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