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.AlignViewport;
  48 import jalview.gui.AlignmentPanel;
  49 import jalview.gui.Desktop;
  50 import jalview.gui.FeatureRenderer;
  51 import jalview.gui.Jalview2XML;
  52 import jalview.gui.JvOptionPane;
  53 import jalview.gui.PopupMenu;
  54 import jalview.gui.SliderPanel;
  55 import jalview.renderer.ResidueShaderI;
  56 import jalview.schemes.AnnotationColourGradient;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ColourSchemeI;
  59 import jalview.schemes.ColourSchemeProperty;
  60 import jalview.schemes.FeatureColour;
  61 import jalview.schemes.JalviewColourScheme;
  62 import jalview.schemes.RNAHelicesColour;
  63 import jalview.schemes.StrandColourScheme;
  64 import jalview.schemes.TCoffeeColourScheme;
  65 import jalview.structure.StructureImportSettings;
  66 import jalview.util.matcher.Condition;
  67 import jalview.viewmodel.AlignmentViewport;
  68
  69 import java.awt.Color;
  70 import java.io.File;
  71 import java.io.IOException;
  72 import java.util.ArrayList;
  73 import java.util.HashMap;
  74 import java.util.List;
  75 import java.util.Map;
  76
  77 import org.testng.Assert;
  78 import org.testng.AssertJUnit;
  79 import org.testng.annotations.BeforeClass;
  80 import org.testng.annotations.Test;
  81
  82 @Test(singleThreaded = true)
  83 public class Jalview2xmlTests extends Jalview2xmlBase
  84 {
  85
  86   @Override
  87   @BeforeClass(alwaysRun = true)
  88   public void setUpJvOptionPane()
  89   {
  90     JvOptionPane.setInteractiveMode(false);
  91     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  92   }
  93
  94   @Test(groups = { "Functional" })
  95   public void testRNAStructureRecovery() throws Exception
  96   {
  97     String inFile = "examples/RF00031_folded.stk";
  98     String tfile = File.createTempFile("JalviewTest", ".jvp")
  99             .getAbsolutePath();
 100     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 101             DataSourceType.FILE);
 102     assertNotNull(af, "Didn't read input file " + inFile);
 103     int olddsann = countDsAnn(af.getViewport());
 104     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 105     af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
 106             .toString());
 107     assertTrue(
 108             af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 109             "Couldn't apply RNA helices colourscheme");
 110     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 111             "Failed to store as a project.");
 112     af.closeMenuItem_actionPerformed(true);
 113     af = null;
 114     af = new FileLoader()
 115             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 116     assertNotNull(af, "Failed to import new project");
 117     int newdsann = countDsAnn(af.getViewport());
 118     assertEquals(olddsann, newdsann,
 119             "Differing numbers of dataset sequence annotation\nOriginally "
 120                     + olddsann + " and now " + newdsann);
 121     System.out
 122             .println("Read in same number of annotations as originally present ("
 123                     + olddsann + ")");
 124     assertTrue(
 125
 126     af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 127             "RNA helices colourscheme was not applied on import.");
 128   }
 129
 130   @Test(groups = { "Functional" })
 131   public void testTCoffeeScores() throws Exception
 132   {
 133     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
 134     String tfile = File.createTempFile("JalviewTest", ".jvp")
 135             .getAbsolutePath();
 136     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 137             DataSourceType.FILE);
 138     assertNotNull(af, "Didn't read input file " + inFile);
 139     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 140     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 141             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 142     assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
 143             .getAlignment(), af.getViewport().getGlobalColourScheme()
 144             .getSchemeName()), "Recognise T-Coffee score from string");
 145
 146     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 147             "Failed to store as a project.");
 148     af.closeMenuItem_actionPerformed(true);
 149     af = null;
 150     af = new FileLoader()
 151             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 152     assertNotNull(af, "Failed to import new project");
 153     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 154             TCoffeeColourScheme.class,
 155             "Didn't set T-coffee colourscheme for imported project.");
 156     System.out
 157             .println("T-Coffee score shading successfully recovered from project.");
 158   }
 159
 160   @Test(groups = { "Functional" })
 161   public void testColourByAnnotScores() throws Exception
 162   {
 163     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
 164     String tfile = File.createTempFile("JalviewTest", ".jvp")
 165             .getAbsolutePath();
 166     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 167             DataSourceType.FILE);
 168     assertNotNull(af, "Didn't read input file " + inFile);
 169     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 170     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 171             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 172     assertTrue(
 173
 174     aa != null && aa.length > 0,
 175             "Didn't find any IUPred annotation to use to shade alignment.");
 176     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 177             AnnotationColourGradient.ABOVE_THRESHOLD);
 178     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
 179             null, AnnotationColourGradient.BELOW_THRESHOLD);
 180     cs.setSeqAssociated(true);
 181     gcs.setSeqAssociated(true);
 182     af.changeColour(cs);
 183     SequenceGroup sg = new SequenceGroup();
 184     sg.setStartRes(57);
 185     sg.setEndRes(92);
 186     sg.cs.setColourScheme(gcs);
 187     af.getViewport().getAlignment().addGroup(sg);
 188     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 189     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 190     af.alignPanel.alignmentChanged();
 191     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 192             "Failed to store as a project.");
 193     af.closeMenuItem_actionPerformed(true);
 194     af = null;
 195     af = new FileLoader()
 196             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 197     assertNotNull(af, "Failed to import new project");
 198
 199     // check for group and alignment colourschemes
 200
 201     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 202     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
 203             .get(0).getColourScheme();
 204     assertNotNull(_rcs, "Didn't recover global colourscheme");
 205     assertTrue(_rcs instanceof AnnotationColourGradient,
 206             "Didn't recover annotation colour global scheme");
 207     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 208     assertTrue(__rcs.isSeqAssociated(),
 209             "Annotation colourscheme wasn't sequence associated");
 210
 211     boolean diffseqcols = false, diffgseqcols = false;
 212     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 213     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 214             && (!diffseqcols || !diffgseqcols); p++)
 215     {
 216       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 217               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 218       {
 219         diffseqcols = true;
 220       }
 221     }
 222     assertTrue(diffseqcols, "Got Different sequence colours");
 223     System.out
 224             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 225
 226     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 227     assertTrue(_rgcs instanceof AnnotationColourGradient,
 228             "Didn't recover annotation colour group colourscheme");
 229     __rcs = (AnnotationColourGradient) _rgcs;
 230     assertTrue(__rcs.isSeqAssociated(),
 231             "Group Annotation colourscheme wasn't sequence associated");
 232
 233     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 234             && (!diffseqcols || !diffgseqcols); p++)
 235     {
 236       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
 237               .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
 238       {
 239         diffgseqcols = true;
 240       }
 241     }
 242     assertTrue(diffgseqcols, "Got Different group sequence colours");
 243     System.out
 244             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
 245   }
 246
 247   @Test(groups = { "Functional" })
 248   public void gatherViewsHere() throws Exception
 249   {
 250     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
 251             .getAlignFrames().length;
 252     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 253             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 254     assertNotNull(af, "Didn't read in the example file correctly.");
 255     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 256             "Didn't gather the views in the example file.");
 257
 258   }
 259
 260   /**
 261    * Test for JAL-2223 - multiple mappings in View Mapping report
 262    *
 263    * @throws Exception
 264    */
 265   @Test(groups = { "Functional" })
 266   public void noDuplicatePdbMappingsMade() throws Exception
 267   {
 268     StructureImportSettings.setProcessSecondaryStructure(true);
 269     StructureImportSettings.setVisibleChainAnnotation(true);
 270     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 271             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 272     assertNotNull(af, "Didn't read in the example file correctly.");
 273
 274     // locate Jmol viewer
 275     // count number of PDB mappings the structure selection manager holds -
 276     String pdbFile = af.getCurrentView().getStructureSelectionManager()
 277             .findFileForPDBId("1A70");
 278     assertEquals(
 279             af.getCurrentView().getStructureSelectionManager()
 280                     .getMapping(pdbFile).length,
 281             2, "Expected only two mappings for 1A70");
 282
 283   }
 284
 285   @Test(groups = { "Functional" })
 286   public void viewRefPdbAnnotation() throws Exception
 287   {
 288     StructureImportSettings.setProcessSecondaryStructure(true);
 289     StructureImportSettings.setVisibleChainAnnotation(true);
 290     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 291             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 292     assertNotNull(af, "Didn't read in the example file correctly.");
 293     AlignmentViewPanel sps = null;
 294     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 295     {
 296       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 297       {
 298         sps = ap;
 299         break;
 300       }
 301     }
 302     assertNotNull(sps, "Couldn't find the structure view");
 303     AlignmentAnnotation refan = null;
 304     for (AlignmentAnnotation ra : sps.getAlignment()
 305             .getAlignmentAnnotation())
 306     {
 307       if (ra.graph != 0)
 308       {
 309         refan = ra;
 310         break;
 311       }
 312     }
 313     assertNotNull(refan, "Annotation secondary structure not found.");
 314     SequenceI sq = sps.getAlignment().findName("1A70|");
 315     assertNotNull(sq, "Couldn't find 1a70 null chain");
 316     // compare the manually added temperature factor annotation
 317     // to the track automatically transferred from the pdb structure on load
 318     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 319             "1a70 has no annotation");
 320     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 321     {
 322       AlignmentAnnotation alaa;
 323       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 324       alaa.adjustForAlignment();
 325       if (ala.graph == refan.graph)
 326       {
 327         for (int p = 0; p < ala.annotations.length; p++)
 328         {
 329           sq.findPosition(p);
 330           try
 331           {
 332             assertTrue(
 333                     (alaa.annotations[p] == null && refan.annotations[p] == null)
 334                             || alaa.annotations[p].value == refan.annotations[p].value,
 335                     "Mismatch at alignment position " + p);
 336           } catch (NullPointerException q)
 337           {
 338             Assert.fail("Mismatch of alignment annotations at position "
 339                     + p + " Ref seq ann: " + refan.annotations[p]
 340                     + " alignment " + alaa.annotations[p]);
 341           }
 342         }
 343       }
 344     }
 345
 346   }
 347
 348   @Test(groups = { "Functional" })
 349   public void testCopyViewSettings() throws Exception
 350   {
 351     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 352             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 353     assertNotNull(af, "Didn't read in the example file correctly.");
 354     AlignmentViewPanel sps = null, groups = null;
 355     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 356     {
 357       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 358       {
 359         sps = ap;
 360       }
 361       if (ap.getViewName().contains("MAFFT"))
 362       {
 363         groups = ap;
 364       }
 365     }
 366     assertNotNull(sps, "Couldn't find the structure view");
 367     assertNotNull(groups, "Couldn't find the MAFFT view");
 368
 369     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 370     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 371     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 372
 373     groups.getAlignViewport().setViewStyle(structureStyle);
 374     AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
 375             .getViewStyle()));
 376     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
 377             .getViewStyle()));
 378
 379   }
 380
 381   /**
 382    * test store and recovery of expanded views
 383    *
 384    * @throws Exception
 385    */
 386   @Test(groups = { "Functional" }, enabled = true)
 387   public void testStoreAndRecoverExpandedviews() throws Exception
 388   {
 389     Desktop.instance.closeAll_actionPerformed(null);
 390
 391     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 392             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 393     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 394     String afid = af.getViewport().getSequenceSetId();
 395
 396     // check FileLoader returned a reference to the one alignFrame that is
 397     // actually on the Desktop
 398     assertSame(
 399             af,
 400             Desktop.getAlignFrameFor(af.getViewport()),
 401             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 402
 403     Desktop.explodeViews(af);
 404
 405     int oldviews = Desktop.getAlignFrames().length;
 406     Assert.assertEquals(Desktop.getAlignFrames().length,
 407             Desktop.getAlignmentPanels(afid).length);
 408     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 409     try
 410     {
 411       new Jalview2XML(false).saveState(tfile);
 412     } catch (Error e)
 413     {
 414       Assert.fail("Didn't save the expanded view state", e);
 415     } catch (Exception e)
 416     {
 417       Assert.fail("Didn't save the expanded view state", e);
 418     }
 419     Desktop.instance.closeAll_actionPerformed(null);
 420     if (Desktop.getAlignFrames() != null)
 421     {
 422       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 423     }
 424     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 425             DataSourceType.FILE);
 426     Assert.assertNotNull(af);
 427     Assert.assertEquals(
 428             Desktop.getAlignFrames().length,
 429             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
 430     Assert.assertEquals(
 431             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
 432             oldviews);
 433   }
 434
 435   /**
 436    * Test save and reload of a project with a different representative sequence
 437    * in each view.
 438    *
 439    * @throws Exception
 440    */
 441   @Test(groups = { "Functional" })
 442   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 443   {
 444     Desktop.instance.closeAll_actionPerformed(null);
 445     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 446             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 447     assertNotNull(af, "Didn't read in the example file correctly.");
 448     String afid = af.getViewport().getSequenceSetId();
 449
 450     // remember reference sequence for each panel
 451     Map<String, SequenceI> refseqs = new HashMap<>();
 452
 453     /*
 454      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 455      * as reference sequence for itself and the preceding sequence
 456      */
 457     int n = 1;
 458     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 459     {
 460       AlignViewportI av = ap.getAlignViewport();
 461       AlignmentI alignment = ap.getAlignment();
 462       int repIndex = n % alignment.getHeight();
 463       SequenceI rep = alignment.getSequenceAt(repIndex);
 464       refseqs.put(ap.getViewName(), rep);
 465
 466       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 467       // todo refactor this to an alignment view controller
 468       av.setDisplayReferenceSeq(true);
 469       av.setColourByReferenceSeq(true);
 470       av.getAlignment().setSeqrep(rep);
 471
 472       n++;
 473     }
 474     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 475             ".jvp");
 476     try
 477     {
 478       new Jalview2XML(false).saveState(tfile);
 479     } catch (Throwable e)
 480     {
 481       Assert.fail("Didn't save the expanded view state", e);
 482     }
 483     Desktop.instance.closeAll_actionPerformed(null);
 484     if (Desktop.getAlignFrames() != null)
 485     {
 486       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 487     }
 488
 489     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 490             DataSourceType.FILE);
 491     afid = af.getViewport().getSequenceSetId();
 492
 493     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 494     {
 495       // check representative
 496       AlignmentI alignment = ap.getAlignment();
 497       SequenceI rep = alignment.getSeqrep();
 498       Assert.assertNotNull(rep,
 499               "Couldn't restore sequence representative from project");
 500       // can't use a strong equals here, because by definition, the sequence IDs
 501       // will be different.
 502       // could set vamsas session save/restore flag to preserve IDs across
 503       // load/saves.
 504       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 505               rep.toString(),
 506               "Representative wasn't the same when recovered.");
 507       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 508               "Display reference sequence view setting not set.");
 509       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 510               "Colour By Reference Seq view setting not set.");
 511     }
 512   }
 513
 514   @Test(groups = { "Functional" })
 515   public void testIsVersionStringLaterThan()
 516   {
 517     /*
 518      * No version / development / test / autobuild is leniently assumed to be
 519      * compatible
 520      */
 521     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 522     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 523     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 524     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 525             "Development Build"));
 526     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 527             "DEVELOPMENT BUILD"));
 528     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 529             "Development Build"));
 530     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 531     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 532     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 533     assertTrue(Jalview2XML
 534             .isVersionStringLaterThan(null, "Automated Build"));
 535     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 536             "Automated Build"));
 537     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 538             "AUTOMATED BUILD"));
 539
 540     /*
 541      * same version returns true i.e. compatible
 542      */
 543     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 544     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 545     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 546     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 547     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 548
 549     /*
 550      * later version returns true
 551      */
 552     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 553     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 554     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 555     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 556     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 557
 558     /*
 559      * earlier version returns false
 560      */
 561     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 562     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 563     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 564     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 565     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 566   }
 567
 568   /**
 569    * Test save and reload of a project with a different sequence group (and
 570    * representative sequence) in each view.
 571    *
 572    * @throws Exception
 573    */
 574   @Test(groups = { "Functional" })
 575   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 576   {
 577     Desktop.instance.closeAll_actionPerformed(null);
 578     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 579             "examples/uniref50.fa", DataSourceType.FILE);
 580     assertNotNull(af, "Didn't read in the example file correctly.");
 581     String afid = af.getViewport().getSequenceSetId();
 582     // make a second view of the alignment
 583     af.newView_actionPerformed(null);
 584
 585     /*
 586      * remember representative and hidden sequences marked
 587      * on each panel
 588      */
 589     Map<String, SequenceI> repSeqs = new HashMap<>();
 590     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 591
 592     /*
 593      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 594      * as reference sequence for itself and the preceding sequence
 595      */
 596     int n = 1;
 597     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 598     {
 599       AlignViewportI av = ap.getAlignViewport();
 600       AlignmentI alignment = ap.getAlignment();
 601       int repIndex = n % alignment.getHeight();
 602       // ensure at least one preceding sequence i.e. index >= 1
 603       repIndex = Math.max(repIndex, 1);
 604       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 605       repSeqs.put(ap.getViewName(), repSeq);
 606       List<String> hiddenNames = new ArrayList<>();
 607       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 608
 609       /*
 610        * have rep sequence represent itself and the one before it
 611        * this hides the group (except for the rep seq)
 612        */
 613       SequenceGroup sg = new SequenceGroup();
 614       sg.addSequence(repSeq, false);
 615       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 616       sg.addSequence(precedingSeq, false);
 617       sg.setSeqrep(repSeq);
 618       assertTrue(sg.getSequences().contains(repSeq));
 619       assertTrue(sg.getSequences().contains(precedingSeq));
 620       av.setSelectionGroup(sg);
 621       assertSame(repSeq, sg.getSeqrep());
 622
 623       /*
 624        * represent group with sequence adds to a map of hidden rep sequences
 625        * (it does not create a group on the alignment)
 626        */
 627       ((AlignmentViewport) av).hideSequences(repSeq, true);
 628       assertSame(repSeq, sg.getSeqrep());
 629       assertTrue(sg.getSequences().contains(repSeq));
 630       assertTrue(sg.getSequences().contains(precedingSeq));
 631       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 632       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 633               .getHiddenRepSequences();
 634       assertNotNull(hiddenRepSeqsMap);
 635       assertEquals(1, hiddenRepSeqsMap.size());
 636       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 637       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 638       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 639       hiddenNames.add(precedingSeq.getName());
 640
 641       n++;
 642     }
 643     File tfile = File
 644             .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
 645     try
 646     {
 647       new Jalview2XML(false).saveState(tfile);
 648     } catch (Throwable e)
 649     {
 650       Assert.fail("Didn't save the expanded view state", e);
 651     }
 652     Desktop.instance.closeAll_actionPerformed(null);
 653     if (Desktop.getAlignFrames() != null)
 654     {
 655       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 656     }
 657
 658     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 659             DataSourceType.FILE);
 660     afid = af.getViewport().getSequenceSetId();
 661
 662     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 663     {
 664       String viewName = ap.getViewName();
 665       AlignViewportI av = ap.getAlignViewport();
 666       AlignmentI alignment = ap.getAlignment();
 667       List<SequenceGroup> groups = alignment.getGroups();
 668       assertNotNull(groups);
 669       assertTrue(groups.isEmpty(), "Alignment has groups");
 670       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 671               .getHiddenRepSequences();
 672       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 673       assertEquals(1, hiddenRepSeqsMap.size());
 674       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 675               hiddenRepSeqsMap.keySet().iterator().next()
 676                       .getDisplayId(true));
 677
 678       /*
 679        * verify hidden sequences in restored panel
 680        */
 681       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 682       HiddenSequences hs = alignment.getHiddenSequences();
 683       assertEquals(
 684               hidden.size(),
 685               hs.getSize(),
 686               "wrong number of restored hidden sequences in "
 687                       + ap.getViewName());
 688     }
 689   }
 690
 691   /**
 692    * Test save and reload of PDBEntry in Jalview project
 693    *
 694    * @throws Exception
 695    */
 696   @Test(groups = { "Functional" })
 697   public void testStoreAndRecoverPDBEntry() throws Exception
 698   {
 699     Desktop.instance.closeAll_actionPerformed(null);
 700     String exampleFile = "examples/3W5V.pdb";
 701     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 702             DataSourceType.FILE);
 703     assertNotNull(af, "Didn't read in the example file correctly.");
 704     String afid = af.getViewport().getSequenceSetId();
 705
 706     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 707     System.out.println();
 708     AlignmentViewPanel ap = alignPanels[0];
 709     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 710     String testFile = tfileBase + exampleFile;
 711     AlignmentI alignment = ap.getAlignment();
 712     System.out.println("blah");
 713     SequenceI[] seqs = alignment.getSequencesArray();
 714     Assert.assertNotNull(seqs[0]);
 715     Assert.assertNotNull(seqs[1]);
 716     Assert.assertNotNull(seqs[2]);
 717     Assert.assertNotNull(seqs[3]);
 718     Assert.assertNotNull(seqs[0].getDatasetSequence());
 719     Assert.assertNotNull(seqs[1].getDatasetSequence());
 720     Assert.assertNotNull(seqs[2].getDatasetSequence());
 721     Assert.assertNotNull(seqs[3].getDatasetSequence());
 722     PDBEntry[] pdbEntries = new PDBEntry[4];
 723     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 724     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 725     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 726     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 727     Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
 728             .get(0), pdbEntries[0]);
 729     Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
 730             .get(0), pdbEntries[1]);
 731     Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
 732             .get(0), pdbEntries[2]);
 733     Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
 734             .get(0), pdbEntries[3]);
 735
 736     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 737     try
 738     {
 739       new Jalview2XML(false).saveState(tfile);
 740     } catch (Throwable e)
 741     {
 742       Assert.fail("Didn't save the state", e);
 743     }
 744     Desktop.instance.closeAll_actionPerformed(null);
 745     if (Desktop.getAlignFrames() != null)
 746     {
 747       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 748     }
 749
 750     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 751             tfile.getAbsolutePath(), DataSourceType.FILE);
 752     String rfid = restoredFrame.getViewport().getSequenceSetId();
 753     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 754     AlignmentViewPanel rap = rAlignPanels[0];
 755     AlignmentI rAlignment = rap.getAlignment();
 756     System.out.println("blah");
 757     SequenceI[] rseqs = rAlignment.getSequencesArray();
 758     Assert.assertNotNull(rseqs[0]);
 759     Assert.assertNotNull(rseqs[1]);
 760     Assert.assertNotNull(rseqs[2]);
 761     Assert.assertNotNull(rseqs[3]);
 762     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 763     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 764     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 765     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 766
 767     // The Asserts below are expected to fail until the PDB chainCode is
 768     // recoverable from a Jalview projects
 769     for (int chain = 0; chain < 4; chain++)
 770     {
 771       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 772               .get(0);
 773       PDBEntry expected = pdbEntries[chain];
 774       Assert.assertEquals(recov.getId(), expected.getId(),
 775               "Mismatch PDB ID");
 776       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 777               "Mismatch PDB ID");
 778       Assert.assertEquals(recov.getType(), expected.getType(),
 779               "Mismatch PDBEntry 'Type'");
 780       Assert.assertNotNull(recov.getFile(),
 781               "Recovered PDBEntry should have a non-null file entry");
 782     }
 783   }
 784
 785   /**
 786    * Configure an alignment and a sub-group each with distinct colour schemes,
 787    * Conservation and PID thresholds, and confirm these are restored from the
 788    * saved project.
 789    *
 790    * @throws IOException
 791    */
 792   @Test(groups = { "Functional" })
 793   public void testStoreAndRecoverColourThresholds() throws IOException
 794   {
 795     Desktop.instance.closeAll_actionPerformed(null);
 796     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 797             "examples/uniref50.fa", DataSourceType.FILE);
 798
 799     AlignViewport av = af.getViewport();
 800     AlignmentI al = av.getAlignment();
 801
 802     /*
 803      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 804      */
 805     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 806     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 807     af.abovePIDThreshold_actionPerformed(true);
 808     SliderPanel sp = SliderPanel.getSliderPanel();
 809     assertFalse(sp.isForConservation());
 810     sp.valueChanged(10);
 811     af.conservationMenuItem_actionPerformed(true);
 812     sp = SliderPanel.getSliderPanel();
 813     assertTrue(sp.isForConservation());
 814     sp.valueChanged(20);
 815     ResidueShaderI rs = av.getResidueShading();
 816     assertEquals(rs.getThreshold(), 10);
 817     assertTrue(rs.conservationApplied());
 818     assertEquals(rs.getConservationInc(), 20);
 819
 820     /*
 821      * create a group with Strand colouring, 30% Conservation
 822      * and 40% PID threshold
 823      */
 824     SequenceGroup sg = new SequenceGroup();
 825     sg.addSequence(al.getSequenceAt(0), false);
 826     sg.setStartRes(15);
 827     sg.setEndRes(25);
 828     av.setSelectionGroup(sg);
 829     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 830     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
 831             .toString());
 832     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 833     assertEquals(al.getGroups().size(), 1);
 834     assertSame(al.getGroups().get(0), sg);
 835     popupMenu.conservationMenuItem_actionPerformed(true);
 836     sp = SliderPanel.getSliderPanel();
 837     assertTrue(sp.isForConservation());
 838     sp.valueChanged(30);
 839     popupMenu.abovePIDColour_actionPerformed(true);
 840     sp = SliderPanel.getSliderPanel();
 841     assertFalse(sp.isForConservation());
 842     sp.valueChanged(40);
 843     assertTrue(sg.getGroupColourScheme().conservationApplied());
 844     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 845     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 846
 847     /*
 848      * save project, close windows, reload project, verify
 849      */
 850     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 851             ".jvp");
 852     tfile.deleteOnExit();
 853     new Jalview2XML(false).saveState(tfile);
 854     Desktop.instance.closeAll_actionPerformed(null);
 855     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 856             DataSourceType.FILE);
 857     Assert.assertNotNull(af, "Failed to reload project");
 858
 859     /*
 860      * verify alignment (background) colouring
 861      */
 862     rs = af.getViewport().getResidueShading();
 863     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 864     assertEquals(rs.getThreshold(), 10);
 865     assertTrue(rs.conservationApplied());
 866     assertEquals(rs.getConservationInc(), 20);
 867
 868     /*
 869      * verify group colouring
 870      */
 871     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 872     rs = af.getViewport().getAlignment().getGroups().get(0)
 873             .getGroupColourScheme();
 874     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 875     assertEquals(rs.getThreshold(), 40);
 876     assertTrue(rs.conservationApplied());
 877     assertEquals(rs.getConservationInc(), 30);
 878   }
 879
 880   /**
 881    * Test save and reload of feature colour schemes and filter settings
 882    *
 883    * @throws IOException
 884    */
 885   @Test(groups = { "Functional" })
 886   public void testSaveLoadFeatureColoursAndFilters() throws IOException
 887   {
 888     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 889             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 890     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 891
 892     /*
 893      * add some features to the sequence
 894      */
 895     int score = 1;
 896     addFeatures(seq1, "type1", score++);
 897     addFeatures(seq1, "type2", score++);
 898     addFeatures(seq1, "type3", score++);
 899     addFeatures(seq1, "type4", score++);
 900     addFeatures(seq1, "type5", score++);
 901
 902     /*
 903      * set colour schemes for features
 904      */
 905     FeatureRenderer fr = af.getFeatureRenderer();
 906     fr.findAllFeatures(true);
 907
 908     // type1: red
 909     fr.setColour("type1", new FeatureColour(Color.red));
 910
 911     // type2: by label
 912     FeatureColourI byLabel = new FeatureColour();
 913     byLabel.setColourByLabel(true);
 914     fr.setColour("type2", byLabel);
 915
 916     // type3: by score above threshold
 917     FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
 918             10);
 919     byScore.setAboveThreshold(true);
 920     byScore.setThreshold(2f);
 921     fr.setColour("type3", byScore);
 922
 923     // type4: by attribute AF
 924     FeatureColourI byAF = new FeatureColour();
 925     byAF.setColourByLabel(true);
 926     byAF.setAttributeName("AF");
 927     fr.setColour("type4", byAF);
 928
 929     // type5: by attribute CSQ:PolyPhen below threshold
 930     FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
 931             1, 10);
 932     byPolyPhen.setBelowThreshold(true);
 933     byPolyPhen.setThreshold(3f);
 934     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 935     fr.setColour("type5", byPolyPhen);
 936
 937     /*
 938      * set filters for feature types
 939      */
 940
 941     // filter type1 features by (label contains "x")
 942     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 943     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 944     fr.setFeatureFilter("type1", filterByX);
 945
 946     // filter type2 features by (score <= 2.4 and score > 1.1)
 947     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 948     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 949     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 950     fr.setFeatureFilter("type2", filterByScore);
 951
 952     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 953     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 954     filterByXY
 955             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 956     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 957             "PolyPhen"));
 958     fr.setFeatureFilter("type3", filterByXY);
 959
 960     /*
 961      * save as Jalview project
 962      */
 963     File tfile = File.createTempFile("JalviewTest", ".jvp");
 964     tfile.deleteOnExit();
 965     String filePath = tfile.getAbsolutePath();
 966     assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
 967             "Failed to store as a project.");
 968
 969     /*
 970      * close current alignment and load the saved project
 971      */
 972     af.closeMenuItem_actionPerformed(true);
 973     af = null;
 974     af = new FileLoader()
 975             .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
 976     assertNotNull(af, "Failed to import new project");
 977
 978     /*
 979      * verify restored feature colour schemes and filters
 980      */
 981     fr = af.getFeatureRenderer();
 982     FeatureColourI fc = fr.getFeatureStyle("type1");
 983     assertTrue(fc.isSimpleColour());
 984     assertEquals(fc.getColour(), Color.red);
 985     fc = fr.getFeatureStyle("type2");
 986     assertTrue(fc.isColourByLabel());
 987     fc = fr.getFeatureStyle("type3");
 988     assertTrue(fc.isGraduatedColour());
 989     assertNull(fc.getAttributeName());
 990     assertTrue(fc.isAboveThreshold());
 991     assertEquals(fc.getThreshold(), 2f);
 992     fc = fr.getFeatureStyle("type4");
 993     assertTrue(fc.isColourByLabel());
 994     assertTrue(fc.isColourByAttribute());
 995     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 996     fc = fr.getFeatureStyle("type5");
 997     assertTrue(fc.isGraduatedColour());
 998     assertTrue(fc.isColourByAttribute());
 999     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1000     assertTrue(fc.isBelowThreshold());
1001     assertEquals(fc.getThreshold(), 3f);
1002
1003     assertEquals(fr.getFeatureFilter("type1").toStableString(),
1004             "Label Contains x");
1005     assertEquals(fr.getFeatureFilter("type2").toStableString(),
1006             "(Score LE 2.4) AND (Score GT 1.1)");
1007     assertEquals(fr.getFeatureFilter("type3").toStableString(),
1008             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
1009   }
1010
1011   private void addFeature(SequenceI seq, String featureType, int score)
1012   {
1013     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1014             score, "grp");
1015     sf.setValue("AF", score);
1016     sf.setValue("CSQ", new HashMap<String, String>()
1017     {
1018       {
1019         put("PolyPhen", Integer.toString(score));
1020       }
1021     });
1022     seq.addSequenceFeature(sf);
1023   }
1024
1025   /**
1026    * Adds two features of the given type to the given sequence, also setting the
1027    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1028    *
1029    * @param seq
1030    * @param featureType
1031    * @param score
1032    */
1033   private void addFeatures(SequenceI seq, String featureType, int score)
1034   {
1035     addFeature(seq, featureType, score++);
1036     addFeature(seq, featureType, score);
1037   }
1038 }