test/jalview/project/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.project;
  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.JvOptionPane;
  52 import jalview.gui.PopupMenu;
  53 import jalview.gui.SliderPanel;
  54 import jalview.io.DataSourceType;
  55 import jalview.io.FileFormat;
  56 import jalview.io.FileLoader;
  57 import jalview.io.Jalview2xmlBase;
  58 import jalview.renderer.ResidueShaderI;
  59 import jalview.schemes.AnnotationColourGradient;
  60 import jalview.schemes.BuriedColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.ColourSchemeProperty;
  63 import jalview.schemes.FeatureColour;
  64 import jalview.schemes.JalviewColourScheme;
  65 import jalview.schemes.RNAHelicesColour;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.structure.StructureImportSettings;
  69 import jalview.util.matcher.Condition;
  70 import jalview.viewmodel.AlignmentViewport;
  71
  72 import java.awt.Color;
  73 import java.io.File;
  74 import java.io.IOException;
  75 import java.util.ArrayList;
  76 import java.util.HashMap;
  77 import java.util.List;
  78 import java.util.Map;
  79
  80 import org.testng.Assert;
  81 import org.testng.AssertJUnit;
  82 import org.testng.annotations.BeforeClass;
  83 import org.testng.annotations.Test;
  84
  85 @Test(singleThreaded = true)
  86 public class Jalview2xmlTests extends Jalview2xmlBase
  87 {
  88
  89   @Override
  90   @BeforeClass(alwaysRun = true)
  91   public void setUpJvOptionPane()
  92   {
  93     JvOptionPane.setInteractiveMode(false);
  94     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  95   }
  96
  97   @Test(groups = { "Functional" })
  98   public void testRNAStructureRecovery() throws Exception
  99   {
 100     String inFile = "examples/RF00031_folded.stk";
 101     String tfile = File.createTempFile("JalviewTest", ".jvp")
 102             .getAbsolutePath();
 103     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 104             DataSourceType.FILE);
 105     assertNotNull(af, "Didn't read input file " + inFile);
 106     int olddsann = countDsAnn(af.getViewport());
 107     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 108     af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
 109             .toString());
 110     assertTrue(
 111             af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 112             "Couldn't apply RNA helices colourscheme");
 113     af.saveAlignment(tfile, FileFormat.Jalview);
 114     assertTrue(af.isSaveAlignmentSuccessful(),
 115             "Failed to store as a project.");
 116     af.closeMenuItem_actionPerformed(true);
 117     af = null;
 118     af = new FileLoader()
 119             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 120     assertNotNull(af, "Failed to import new project");
 121     int newdsann = countDsAnn(af.getViewport());
 122     assertEquals(olddsann, newdsann,
 123             "Differing numbers of dataset sequence annotation\nOriginally "
 124                     + olddsann + " and now " + newdsann);
 125     System.out
 126             .println("Read in same number of annotations as originally present ("
 127                     + olddsann + ")");
 128     assertTrue(
 129
 130     af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 131             "RNA helices colourscheme was not applied on import.");
 132   }
 133
 134   @Test(groups = { "Functional" })
 135   public void testTCoffeeScores() throws Exception
 136   {
 137     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
 138     String tfile = File.createTempFile("JalviewTest", ".jvp")
 139             .getAbsolutePath();
 140     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 141             DataSourceType.FILE);
 142     assertNotNull(af, "Didn't read input file " + inFile);
 143     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 144     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 145             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 146     assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
 147             .getAlignment(), af.getViewport().getGlobalColourScheme()
 148             .getSchemeName()), "Recognise T-Coffee score from string");
 149
 150     af.saveAlignment(tfile, FileFormat.Jalview);
 151     assertTrue(af.isSaveAlignmentSuccessful(),
 152             "Failed to store as a project.");
 153     af.closeMenuItem_actionPerformed(true);
 154     af = null;
 155     af = new FileLoader()
 156             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 157     assertNotNull(af, "Failed to import new project");
 158     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 159             TCoffeeColourScheme.class,
 160             "Didn't set T-coffee colourscheme for imported project.");
 161     System.out
 162             .println("T-Coffee score shading successfully recovered from project.");
 163   }
 164
 165   @Test(groups = { "Functional" })
 166   public void testColourByAnnotScores() throws Exception
 167   {
 168     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
 169     String tfile = File.createTempFile("JalviewTest", ".jvp")
 170             .getAbsolutePath();
 171     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 172             DataSourceType.FILE);
 173     assertNotNull(af, "Didn't read input file " + inFile);
 174     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 175     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 176             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 177     assertTrue(
 178
 179     aa != null && aa.length > 0,
 180             "Didn't find any IUPred annotation to use to shade alignment.");
 181     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 182             AnnotationColourGradient.ABOVE_THRESHOLD);
 183     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
 184             null, AnnotationColourGradient.BELOW_THRESHOLD);
 185     cs.setSeqAssociated(true);
 186     gcs.setSeqAssociated(true);
 187     af.changeColour(cs);
 188     SequenceGroup sg = new SequenceGroup();
 189     sg.setStartRes(57);
 190     sg.setEndRes(92);
 191     sg.cs.setColourScheme(gcs);
 192     af.getViewport().getAlignment().addGroup(sg);
 193     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 194     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 195     af.alignPanel.alignmentChanged();
 196     af.saveAlignment(tfile, FileFormat.Jalview);
 197     assertTrue(af.isSaveAlignmentSuccessful(),
 198             "Failed to store as a project.");
 199     af.closeMenuItem_actionPerformed(true);
 200     af = null;
 201     af = new FileLoader()
 202             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 203     assertNotNull(af, "Failed to import new project");
 204
 205     // check for group and alignment colourschemes
 206
 207     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 208     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
 209             .get(0).getColourScheme();
 210     assertNotNull(_rcs, "Didn't recover global colourscheme");
 211     assertTrue(_rcs instanceof AnnotationColourGradient,
 212             "Didn't recover annotation colour global scheme");
 213     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 214     assertTrue(__rcs.isSeqAssociated(),
 215             "Annotation colourscheme wasn't sequence associated");
 216
 217     boolean diffseqcols = false, diffgseqcols = false;
 218     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 219     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 220             && (!diffseqcols || !diffgseqcols); p++)
 221     {
 222       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 223               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 224       {
 225         diffseqcols = true;
 226       }
 227     }
 228     assertTrue(diffseqcols, "Got Different sequence colours");
 229     System.out
 230             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 231
 232     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 233     assertTrue(_rgcs instanceof AnnotationColourGradient,
 234             "Didn't recover annotation colour group colourscheme");
 235     __rcs = (AnnotationColourGradient) _rgcs;
 236     assertTrue(__rcs.isSeqAssociated(),
 237             "Group Annotation colourscheme wasn't sequence associated");
 238
 239     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 240             && (!diffseqcols || !diffgseqcols); p++)
 241     {
 242       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
 243               .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
 244       {
 245         diffgseqcols = true;
 246       }
 247     }
 248     assertTrue(diffgseqcols, "Got Different group sequence colours");
 249     System.out
 250             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
 251   }
 252
 253   @Test(groups = { "Functional" })
 254   public void gatherViewsHere() throws Exception
 255   {
 256     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
 257             .getAlignFrames().length;
 258     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 259             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 260     assertNotNull(af, "Didn't read in the example file correctly.");
 261     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 262             "Didn't gather the views in the example file.");
 263
 264   }
 265
 266   /**
 267    * Test for JAL-2223 - multiple mappings in View Mapping report
 268    *
 269    * @throws Exception
 270    */
 271   @Test(groups = { "Functional" })
 272   public void noDuplicatePdbMappingsMade() throws Exception
 273   {
 274     StructureImportSettings.setProcessSecondaryStructure(true);
 275     StructureImportSettings.setVisibleChainAnnotation(true);
 276     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 277             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 278     assertNotNull(af, "Didn't read in the example file correctly.");
 279
 280     // locate Jmol viewer
 281     // count number of PDB mappings the structure selection manager holds -
 282     String pdbFile = af.getCurrentView().getStructureSelectionManager()
 283             .findFileForPDBId("1A70");
 284     assertEquals(
 285             af.getCurrentView().getStructureSelectionManager()
 286                     .getMapping(pdbFile).length,
 287             2, "Expected only two mappings for 1A70");
 288
 289   }
 290
 291   @Test(groups = { "Functional" })
 292   public void viewRefPdbAnnotation() throws Exception
 293   {
 294     StructureImportSettings.setProcessSecondaryStructure(true);
 295     StructureImportSettings.setVisibleChainAnnotation(true);
 296     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 297             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 298     assertNotNull(af, "Didn't read in the example file correctly.");
 299     AlignmentViewPanel sps = null;
 300     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 301     {
 302       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 303       {
 304         sps = ap;
 305         break;
 306       }
 307     }
 308     assertNotNull(sps, "Couldn't find the structure view");
 309     AlignmentAnnotation refan = null;
 310     for (AlignmentAnnotation ra : sps.getAlignment()
 311             .getAlignmentAnnotation())
 312     {
 313       if (ra.graph != 0)
 314       {
 315         refan = ra;
 316         break;
 317       }
 318     }
 319     assertNotNull(refan, "Annotation secondary structure not found.");
 320     SequenceI sq = sps.getAlignment().findName("1A70|");
 321     assertNotNull(sq, "Couldn't find 1a70 null chain");
 322     // compare the manually added temperature factor annotation
 323     // to the track automatically transferred from the pdb structure on load
 324     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 325             "1a70 has no annotation");
 326     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 327     {
 328       AlignmentAnnotation alaa;
 329       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 330       alaa.adjustForAlignment();
 331       if (ala.graph == refan.graph)
 332       {
 333         for (int p = 0; p < ala.annotations.length; p++)
 334         {
 335           sq.findPosition(p);
 336           try
 337           {
 338             assertTrue(
 339                     (alaa.annotations[p] == null && refan.annotations[p] == null)
 340                             || alaa.annotations[p].value == refan.annotations[p].value,
 341                     "Mismatch at alignment position " + p);
 342           } catch (NullPointerException q)
 343           {
 344             Assert.fail("Mismatch of alignment annotations at position "
 345                     + p + " Ref seq ann: " + refan.annotations[p]
 346                     + " alignment " + alaa.annotations[p]);
 347           }
 348         }
 349       }
 350     }
 351
 352   }
 353
 354   @Test(groups = { "Functional" })
 355   public void testCopyViewSettings() throws Exception
 356   {
 357     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 358             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 359     assertNotNull(af, "Didn't read in the example file correctly.");
 360     AlignmentViewPanel sps = null, groups = null;
 361     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 362     {
 363       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 364       {
 365         sps = ap;
 366       }
 367       if (ap.getViewName().contains("MAFFT"))
 368       {
 369         groups = ap;
 370       }
 371     }
 372     assertNotNull(sps, "Couldn't find the structure view");
 373     assertNotNull(groups, "Couldn't find the MAFFT view");
 374
 375     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 376     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 377     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 378
 379     groups.getAlignViewport().setViewStyle(structureStyle);
 380     AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
 381             .getViewStyle()));
 382     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
 383             .getViewStyle()));
 384
 385   }
 386
 387   /**
 388    * test store and recovery of expanded views
 389    *
 390    * @throws Exception
 391    */
 392   @Test(groups = { "Functional" }, enabled = true)
 393   public void testStoreAndRecoverExpandedviews() throws Exception
 394   {
 395     Desktop.instance.closeAll_actionPerformed(null);
 396
 397     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 398             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 399     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 400     String afid = af.getViewport().getSequenceSetId();
 401
 402     // check FileLoader returned a reference to the one alignFrame that is
 403     // actually on the Desktop
 404     assertSame(
 405             af,
 406             Desktop.getAlignFrameFor(af.getViewport()),
 407             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 408
 409     Desktop.explodeViews(af);
 410
 411     int oldviews = Desktop.getAlignFrames().length;
 412     Assert.assertEquals(Desktop.getAlignFrames().length,
 413             Desktop.getAlignmentPanels(afid).length);
 414     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 415     try
 416     {
 417       new Jalview2XML(false).saveState(tfile);
 418     } catch (Error e)
 419     {
 420       Assert.fail("Didn't save the expanded view state", e);
 421     } catch (Exception e)
 422     {
 423       Assert.fail("Didn't save the expanded view state", e);
 424     }
 425     Desktop.instance.closeAll_actionPerformed(null);
 426     if (Desktop.getAlignFrames() != null)
 427     {
 428       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 429     }
 430     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 431             DataSourceType.FILE);
 432     Assert.assertNotNull(af);
 433     Assert.assertEquals(
 434             Desktop.getAlignFrames().length,
 435             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
 436     Assert.assertEquals(
 437             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
 438             oldviews);
 439   }
 440
 441   /**
 442    * Test save and reload of a project with a different representative sequence
 443    * in each view.
 444    *
 445    * @throws Exception
 446    */
 447   @Test(groups = { "Functional" })
 448   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 449   {
 450     Desktop.instance.closeAll_actionPerformed(null);
 451     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 452             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 453     assertNotNull(af, "Didn't read in the example file correctly.");
 454     String afid = af.getViewport().getSequenceSetId();
 455
 456     // remember reference sequence for each panel
 457     Map<String, SequenceI> refseqs = new HashMap<>();
 458
 459     /*
 460      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 461      * as reference sequence for itself and the preceding sequence
 462      */
 463     int n = 1;
 464     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 465     {
 466       AlignViewportI av = ap.getAlignViewport();
 467       AlignmentI alignment = ap.getAlignment();
 468       int repIndex = n % alignment.getHeight();
 469       SequenceI rep = alignment.getSequenceAt(repIndex);
 470       refseqs.put(ap.getViewName(), rep);
 471
 472       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 473       // todo refactor this to an alignment view controller
 474       av.setDisplayReferenceSeq(true);
 475       av.setColourByReferenceSeq(true);
 476       av.getAlignment().setSeqrep(rep);
 477
 478       n++;
 479     }
 480     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 481             ".jvp");
 482     try
 483     {
 484       new Jalview2XML(false).saveState(tfile);
 485     } catch (Throwable e)
 486     {
 487       Assert.fail("Didn't save the expanded view state", e);
 488     }
 489     Desktop.instance.closeAll_actionPerformed(null);
 490     if (Desktop.getAlignFrames() != null)
 491     {
 492       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 493     }
 494
 495     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 496             DataSourceType.FILE);
 497     afid = af.getViewport().getSequenceSetId();
 498
 499     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 500     {
 501       // check representative
 502       AlignmentI alignment = ap.getAlignment();
 503       SequenceI rep = alignment.getSeqrep();
 504       Assert.assertNotNull(rep,
 505               "Couldn't restore sequence representative from project");
 506       // can't use a strong equals here, because by definition, the sequence IDs
 507       // will be different.
 508       // could set vamsas session save/restore flag to preserve IDs across
 509       // load/saves.
 510       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 511               rep.toString(),
 512               "Representative wasn't the same when recovered.");
 513       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 514               "Display reference sequence view setting not set.");
 515       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 516               "Colour By Reference Seq view setting not set.");
 517     }
 518   }
 519
 520   @Test(groups = { "Functional" })
 521   public void testIsVersionStringLaterThan()
 522   {
 523     /*
 524      * No version / development / test / autobuild is leniently assumed to be
 525      * compatible
 526      */
 527     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 528     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 529     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 530     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 531             "Development Build"));
 532     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 533             "DEVELOPMENT BUILD"));
 534     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 535             "Development Build"));
 536     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 537     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 538     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 539     assertTrue(Jalview2XML
 540             .isVersionStringLaterThan(null, "Automated Build"));
 541     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 542             "Automated Build"));
 543     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 544             "AUTOMATED BUILD"));
 545
 546     /*
 547      * same version returns true i.e. compatible
 548      */
 549     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 550     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 551     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 552     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 553     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 554
 555     /*
 556      * later version returns true
 557      */
 558     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 559     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 560     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 561     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 562     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 563
 564     /*
 565      * earlier version returns false
 566      */
 567     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 568     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 569     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 570     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 571     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 572   }
 573
 574   /**
 575    * Test save and reload of a project with a different sequence group (and
 576    * representative sequence) in each view.
 577    *
 578    * @throws Exception
 579    */
 580   @Test(groups = { "Functional" })
 581   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 582   {
 583     Desktop.instance.closeAll_actionPerformed(null);
 584     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 585             "examples/uniref50.fa", DataSourceType.FILE);
 586     assertNotNull(af, "Didn't read in the example file correctly.");
 587     String afid = af.getViewport().getSequenceSetId();
 588     // make a second view of the alignment
 589     af.newView_actionPerformed(null);
 590
 591     /*
 592      * remember representative and hidden sequences marked
 593      * on each panel
 594      */
 595     Map<String, SequenceI> repSeqs = new HashMap<>();
 596     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 597
 598     /*
 599      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 600      * as reference sequence for itself and the preceding sequence
 601      */
 602     int n = 1;
 603     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 604     {
 605       AlignViewportI av = ap.getAlignViewport();
 606       AlignmentI alignment = ap.getAlignment();
 607       int repIndex = n % alignment.getHeight();
 608       // ensure at least one preceding sequence i.e. index >= 1
 609       repIndex = Math.max(repIndex, 1);
 610       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 611       repSeqs.put(ap.getViewName(), repSeq);
 612       List<String> hiddenNames = new ArrayList<>();
 613       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 614
 615       /*
 616        * have rep sequence represent itself and the one before it
 617        * this hides the group (except for the rep seq)
 618        */
 619       SequenceGroup sg = new SequenceGroup();
 620       sg.addSequence(repSeq, false);
 621       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 622       sg.addSequence(precedingSeq, false);
 623       sg.setSeqrep(repSeq);
 624       assertTrue(sg.getSequences().contains(repSeq));
 625       assertTrue(sg.getSequences().contains(precedingSeq));
 626       av.setSelectionGroup(sg);
 627       assertSame(repSeq, sg.getSeqrep());
 628
 629       /*
 630        * represent group with sequence adds to a map of hidden rep sequences
 631        * (it does not create a group on the alignment)
 632        */
 633       ((AlignmentViewport) av).hideSequences(repSeq, true);
 634       assertSame(repSeq, sg.getSeqrep());
 635       assertTrue(sg.getSequences().contains(repSeq));
 636       assertTrue(sg.getSequences().contains(precedingSeq));
 637       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 638       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 639               .getHiddenRepSequences();
 640       assertNotNull(hiddenRepSeqsMap);
 641       assertEquals(1, hiddenRepSeqsMap.size());
 642       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 643       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 644       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 645       hiddenNames.add(precedingSeq.getName());
 646
 647       n++;
 648     }
 649     File tfile = File
 650             .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
 651     try
 652     {
 653       new Jalview2XML(false).saveState(tfile);
 654     } catch (Throwable e)
 655     {
 656       Assert.fail("Didn't save the expanded view state", e);
 657     }
 658     Desktop.instance.closeAll_actionPerformed(null);
 659     if (Desktop.getAlignFrames() != null)
 660     {
 661       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 662     }
 663
 664     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 665             DataSourceType.FILE);
 666     afid = af.getViewport().getSequenceSetId();
 667
 668     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 669     {
 670       String viewName = ap.getViewName();
 671       AlignViewportI av = ap.getAlignViewport();
 672       AlignmentI alignment = ap.getAlignment();
 673       List<SequenceGroup> groups = alignment.getGroups();
 674       assertNotNull(groups);
 675       assertTrue(groups.isEmpty(), "Alignment has groups");
 676       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 677               .getHiddenRepSequences();
 678       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 679       assertEquals(1, hiddenRepSeqsMap.size());
 680       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 681               hiddenRepSeqsMap.keySet().iterator().next()
 682                       .getDisplayId(true));
 683
 684       /*
 685        * verify hidden sequences in restored panel
 686        */
 687       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 688       HiddenSequences hs = alignment.getHiddenSequences();
 689       assertEquals(
 690               hidden.size(),
 691               hs.getSize(),
 692               "wrong number of restored hidden sequences in "
 693                       + ap.getViewName());
 694     }
 695   }
 696
 697   /**
 698    * Test save and reload of PDBEntry in Jalview project
 699    *
 700    * @throws Exception
 701    */
 702   @Test(groups = { "Functional" })
 703   public void testStoreAndRecoverPDBEntry() throws Exception
 704   {
 705     Desktop.instance.closeAll_actionPerformed(null);
 706     String exampleFile = "examples/3W5V.pdb";
 707     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 708             DataSourceType.FILE);
 709     assertNotNull(af, "Didn't read in the example file correctly.");
 710     String afid = af.getViewport().getSequenceSetId();
 711
 712     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 713     System.out.println();
 714     AlignmentViewPanel ap = alignPanels[0];
 715     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 716     String testFile = tfileBase + exampleFile;
 717     AlignmentI alignment = ap.getAlignment();
 718     System.out.println("blah");
 719     SequenceI[] seqs = alignment.getSequencesArray();
 720     Assert.assertNotNull(seqs[0]);
 721     Assert.assertNotNull(seqs[1]);
 722     Assert.assertNotNull(seqs[2]);
 723     Assert.assertNotNull(seqs[3]);
 724     Assert.assertNotNull(seqs[0].getDatasetSequence());
 725     Assert.assertNotNull(seqs[1].getDatasetSequence());
 726     Assert.assertNotNull(seqs[2].getDatasetSequence());
 727     Assert.assertNotNull(seqs[3].getDatasetSequence());
 728     PDBEntry[] pdbEntries = new PDBEntry[4];
 729     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 730     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 731     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 732     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 733     Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
 734             .get(0), pdbEntries[0]);
 735     Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
 736             .get(0), pdbEntries[1]);
 737     Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
 738             .get(0), pdbEntries[2]);
 739     Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
 740             .get(0), pdbEntries[3]);
 741
 742     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 743     try
 744     {
 745       new Jalview2XML(false).saveState(tfile);
 746     } catch (Throwable e)
 747     {
 748       Assert.fail("Didn't save the state", e);
 749     }
 750     Desktop.instance.closeAll_actionPerformed(null);
 751     if (Desktop.getAlignFrames() != null)
 752     {
 753       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 754     }
 755
 756     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 757             tfile.getAbsolutePath(), DataSourceType.FILE);
 758     String rfid = restoredFrame.getViewport().getSequenceSetId();
 759     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 760     AlignmentViewPanel rap = rAlignPanels[0];
 761     AlignmentI rAlignment = rap.getAlignment();
 762     System.out.println("blah");
 763     SequenceI[] rseqs = rAlignment.getSequencesArray();
 764     Assert.assertNotNull(rseqs[0]);
 765     Assert.assertNotNull(rseqs[1]);
 766     Assert.assertNotNull(rseqs[2]);
 767     Assert.assertNotNull(rseqs[3]);
 768     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 769     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 770     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 771     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 772
 773     // The Asserts below are expected to fail until the PDB chainCode is
 774     // recoverable from a Jalview projects
 775     for (int chain = 0; chain < 4; chain++)
 776     {
 777       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 778               .get(0);
 779       PDBEntry expected = pdbEntries[chain];
 780       Assert.assertEquals(recov.getId(), expected.getId(),
 781               "Mismatch PDB ID");
 782       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 783               "Mismatch PDB ID");
 784       Assert.assertEquals(recov.getType(), expected.getType(),
 785               "Mismatch PDBEntry 'Type'");
 786       Assert.assertNotNull(recov.getFile(),
 787               "Recovered PDBEntry should have a non-null file entry");
 788     }
 789   }
 790
 791   /**
 792    * Configure an alignment and a sub-group each with distinct colour schemes,
 793    * Conservation and PID thresholds, and confirm these are restored from the
 794    * saved project.
 795    *
 796    * @throws IOException
 797    */
 798   @Test(groups = { "Functional" })
 799   public void testStoreAndRecoverColourThresholds() throws IOException
 800   {
 801     Desktop.instance.closeAll_actionPerformed(null);
 802     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 803             "examples/uniref50.fa", DataSourceType.FILE);
 804
 805     AlignViewport av = af.getViewport();
 806     AlignmentI al = av.getAlignment();
 807
 808     /*
 809      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 810      */
 811     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 812     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 813     af.abovePIDThreshold_actionPerformed(true);
 814     SliderPanel sp = SliderPanel.getSliderPanel();
 815     assertFalse(sp.isForConservation());
 816     sp.valueChanged(10);
 817     af.conservationMenuItem_actionPerformed(true);
 818     sp = SliderPanel.getSliderPanel();
 819     assertTrue(sp.isForConservation());
 820     sp.valueChanged(20);
 821     ResidueShaderI rs = av.getResidueShading();
 822     assertEquals(rs.getThreshold(), 10);
 823     assertTrue(rs.conservationApplied());
 824     assertEquals(rs.getConservationInc(), 20);
 825
 826     /*
 827      * create a group with Strand colouring, 30% Conservation
 828      * and 40% PID threshold
 829      */
 830     SequenceGroup sg = new SequenceGroup();
 831     sg.addSequence(al.getSequenceAt(0), false);
 832     sg.setStartRes(15);
 833     sg.setEndRes(25);
 834     av.setSelectionGroup(sg);
 835     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 836     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
 837             .toString());
 838     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 839     assertEquals(al.getGroups().size(), 1);
 840     assertSame(al.getGroups().get(0), sg);
 841     popupMenu.conservationMenuItem_actionPerformed(true);
 842     sp = SliderPanel.getSliderPanel();
 843     assertTrue(sp.isForConservation());
 844     sp.valueChanged(30);
 845     popupMenu.abovePIDColour_actionPerformed(true);
 846     sp = SliderPanel.getSliderPanel();
 847     assertFalse(sp.isForConservation());
 848     sp.valueChanged(40);
 849     assertTrue(sg.getGroupColourScheme().conservationApplied());
 850     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 851     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 852
 853     /*
 854      * save project, close windows, reload project, verify
 855      */
 856     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 857             ".jvp");
 858     tfile.deleteOnExit();
 859     new Jalview2XML(false).saveState(tfile);
 860     Desktop.instance.closeAll_actionPerformed(null);
 861     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 862             DataSourceType.FILE);
 863     Assert.assertNotNull(af, "Failed to reload project");
 864
 865     /*
 866      * verify alignment (background) colouring
 867      */
 868     rs = af.getViewport().getResidueShading();
 869     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 870     assertEquals(rs.getThreshold(), 10);
 871     assertTrue(rs.conservationApplied());
 872     assertEquals(rs.getConservationInc(), 20);
 873
 874     /*
 875      * verify group colouring
 876      */
 877     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 878     rs = af.getViewport().getAlignment().getGroups().get(0)
 879             .getGroupColourScheme();
 880     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 881     assertEquals(rs.getThreshold(), 40);
 882     assertTrue(rs.conservationApplied());
 883     assertEquals(rs.getConservationInc(), 30);
 884   }
 885
 886   /**
 887    * Test save and reload of feature colour schemes and filter settings
 888    *
 889    * @throws IOException
 890    */
 891   @Test(groups = { "Functional" })
 892   public void testSaveLoadFeatureColoursAndFilters() throws IOException
 893   {
 894     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 895             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 896     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 897
 898     /*
 899      * add some features to the sequence
 900      */
 901     int score = 1;
 902     addFeatures(seq1, "type1", score++);
 903     addFeatures(seq1, "type2", score++);
 904     addFeatures(seq1, "type3", score++);
 905     addFeatures(seq1, "type4", score++);
 906     addFeatures(seq1, "type5", score++);
 907
 908     /*
 909      * set colour schemes for features
 910      */
 911     FeatureRenderer fr = af.getFeatureRenderer();
 912     fr.findAllFeatures(true);
 913
 914     // type1: red
 915     fr.setColour("type1", new FeatureColour(Color.red));
 916
 917     // type2: by label
 918     FeatureColourI byLabel = new FeatureColour();
 919     byLabel.setColourByLabel(true);
 920     fr.setColour("type2", byLabel);
 921
 922     // type3: by score above threshold
 923     FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
 924             10);
 925     byScore.setAboveThreshold(true);
 926     byScore.setThreshold(2f);
 927     fr.setColour("type3", byScore);
 928
 929     // type4: by attribute AF
 930     FeatureColourI byAF = new FeatureColour();
 931     byAF.setColourByLabel(true);
 932     byAF.setAttributeName("AF");
 933     fr.setColour("type4", byAF);
 934
 935     // type5: by attribute CSQ:PolyPhen below threshold
 936     FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
 937             1, 10);
 938     byPolyPhen.setBelowThreshold(true);
 939     byPolyPhen.setThreshold(3f);
 940     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 941     fr.setColour("type5", byPolyPhen);
 942
 943     /*
 944      * set filters for feature types
 945      */
 946
 947     // filter type1 features by (label contains "x")
 948     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 949     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 950     fr.setFeatureFilter("type1", filterByX);
 951
 952     // filter type2 features by (score <= 2.4 and score > 1.1)
 953     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 954     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 955     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 956     fr.setFeatureFilter("type2", filterByScore);
 957
 958     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 959     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 960     filterByXY
 961             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 962     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 963             "PolyPhen"));
 964     fr.setFeatureFilter("type3", filterByXY);
 965
 966     /*
 967      * save as Jalview project
 968      */
 969     File tfile = File.createTempFile("JalviewTest", ".jvp");
 970     tfile.deleteOnExit();
 971     String filePath = tfile.getAbsolutePath();
 972     af.saveAlignment(filePath, FileFormat.Jalview);
 973     assertTrue(af.isSaveAlignmentSuccessful(),
 974             "Failed to store as a project.");
 975
 976     /*
 977      * close current alignment and load the saved project
 978      */
 979     af.closeMenuItem_actionPerformed(true);
 980     af = null;
 981     af = new FileLoader()
 982             .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
 983     assertNotNull(af, "Failed to import new project");
 984
 985     /*
 986      * verify restored feature colour schemes and filters
 987      */
 988     fr = af.getFeatureRenderer();
 989     FeatureColourI fc = fr.getFeatureStyle("type1");
 990     assertTrue(fc.isSimpleColour());
 991     assertEquals(fc.getColour(), Color.red);
 992     fc = fr.getFeatureStyle("type2");
 993     assertTrue(fc.isColourByLabel());
 994     fc = fr.getFeatureStyle("type3");
 995     assertTrue(fc.isGraduatedColour());
 996     assertNull(fc.getAttributeName());
 997     assertTrue(fc.isAboveThreshold());
 998     assertEquals(fc.getThreshold(), 2f);
 999     fc = fr.getFeatureStyle("type4");
1000     assertTrue(fc.isColourByLabel());
1001     assertTrue(fc.isColourByAttribute());
1002     assertEquals(fc.getAttributeName(), new String[] { "AF" });
1003     fc = fr.getFeatureStyle("type5");
1004     assertTrue(fc.isGraduatedColour());
1005     assertTrue(fc.isColourByAttribute());
1006     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1007     assertTrue(fc.isBelowThreshold());
1008     assertEquals(fc.getThreshold(), 3f);
1009
1010     assertEquals(fr.getFeatureFilter("type1").toStableString(),
1011             "Label Contains x");
1012     assertEquals(fr.getFeatureFilter("type2").toStableString(),
1013             "(Score LE 2.4) AND (Score GT 1.1)");
1014     assertEquals(fr.getFeatureFilter("type3").toStableString(),
1015             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
1016   }
1017
1018   private void addFeature(SequenceI seq, String featureType, int score)
1019   {
1020     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1021             score, "grp");
1022     sf.setValue("AF", score);
1023     sf.setValue("CSQ", new HashMap<String, String>()
1024     {
1025       {
1026         put("PolyPhen", Integer.toString(score));
1027       }
1028     });
1029     seq.addSequenceFeature(sf);
1030   }
1031
1032   /**
1033    * Adds two features of the given type to the given sequence, also setting the
1034    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1035    *
1036    * @param seq
1037    * @param featureType
1038    * @param score
1039    */
1040   private void addFeatures(SequenceI seq, String featureType, int score)
1041   {
1042     addFeature(seq, featureType, score++);
1043     addFeature(seq, featureType, score);
1044   }
1045 }