotNull(af, "Failed to import new project");
 116     int newdsann = countDsAnn(af.getViewport());
 117     assertEquals(olddsann, newdsann,
 118             "Differing numbers of dataset sequence annotation\nOriginally "
 119                     + olddsann + " and now " + newdsann);
 120     System.out
 121             .println("Read in same number of annotations as originally present ("
 122                     + olddsann + ")");
 123     assertTrue(
 124
 125     af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 126             "RNA helices colourscheme was not applied on import.");
 127   }
 128
 129   @Test(groups = { "Functional" })
 130   public void testTCoffeeScores() throws Exception
 131   {
 132     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
 133     String tfile = File.createTempFile("JalviewTest", ".jvp")
 134             .getAbsolutePath();
 135     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 136             DataSourceType.FILE);
 137     assertNotNull(af, "Didn't read input file " + inFile);
 138     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 139     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 140             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 141     assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
 142             .getAlignment(), af.getViewport().getGlobalColourScheme()
 143             .getSchemeName()), "Recognise T-Coffee score from string");
 144
 145     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 146             "Failed to store as a project.");
 147     af.closeMenuItem_actionPerformed(true);
 148     af = null;
 149     af = new FileLoader()
 150             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 151     assertNotNull(af, "Failed to import new project");
 152     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 153             TCoffeeColourScheme.class,
 154             "Didn't set T-coffee colourscheme for imported project.");
 155     System.out
 156             .println("T-Coffee score shading successfully recovered from project.");
 157   }
 158
 159   @Test(groups = { "Functional" })
 160   public void testColourByAnnotScores() throws Exception
 161   {
 162     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
 163     String tfile = File.createTempFile("JalviewTest", ".jvp")
 164             .getAbsolutePath();
 165     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 166             DataSourceType.FILE);
 167     assertNotNull(af, "Didn't read input file " + inFile);
 168     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 169     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 170             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 171     assertTrue(
 172
 173     aa != null && aa.length > 0,
 174             "Didn't find any IUPred annotation to use to shade alignment.");
 175     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 176             AnnotationColourGradient.ABOVE_THRESHOLD);
 177     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
 178             null, AnnotationColourGradient.BELOW_THRESHOLD);
 179     cs.setSeqAssociated(true);
 180     gcs.setSeqAssociated(true);
 181     af.changeColour(cs);
 182     SequenceGroup sg = new SequenceGroup();
 183     sg.setStartRes(57);
 184     sg.setEndRes(92);
 185     sg.cs.setColourScheme(gcs);
 186     af.getViewport().getAlignment().addGroup(sg);
 187     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 188     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 189     af.alignPanel.alignmentChanged();
 190     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 191             "Failed to store as a project.");
 192     af.closeMenuItem_actionPerformed(true);
 193     af = null;
 194     af = new FileLoader()
 195             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 196     assertNotNull(af, "Failed to import new project");
 197
 198     // check for group and alignment colourschemes
 199
 200     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 201     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
 202             .get(0).getColourScheme();
 203     assertNotNull(_rcs, "Didn't recover global colourscheme");
 204     assertTrue(_rcs instanceof AnnotationColourGradient,
 205             "Didn't recover annotation colour global scheme");
 206     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 207     assertTrue(__rcs.isSeqAssociated(),
 208             "Annotation colourscheme wasn't sequence associated");
 209
 210     boolean diffseqcols = false, diffgseqcols = false;
 211     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 212     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 213             && (!diffseqcols || !diffgseqcols); p++)
 214     {
 215       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 216               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 217       {
 218         diffseqcols = true;
 219       }
 220     }
 221     assertTrue(diffseqcols, "Got Different sequence colours");
 222     System.out
 223             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 224
 225     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 226     assertTrue(_rgcs instanceof AnnotationColourGradient,
 227             "Didn't recover annotation colour group colourscheme");
 228     __rcs = (AnnotationColourGradient) _rgcs;
 229     assertTrue(__rcs.isSeqAssociated(),
 230             "Group Annotation colourscheme wasn't sequence associated");
 231
 232     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 233             && (!diffseqcols || !diffgseqcols); p++)
 234     {
 235       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
 236               .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
 237       {
 238         diffgseqcols = true;
 239       }
 240     }
 241     assertTrue(diffgseqcols, "Got Different group sequence colours");
 242     System.out
 243             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
 244   }
 245
 246   @Test(groups = { "Functional" })
 247   public void gatherViewsHere() throws Exception
 248   {
 249     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
 250             .getAlignFrames().length;
 251     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 252             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 253     assertNotNull(af, "Didn't read in the example file correctly.");
 254     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 255             "Didn't gather the views in the example file.");
 256
 257   }
 258
 259   @Test(groups = { "Functional" })
 260   public void viewRefPdbAnnotation() throws Exception
 261   {
 262     StructureImportSettings.setProcessSecondaryStructure(true);
 263     StructureImportSettings.setVisibleChainAnnotation(true);
 264     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 265             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 266     assertNotNull(af, "Didn't read in the example file correctly.");
 267     AlignmentViewPanel sps = null;
 268     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 269     {
 270       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 271       {
 272         sps = ap;
 273         break;
 274       }
 275     }
 276     assertNotNull(sps, "Couldn't find the structure view");
 277     AlignmentAnnotation refan = null;
 278     for (AlignmentAnnotation ra : sps.getAlignment()
 279             .getAlignmentAnnotation())
 280     {
 281       if (ra.graph != 0)
 282       {
 283         refan = ra;
 284         break;
 285       }
 286     }
 287     assertNotNull(refan, "Annotation secondary structure not found.");
 288     SequenceI sq = sps.getAlignment().findName("1A70|");
 289     assertNotNull(sq, "Couldn't find 1a70 null chain");
 290     // compare the manually added temperature factor annotation
 291     // to the track automatically transferred from the pdb structure on load
 292     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 293             "1a70 has no annotation");
 294     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 295     {
 296       AlignmentAnnotation alaa;
 297       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 298       alaa.adjustForAlignment();
 299       if (ala.graph == refan.graph)
 300       {
 301         for (int p = 0; p < ala.annotations.length; p++)
 302         {
 303           sq.findPosition(p);
 304           try
 305           {
 306             assertTrue(
 307                     (alaa.annotations[p] == null && refan.annotations[p] == null)
 308                             || alaa.annotations[p].value == refan.annotations[p].value,
 309                     "Mismatch at alignment position " + p);
 310           } catch (NullPointerException q)
 311           {
 312             Assert.fail("Mismatch of alignment annotations at position "
 313                     + p + " Ref seq ann: " + refan.annotations[p]
 314                     + " alignment " + alaa.annotations[p]);
 315           }
 316         }
 317       }
 318     }
 319
 320   }
 321
 322   @Test(groups = { "Functional" })
 323   public void testCopyViewSettings() throws Exception
 324   {
 325     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 326             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 327     assertNotNull(af, "Didn't read in the example file correctly.");
 328     AlignmentViewPanel sps = null, groups = null;
 329     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 330     {
 331       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 332       {
 333         sps = ap;
 334       }
 335       if (ap.getViewName().contains("MAFFT"))
 336       {
 337         groups = ap;
 338       }
 339     }
 340     assertNotNull(sps, "Couldn't find the structure view");
 341     assertNotNull(groups, "Couldn't find the MAFFT view");
 342
 343     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 344     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 345     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 346
 347     groups.getAlignViewport().setViewStyle(structureStyle);
 348     AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
 349             .getViewStyle()));
 350     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
 351             .getViewStyle()));
 352
 353   }
 354
 355   /**
 356    * test store and recovery of expanded views
 357    *
 358    * @throws Exception
 359    */
 360   @Test(groups = { "Functional" }, enabled = true)
 361   public void testStoreAndRecoverExpandedviews() throws Exception
 362   {
 363     Desktop.instance.closeAll_actionPerformed(null);
 364
 365     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 366             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 367     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 368     String afid = af.getViewport().getSequenceSetId();
 369
 370     // check FileLoader returned a reference to the one alignFrame that is
 371     // actually on the Desktop
 372     assertSame(
 373             af,
 374             Desktop.getAlignFrameFor(af.getViewport()),
 375             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 376
 377     Desktop.explodeViews(af);
 378
 379     int oldviews = Desktop.getAlignFrames().length;
 380     Assert.assertEquals(Desktop.getAlignFrames().length,
 381             Desktop.getAlignmentPanels(afid).length);
 382     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 383     try
 384     {
 385       new Jalview2XML(false).saveState(tfile);
 386     } catch (Error e)
 387     {
 388       Assert.fail("Didn't save the expanded view state", e);
 389     } catch (Exception e)
 390     {
 391       Assert.fail("Didn't save the expanded view state", e);
 392     }
 393     Desktop.instance.closeAll_actionPerformed(null);
 394     if (Desktop.getAlignFrames() != null)
 395     {
 396       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 397     }
 398     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 399             DataSourceType.FILE);
 400     Assert.assertNotNull(af);
 401     Assert.assertEquals(
 402             Desktop.getAlignFrames().length,
 403             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
 404     Assert.assertEquals(
 405             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
 406             oldviews);
 407   }
 408
 409   /**
 410    * Test save and reload of a project with a different representative sequence
 411    * in each view.
 412    *
 413    * @throws Exception
 414    */
 415   @Test(groups = { "Functional" })
 416   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 417   {
 418     Desktop.instance.closeAll_actionPerformed(null);
 419     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 420             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 421     assertNotNull(af, "Didn't read in the example file correctly.");
 422     String afid = af.getViewport().getSequenceSetId();
 423
 424     // remember reference sequence for each panel
 425     Map<String, SequenceI> refseqs = new HashMap<>();
 426
 427     /*
 428      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 429      * as reference sequence for itself and the preceding sequence
 430      */
 431     int n = 1;
 432     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 433     {
 434       AlignViewportI av = ap.getAlignViewport();
 435       AlignmentI alignment = ap.getAlignment();
 436       int repIndex = n % alignment.getHeight();
 437       SequenceI rep = alignment.getSequenceAt(repIndex);
 438       refseqs.put(ap.getViewName(), rep);
 439
 440       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 441       // todo refactor this to an alignment view controller
 442       av.setDisplayReferenceSeq(true);
 443       av.setColourByReferenceSeq(true);
 444       av.getAlignment().setSeqrep(rep);
 445
 446       n++;
 447     }
 448     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 449             ".jvp");
 450     try
 451     {
 452       new Jalview2XML(false).saveState(tfile);
 453     } catch (Throwable e)
 454     {
 455       Assert.fail("Didn't save the expanded view state", e);
 456     }
 457     Desktop.instance.closeAll_actionPerformed(null);
 458     if (Desktop.getAlignFrames() != null)
 459     {
 460       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 461     }
 462
 463     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 464             DataSourceType.FILE);
 465     afid = af.getViewport().getSequenceSetId();
 466
 467     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 468     {
 469       // check representative
 470       AlignmentI alignment = ap.getAlignment();
 471       SequenceI rep = alignment.getSeqrep();
 472       Assert.assertNotNull(rep,
 473               "Couldn't restore sequence representative from project");
 474       // can't use a strong equals here, because by definition, the sequence IDs
 475       // will be different.
 476       // could set vamsas session save/restore flag to preserve IDs across
 477       // load/saves.
 478       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 479               rep.toString(),
 480               "Representative wasn't the same when recovered.");
 481       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 482               "Display reference sequence view setting not set.");
 483       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 484               "Colour By Reference Seq view setting not set.");
 485     }
 486   }
 487
 488   @Test(groups = { "Functional" })
 489   public void testIsVersionStringLaterThan()
 490   {
 491     /*
 492      * No version / development / test / autobuild is leniently assumed to be
 493      * compatible
 494      */
 495     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 496     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 497     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 498     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 499             "Development Build"));
 500     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 501             "DEVELOPMENT BUILD"));
 502     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 503             "Development Build"));
 504     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 505     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 506     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 507     assertTrue(Jalview2XML
 508             .isVersionStringLaterThan(null, "Automated Build"));
 509     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 510             "Automated Build"));
 511     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 512             "AUTOMATED BUILD"));
 513
 514     /*
 515      * same version returns true i.e. compatible
 516      */
 517     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 518     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 519     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 520     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 521     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 522
 523     /*
 524      * later version returns true
 525      */
 526     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 527     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 528     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 529     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 530     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 531
 532     /*
 533      * earlier version returns false
 534      */
 535     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 536     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 537     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 538     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 539     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 540   }
 541
 542   /**
 543    * Test save and reload of a project with a different sequence group (and
 544    * representative sequence) in each view.
 545    *
 546    * @throws Exception
 547    */
 548   @Test(groups = { "Functional" })
 549   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 550   {
 551     Desktop.instance.closeAll_actionPerformed(null);
 552     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 553             "examples/uniref50.fa", DataSourceType.FILE);
 554     assertNotNull(af, "Didn't read in the example file correctly.");
 555     String afid = af.getViewport().getSequenceSetId();
 556     // make a second view of the alignment
 557     af.newView_actionPerformed(null);
 558
 559     /*
 560      * remember representative and hidden sequences marked
 561      * on each panel
 562      */
 563     Map<String, SequenceI> repSeqs = new HashMap<>();
 564     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 565
 566     /*
 567      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 568      * as reference sequence for itself and the preceding sequence
 569      */
 570     int n = 1;
 571     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 572     {
 573       AlignViewportI av = ap.getAlignViewport();
 574       AlignmentI alignment = ap.getAlignment();
 575       int repIndex = n % alignment.getHeight();
 576       // ensure at least one preceding sequence i.e. index >= 1
 577       repIndex = Math.max(repIndex, 1);
 578       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 579       repSeqs.put(ap.getViewName(), repSeq);
 580       List<String> hiddenNames = new ArrayList<>();
 581       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 582
 583       /*
 584        * have rep sequence represent itself and the one before it
 585        * this hides the group (except for the rep seq)
 586        */
 587       SequenceGroup sg = new SequenceGroup();
 588       sg.addSequence(repSeq, false);
 589       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 590       sg.addSequence(precedingSeq, false);
 591       sg.setSeqrep(repSeq);
 592       assertTrue(sg.getSequences().contains(repSeq));
 593       assertTrue(sg.getSequences().contains(precedingSeq));
 594       av.setSelectionGroup(sg);
 595       assertSame(repSeq, sg.getSeqrep());
 596
 597       /*
 598        * represent group with sequence adds to a map of hidden rep sequences
 599        * (it does not create a group on the alignment)
 600        */
 601       ((AlignmentViewport) av).hideSequences(repSeq, true);
 602       assertSame(repSeq, sg.getSeqrep());
 603       assertTrue(sg.getSequences().contains(repSeq));
 604       assertTrue(sg.getSequences().contains(precedingSeq));
 605       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 606       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 607               .getHiddenRepSequences();
 608       assertNotNull(hiddenRepSeqsMap);
 609       assertEquals(1, hiddenRepSeqsMap.size());
 610       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 611       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 612       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 613       hiddenNames.add(precedingSeq.getName());
 614
 615       n++;
 616     }
 617     File tfile = File
 618             .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
 619     try
 620     {
 621       new Jalview2XML(false).saveState(tfile);
 622     } catch (Throwable e)
 623     {
 624       Assert.fail("Didn't save the expanded view state", e);
 625     }
 626     Desktop.instance.closeAll_actionPerformed(null);
 627     if (Desktop.getAlignFrames() != null)
 628     {
 629       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 630     }
 631
 632     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 633             DataSourceType.FILE);
 634     afid = af.getViewport().getSequenceSetId();
 635
 636     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 637     {
 638       String viewName = ap.getViewName();
 639       AlignViewportI av = ap.getAlignViewport();
 640       AlignmentI alignment = ap.getAlignment();
 641       List<SequenceGroup> groups = alignment.getGroups();
 642       assertNotNull(groups);
 643       assertTrue(groups.isEmpty(), "Alignment has groups");
 644       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 645               .getHiddenRepSequences();
 646       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 647       assertEquals(1, hiddenRepSeqsMap.size());
 648       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 649               hiddenRepSeqsMap.keySet().iterator().next()
 650                       .getDisplayId(true));
 651
 652       /*
 653        * verify hidden sequences in restored panel
 654        */
 655       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 656       HiddenSequences hs = alignment.getHiddenSequences();
 657       assertEquals(
 658               hidden.size(),
 659               hs.getSize(),
 660               "wrong number of restored hidden sequences in "
 661                       + ap.getViewName());
 662     }
 663   }
 664
 665   /**
 666    * Test save and reload of PDBEntry in Jalview project
 667    *
 668    * @throws Exception
 669    */
 670   @Test(groups = { "Functional" })
 671   public void testStoreAndRecoverPDBEntry() throws Exception
 672   {
 673     Desktop.instance.closeAll_actionPerformed(null);
 674     String exampleFile = "examples/3W5V.pdb";
 675     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 676             DataSourceType.FILE);
 677     assertNotNull(af, "Didn't read in the example file correctly.");
 678     String afid = af.getViewport().getSequenceSetId();
 679
 680     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 681     System.out.println();
 682     AlignmentViewPanel ap = alignPanels[0];
 683     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 684     String testFile = tfileBase + exampleFile;
 685     AlignmentI alignment = ap.getAlignment();
 686     System.out.println("blah");
 687     SequenceI[] seqs = alignment.getSequencesArray();
 688     Assert.assertNotNull(seqs[0]);
 689     Assert.assertNotNull(seqs[1]);
 690     Assert.assertNotNull(seqs[2]);
 691     Assert.assertNotNull(seqs[3]);
 692     Assert.assertNotNull(seqs[0].getDatasetSequence());
 693     Assert.assertNotNull(seqs[1].getDatasetSequence());
 694     Assert.assertNotNull(seqs[2].getDatasetSequence());
 695     Assert.assertNotNull(seqs[3].getDatasetSequence());
 696     PDBEntry[] pdbEntries = new PDBEntry[4];
 697     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 698     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 699     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 700     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 701     Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
 702             .get(0), pdbEntries[0]);
 703     Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
 704             .get(0), pdbEntries[1]);
 705     Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
 706             .get(0), pdbEntries[2]);
 707     Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
 708             .get(0), pdbEntries[3]);
 709
 710     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 711     try
 712     {
 713       new Jalview2XML(false).saveState(tfile);
 714     } catch (Throwable e)
 715     {
 716       Assert.fail("Didn't save the state", e);
 717     }
 718     Desktop.instance.closeAll_actionPerformed(null);
 719     if (Desktop.getAlignFrames() != null)
 720     {
 721       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 722     }
 723
 724     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 725             tfile.getAbsolutePath(), DataSourceType.FILE);
 726     String rfid = restoredFrame.getViewport().getSequenceSetId();
 727     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 728     AlignmentViewPanel rap = rAlignPanels[0];
 729     AlignmentI rAlignment = rap.getAlignment();
 730     System.out.println("blah");
 731     SequenceI[] rseqs = rAlignment.getSequencesArray();
 732     Assert.assertNotNull(rseqs[0]);
 733     Assert.assertNotNull(rseqs[1]);
 734     Assert.assertNotNull(rseqs[2]);
 735     Assert.assertNotNull(rseqs[3]);
 736     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 737     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 738     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 739     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 740
 741     // The Asserts below are expected to fail until the PDB chainCode is
 742     // recoverable from a Jalview projects
 743     for (int chain = 0; chain < 4; chain++)
 744     {
 745       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 746               .get(0);
 747       PDBEntry expected = pdbEntries[chain];
 748       Assert.assertEquals(recov.getId(), expected.getId(),
 749               "Mismatch PDB ID");
 750       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 751               "Mismatch PDB ID");
 752       Assert.assertEquals(recov.getType(), expected.getType(),
 753               "Mismatch PDBEntry 'Type'");
 754       Assert.assertNotNull(recov.getFile(),
 755               "Recovered PDBEntry should have a non-null file entry");
 756     }
 757   }
 758
 759   /**
 760    * Configure an alignment and a sub-group each with distinct colour schemes,
 761    * Conservation and PID thresholds, and confirm these are restored from the
 762    * saved project.
 763    *
 764    * @throws IOException
 765    */
 766   @Test(groups = { "Functional" })
 767   public void testStoreAndRecoverColourThresholds() throws IOException
 768   {
 769     Desktop.instance.closeAll_actionPerformed(null);
 770     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 771             "examples/uniref50.fa", DataSourceType.FILE);
 772
 773     AlignViewportI av = af.getViewport();
 774     AlignmentI al = av.getAlignment();
 775
 776     /*
 777      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 778      */
 779     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 780     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 781     af.abovePIDThreshold_actionPerformed(true);
 782     SliderPanel sp = SliderPanel.getSliderPanel();
 783     assertFalse(sp.isForConservation());
 784     sp.valueChanged(10);
 785     af.conservationMenuItem_actionPerformed(true);
 786     sp = SliderPanel.getSliderPanel();
 787     assertTrue(sp.isForConservation());
 788     sp.valueChanged(20);
 789     ResidueShaderI rs = av.getResidueShading();
 790     assertEquals(rs.getThreshold(), 10);
 791     assertTrue(rs.conservationApplied());
 792     assertEquals(rs.getConservationInc(), 20);
 793
 794     /*
 795      * create a group with Strand colouring, 30% Conservation
 796      * and 40% PID threshold
 797      */
 798     SequenceGroup sg = new SequenceGroup();
 799     sg.addSequence(al.getSequenceAt(0), false);
 800     sg.setStartRes(15);
 801     sg.setEndRes(25);
 802     av.setSelectionGroup(sg);
 803     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 804     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
 805             .toString());
 806     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 807     assertEquals(al.getGroups().size(), 1);
 808     assertSame(al.getGroups().get(0), sg);
 809     popupMenu.conservationMenuItem_actionPerformed(true);
 810     sp = SliderPanel.getSliderPanel();
 811     assertTrue(sp.isForConservation());
 812     sp.valueChanged(30);
 813     popupMenu.abovePIDColour_actionPerformed(true);
 814     sp = SliderPanel.getSliderPanel();
 815     assertFalse(sp.isForConservation());
 816     sp.valueChanged(40);
 817     assertTrue(sg.getGroupColourScheme().conservationApplied());
 818     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 819     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 820
 821     /*
 822      * save project, close windows, reload project, verify
 823      */
 824     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 825             ".jvp");
 826     tfile.deleteOnExit();
 827     new Jalview2XML(false).saveState(tfile);
 828     Desktop.instance.closeAll_actionPerformed(null);
 829     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 830             DataSourceType.FILE);
 831     Assert.assertNotNull(af, "Failed to reload project");
 832
 833     /*
 834      * verify alignment (background) colouring
 835      */
 836     rs = af.getViewport().getResidueShading();
 837     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 838     assertEquals(rs.getThreshold(), 10);
 839     assertTrue(rs.conservationApplied());
 840     assertEquals(rs.getConservationInc(), 20);
 841
 842     /*
 843      * verify group colouring
 844      */
 845     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 846     rs = af.getViewport().getAlignment().getGroups().get(0)
 847             .getGroupColourScheme();
 848     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 849     assertEquals(rs.getThreshold(), 40);
 850     assertTrue(rs.conservationApplied());
 851     assertEquals(rs.getConservationInc(), 30);
 852   }
 853
 854   /**
 855    * Test save and reload of feature colour schemes and filter settings
 856    *
 857    * @throws IOException
 858    */
 859   @Test(groups = { "Functional" })
 860   public void testSaveLoadFeatureColoursAndFilters() throws IOException
 861   {
 862     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 863             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 864     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 865
 866     /*
 867      * add some features to the sequence
 868      */
 869     int score = 1;
 870     addFeatures(seq1, "type1", score++);
 871     addFeatures(seq1, "type2", score++);
 872     addFeatures(seq1, "type3", score++);
 873     addFeatures(seq1, "type4", score++);
 874     addFeatures(seq1, "type5", score++);
 875
 876     /*
 877      * set colour schemes for features
 878      */
 879     FeatureRenderer fr = af.getFeatureRenderer();
 880     fr.findAllFeatures(true);
 881
 882     // type1: red
 883     fr.setColour("type1", new FeatureColour(Color.red));
 884
 885     // type2: by label
 886     FeatureColourI byLabel = new FeatureColour();
 887     byLabel.setColourByLabel(true);
 888     fr.setColour("type2", byLabel);
 889
 890     // type3: by score above threshold
 891     FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
 892             10);
 893     byScore.setAboveThreshold(true);
 894     byScore.setThreshold(2f);
 895     fr.setColour("type3", byScore);
 896
 897     // type4: by attribute AF
 898     FeatureColourI byAF = new FeatureColour();
 899     byAF.setColourByLabel(true);
 900     byAF.setAttributeName("AF");
 901     fr.setColour("type4", byAF);
 902
 903     // type5: by attribute CSQ:PolyPhen below threshold
 904     FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
 905             1, 10);
 906     byPolyPhen.setBelowThreshold(true);
 907     byPolyPhen.setThreshold(3f);
 908     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 909     fr.setColour("type5", byPolyPhen);
 910
 911     /*
 912      * set filters for feature types
 913      */
 914
 915     // filter type1 features by (label contains "x")
 916     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 917     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 918     fr.setFeatureFilter("type1", filterByX);
 919
 920     // filter type2 features by (score <= 2.4 and score > 1.1)
 921     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 922     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 923     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 924     fr.setFeatureFilter("type2", filterByScore);
 925
 926     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 927     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 928     filterByXY
 929             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 930     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 931             "PolyPhen"));
 932     fr.setFeatureFilter("type3", filterByXY);
 933
 934     /*
 935      * save as Jalview project
 936      */
 937     File tfile = File.createTempFile("JalviewTest", ".jvp");
 938     tfile.deleteOnExit();
 939     String filePath = tfile.getAbsolutePath();
 940     assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
 941             "Failed to store as a project.");
 942
 943     /*
 944      * close current alignment and load the saved project
 945      */
 946     af.closeMenuItem_actionPerformed(true);
 947     af = null;
 948     af = new FileLoader()
 949             .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
 950     assertNotNull(af, "Failed to import new project");
 951
 952     /*
 953      * verify restored feature colour schemes and filters
 954      */
 955     fr = af.getFeatureRenderer();
 956     FeatureColourI fc = fr.getFeatureStyle("type1");
 957     assertTrue(fc.isSimpleColour());
 958     assertEquals(fc.getColour(), Color.red);
 959     fc = fr.getFeatureStyle("type2");
 960     assertTrue(fc.isColourByLabel());
 961     fc = fr.getFeatureStyle("type3");
 962     assertTrue(fc.isGraduatedColour());
 963     assertNull(fc.getAttributeName());
 964     assertTrue(fc.isAboveThreshold());
 965     assertEquals(fc.getThreshold(), 2f);
 966     fc = fr.getFeatureStyle("type4");
 967     assertTrue(fc.isColourByLabel());
 968     assertTrue(fc.isColourByAttribute());
 969     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 970     fc = fr.getFeatureStyle("type5");
 971     assertTrue(fc.isGraduatedColour());
 972     assertTrue(fc.isColourByAttribute());
 973     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
 974     assertTrue(fc.isBelowThreshold());
 975     assertEquals(fc.getThreshold(), 3f);
 976
 977     assertEquals(fr.getFeatureFilter("type1").toStableString(),
 978             "Label Contains x");
 979     assertEquals(fr.getFeatureFilter("type2").toStableString(),
 980             "(Score LE 2.4) AND (Score GT 1.1)");
 981     assertEquals(fr.getFeatureFilter("type3").toStableString(),
 982             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
 983   }
 984
 985   private void addFeature(SequenceI seq, String featureType, int score)
 986   {
 987     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
 988             score, "grp");
 989     sf.setValue("AF", score);
 990     sf.setValue("CSQ", new HashMap<String, String>()
 991     {
 992       {
 993         put("PolyPhen", Integer.toString(score));
 994       }
 995     });
 996     seq.addSequenceFeature(sf);
 997   }
 998
 999   /**
1000    * Adds two features of the given type to the given sequence, also setting the
1001    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1002    *
1003    * @param seq
1004    * @param featureType
1005    * @param score
1006    */
1007   private void addFeatures(SequenceI seq, String featureType, int score)
1008   {
1009     addFeature(seq, featureType, score++);
1010     addFeature(seq, featureType, score);
1011   }
1012 }