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.analysis.scoremodels.SimilarityParams;
  31 import jalview.api.AlignViewportI;
  32 import jalview.api.AlignmentViewPanel;
  33 import jalview.api.FeatureColourI;
  34 import jalview.api.ViewStyleI;
  35 import jalview.bin.Jalview;
  36 import jalview.datamodel.AlignmentAnnotation;
  37 import jalview.datamodel.AlignmentI;
  38 import jalview.datamodel.HiddenSequences;
  39 import jalview.datamodel.PDBEntry;
  40 import jalview.datamodel.PDBEntry.Type;
  41 import jalview.datamodel.SequenceCollectionI;
  42 import jalview.datamodel.SequenceFeature;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.datamodel.features.FeatureMatcher;
  46 import jalview.datamodel.features.FeatureMatcherSet;
  47 import jalview.datamodel.features.FeatureMatcherSetI;
  48 import jalview.gui.AlignFrame;
  49 import jalview.gui.AlignViewport;
  50 import jalview.gui.AlignmentPanel;
  51 import jalview.gui.Desktop;
  52 import jalview.gui.FeatureRenderer;
  53 import jalview.gui.JvOptionPane;
  54 import jalview.gui.PCAPanel;
  55 import jalview.gui.PopupMenu;
  56 import jalview.gui.SliderPanel;
  57 import jalview.io.DataSourceType;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileLoader;
  60 import jalview.io.Jalview2xmlBase;
  61 import jalview.renderer.ResidueShaderI;
  62 import jalview.schemes.AnnotationColourGradient;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ColourSchemeI;
  65 import jalview.schemes.ColourSchemeProperty;
  66 import jalview.schemes.FeatureColour;
  67 import jalview.schemes.JalviewColourScheme;
  68 import jalview.schemes.RNAHelicesColour;
  69 import jalview.schemes.StrandColourScheme;
  70 import jalview.schemes.TCoffeeColourScheme;
  71 import jalview.structure.StructureImportSettings;
  72 import jalview.structure.StructureMapping;
  73 import jalview.util.matcher.Condition;
  74 import jalview.viewmodel.AlignmentViewport;
  75
  76 import java.awt.Color;
  77 import java.io.File;
  78 import java.io.IOException;
  79 import java.util.ArrayList;
  80 import java.util.HashMap;
  81 import java.util.List;
  82 import java.util.Map;
  83
  84 import javax.swing.JInternalFrame;
  85
  86 import org.testng.Assert;
  87 import org.testng.AssertJUnit;
  88 import org.testng.annotations.BeforeClass;
  89 import org.testng.annotations.Test;
  90
  91 @Test(singleThreaded = true)
  92 public class Jalview2xmlTests extends Jalview2xmlBase
  93 {
  94
  95   @Override
  96   @BeforeClass(alwaysRun = true)
  97   public void setUpJvOptionPane()
  98   {
  99     JvOptionPane.setInteractiveMode(false);
 100     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
 101     Jalview.setSynchronous(true);
 102   }
 103
 104   @Test(groups = { "Functional" })
 105   public void testRNAStructureRecovery() throws Exception
 106   {
 107     String inFile = "examples/RF00031_folded.stk";
 108     String tfile = File.createTempFile("JalviewTest", ".jvp")
 109             .getAbsolutePath();
 110     // Jalview.setSynchronous(true);
 111     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 112             DataSourceType.FILE);
 113     assertNotNull(af, "Didn't read input file " + inFile);
 114     int olddsann = countDsAnn(af.getViewport());
 115     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 116     af.changeColour_actionPerformed(
 117             JalviewColourScheme.RNAHelices.toString());
 118     assertTrue(
 119             af.getViewport()
 120                     .getGlobalColourScheme() instanceof RNAHelicesColour,
 121             "Couldn't apply RNA helices colourscheme");
 122     af.saveAlignment(tfile, FileFormat.Jalview);
 123     assertTrue(af.isSaveAlignmentSuccessful(),
 124             "Failed to store as a project.");
 125     af.closeMenuItem_actionPerformed(true);
 126     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 127             DataSourceType.FILE);
 128     assertNotNull(af, "Failed to import new project");
 129     int newdsann = countDsAnn(af.getViewport());
 130     assertEquals(olddsann, newdsann,
 131             "Differing numbers of dataset sequence annotation\nOriginally "
 132                     + olddsann + " and now " + newdsann);
 133     System.out.println(
 134             "Read in same number of annotations as originally present ("
 135                     + olddsann + ")");
 136     assertTrue(
 137
 138             af.getViewport()
 139                     .getGlobalColourScheme() instanceof RNAHelicesColour,
 140             "RNA helices colourscheme was not applied on import.");
 141   }
 142
 143   @Test(groups = { "Functional" })
 144   public void testTCoffeeScores() throws Exception
 145   {
 146     String inFile = "examples/uniref50.fa",
 147             inAnnot = "examples/uniref50.score_ascii";
 148     String tfile = File.createTempFile("JalviewTest", ".jvp")
 149             .getAbsolutePath();
 150     // Jalview.setSynchronous(true);
 151     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 152             DataSourceType.FILE);
 153     assertNotNull(af, "Didn't read input file " + inFile);
 154     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 155     AlignViewport viewport = af.getViewport();
 156     assertSame(viewport.getGlobalColourScheme().getClass(),
 157             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 158     assertNotNull(
 159             ColourSchemeProperty.getColourScheme(viewport,
 160                     viewport.getAlignment(),
 161                     viewport.getGlobalColourScheme()
 162                             .getSchemeName()),
 163             "Recognise T-Coffee score from string");
 164
 165     af.saveAlignment(tfile, FileFormat.Jalview);
 166     assertTrue(af.isSaveAlignmentSuccessful(),
 167             "Failed to store as a project.");
 168     af.closeMenuItem_actionPerformed(true);
 169     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 170             DataSourceType.FILE);
 171     assertNotNull(af, "Failed to import new project");
 172     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 173             TCoffeeColourScheme.class,
 174             "Didn't set T-coffee colourscheme for imported project.");
 175     System.out.println(
 176             "T-Coffee score shading successfully recovered from project.");
 177   }
 178
 179   @Test(groups = { "Functional" })
 180   public void testColourByAnnotScores() throws Exception
 181   {
 182     String inFile = "examples/uniref50.fa",
 183             inAnnot = "examples/testdata/uniref50_iupred.jva";
 184     String tfile = File.createTempFile("JalviewTest", ".jvp")
 185             .getAbsolutePath();
 186     // Jalview.setSynchronous(true);
 187     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 188             DataSourceType.FILE);
 189     assertNotNull(af, "Didn't read input file " + inFile);
 190     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 191     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 192             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 193     assertTrue(
 194
 195             aa != null && aa.length > 0,
 196             "Didn't find any IUPred annotation to use to shade alignment.");
 197     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 198             AnnotationColourGradient.ABOVE_THRESHOLD);
 199     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null,
 200             AnnotationColourGradient.BELOW_THRESHOLD);
 201     cs.setSeqAssociated(true);
 202     gcs.setSeqAssociated(true);
 203     af.changeColour(cs);
 204     SequenceGroup sg = new SequenceGroup();
 205     sg.setStartRes(57);
 206     sg.setEndRes(92);
 207     sg.cs.setColourScheme(gcs);
 208     af.getViewport().getAlignment().addGroup(sg);
 209     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 210     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 211     af.alignPanel.alignmentChanged();
 212     af.saveAlignment(tfile, FileFormat.Jalview);
 213     assertTrue(af.isSaveAlignmentSuccessful(),
 214             "Failed to store as a project.");
 215     af.closeMenuItem_actionPerformed(true);
 216     af = null;
 217     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 218             DataSourceType.FILE);
 219     assertNotNull(af, "Failed to import new project");
 220
 221     // check for group and alignment colourschemes
 222
 223     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 224     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0)
 225             .getColourScheme();
 226     assertNotNull(_rcs, "Didn't recover global colourscheme");
 227     assertTrue(_rcs instanceof AnnotationColourGradient,
 228             "Didn't recover annotation colour global scheme");
 229     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 230     assertTrue(__rcs.isSeqAssociated(),
 231             "Annotation colourscheme wasn't sequence associated");
 232
 233     boolean diffseqcols = false, diffgseqcols = false;
 234     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 235     for (int p = 0, pSize = af.getViewport().getAlignment()
 236             .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
 237     {
 238       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 239               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 240       {
 241         diffseqcols = true;
 242       }
 243     }
 244     assertTrue(diffseqcols, "Got Different sequence colours");
 245     System.out.println(
 246             "Per sequence colourscheme (Background) successfully applied and recovered.");
 247
 248     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 249     assertTrue(_rgcs instanceof AnnotationColourGradient,
 250             "Didn't recover annotation colour group colourscheme");
 251     __rcs = (AnnotationColourGradient) _rgcs;
 252     assertTrue(__rcs.isSeqAssociated(),
 253             "Group Annotation colourscheme wasn't sequence associated");
 254
 255     for (int p = 0, pSize = af.getViewport().getAlignment()
 256             .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
 257     {
 258       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
 259               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
 260                       0f))
 261       {
 262         diffgseqcols = true;
 263       }
 264     }
 265     assertTrue(diffgseqcols, "Got Different group sequence colours");
 266     System.out.println(
 267             "Per sequence (Group) colourscheme successfully applied and recovered.");
 268   }
 269
 270   @Test(groups = { "Functional" })
 271   public void gatherViewsHere() throws Exception
 272   {
 273     int origCount = Desktop.getAlignFrames() == null ? 0
 274             : Desktop.getAlignFrames().length;
 275     // Jalview.setSynchronous(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     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 280             "Didn't gather the views in the example file.");
 281
 282   }
 283
 284   /**
 285    * Test for JAL-2223 - multiple mappings in View Mapping report
 286    *
 287    * @throws Exception
 288    */
 289   @Test(groups = { "Functional" })
 290   public void noDuplicatePdbMappingsMade() throws Exception
 291   {
 292     StructureImportSettings.setProcessSecondaryStructure(true);
 293     StructureImportSettings.setVisibleChainAnnotation(true);
 294     // Jalview.setSynchronous(true);
 295     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 296             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 297     assertNotNull(af, "Didn't read in the example file correctly.");
 298
 299     // locate Jmol viewer
 300     // count number of PDB mappings the structure selection manager holds -
 301     String pdbFile = af.getCurrentView().getStructureSelectionManager()
 302             .findFileForPDBId("1A70");
 303     StructureMapping[] x = af.getCurrentView()
 304             .getStructureSelectionManager()//
 305             .getMapping(pdbFile);
 306     assertEquals(x.length,
 307             2, "Expected only two mappings for 1A70");
 308
 309   }
 310
 311   @Test(groups = { "Functional" })
 312   public void viewRefPdbAnnotation() throws Exception
 313   {
 314     StructureImportSettings.setProcessSecondaryStructure(true);
 315     StructureImportSettings.setVisibleChainAnnotation(true);
 316     // Jalview.setSynchronous(true);
 317     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 318             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 319     assertNotNull(af, "Didn't read in the example file correctly.");
 320     AlignmentViewPanel sps = null;
 321     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 322     {
 323       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 324       {
 325         sps = ap;
 326         break;
 327       }
 328     }
 329     assertNotNull(sps, "Couldn't find the structure view");
 330     AlignmentAnnotation refan = null;
 331     for (AlignmentAnnotation ra : sps.getAlignment()
 332             .getAlignmentAnnotation())
 333     {
 334       if (ra.graph != 0)
 335       {
 336         refan = ra;
 337         break;
 338       }
 339     }
 340     assertNotNull(refan, "Annotation secondary structure not found.");
 341     SequenceI sq = sps.getAlignment().findName("1A70|");
 342     assertNotNull(sq, "Couldn't find 1a70 null chain");
 343     // compare the manually added temperature factor annotation
 344     // to the track automatically transferred from the pdb structure on load
 345     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 346             "1a70 has no annotation");
 347     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 348     {
 349       AlignmentAnnotation alaa;
 350       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 351       alaa.adjustForAlignment();
 352       if (ala.graph == refan.graph)
 353       {
 354         for (int p = 0; p < ala.annotations.length; p++)
 355         {
 356           sq.findPosition(p);
 357           try
 358           {
 359             assertTrue((alaa.annotations[p] == null
 360                     && refan.annotations[p] == null)
 361                     || alaa.annotations[p].value == refan.annotations[p].value,
 362                     "Mismatch at alignment position " + p);
 363           } catch (NullPointerException q)
 364           {
 365             Assert.fail("Mismatch of alignment annotations at position " + p
 366                     + " Ref seq ann: " + refan.annotations[p]
 367                     + " alignment " + alaa.annotations[p]);
 368           }
 369         }
 370       }
 371     }
 372
 373   }
 374
 375   @Test(groups = { "Functional" })
 376   public void testCopyViewSettings() throws Exception
 377   {
 378     // Jalview.setSynchronous(true);
 379     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 380             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 381     assertNotNull(af, "Didn't read in the example file correctly.");
 382     AlignmentViewPanel sps = null, groups = null;
 383     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 384     {
 385       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 386       {
 387         sps = ap;
 388       }
 389       if (ap.getViewName().contains("MAFFT"))
 390       {
 391         groups = ap;
 392       }
 393     }
 394     assertNotNull(sps, "Couldn't find the structure view");
 395     assertNotNull(groups, "Couldn't find the MAFFT view");
 396
 397     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 398     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 399     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 400
 401     groups.getAlignViewport().setViewStyle(structureStyle);
 402     AssertJUnit.assertFalse(
 403             groupStyle.sameStyle(groups.getAlignViewport().getViewStyle()));
 404     Assert.assertTrue(structureStyle
 405             .sameStyle(groups.getAlignViewport().getViewStyle()));
 406
 407   }
 408
 409   /**
 410    * test store and recovery of expanded views
 411    *
 412    * @throws Exception
 413    */
 414   @Test(groups = { "Functional" }, enabled = true)
 415   public void testStoreAndRecoverExpandedviews() throws Exception
 416   {
 417     Desktop.getInstance().closeAll_actionPerformed(null);
 418     // Jalview.setSynchronous(true);
 419     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 420             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 421     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 422     String afid = af.getViewport().getSequenceSetId();
 423
 424     // check FileLoader returned a reference to the one alignFrame that is
 425     // actually on the Desktop
 426     assertSame(af, Desktop.getAlignFrameFor(af.getViewport()),
 427             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 428
 429     Desktop.explodeViews(af);
 430
 431     int oldviews = Desktop.getAlignFrames().length;
 432     Assert.assertEquals(Desktop.getAlignFrames().length,
 433             Desktop.getAlignmentPanels(afid).length);
 434     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 435     try
 436     {
 437       new Jalview2XML(false).saveState(tfile);
 438     } catch (Error e)
 439     {
 440       Assert.fail("Didn't save the expanded view state", e);
 441     } catch (Exception e)
 442     {
 443       Assert.fail("Didn't save the expanded view state", e);
 444     }
 445     Desktop.getInstance().closeAll_actionPerformed(null);
 446     if (Desktop.getAlignFrames() != null)
 447     {
 448       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 449     }
 450     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 451             DataSourceType.FILE);
 452     Assert.assertNotNull(af);
 453     Assert.assertEquals(Desktop.getAlignFrames().length,
 454             Desktop.getAlignmentPanels(
 455                     af.getViewport().getSequenceSetId()).length);
 456     Assert.assertEquals(
 457             Desktop.getAlignmentPanels(
 458                     af.getViewport().getSequenceSetId()).length,
 459             oldviews);
 460   }
 461
 462   /**
 463    * Test save and reload of a project with a different representative sequence
 464    * in each view.
 465    *
 466    * @throws Exception
 467    */
 468   @Test(groups = { "Functional" })
 469   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 470   {
 471     Desktop.getInstance().closeAll_actionPerformed(null);
 472     // Jalview.setSynchronous(true);
 473     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 474             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 475     assertNotNull(af, "Didn't read in the example file correctly.");
 476     String afid = af.getViewport().getSequenceSetId();
 477
 478     // remember reference sequence for each panel
 479     Map<String, SequenceI> refseqs = new HashMap<>();
 480
 481     /*
 482      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 483      * as reference sequence for itself and the preceding sequence
 484      */
 485     int n = 1;
 486     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 487     {
 488       AlignViewportI av = ap.getAlignViewport();
 489       AlignmentI alignment = ap.getAlignment();
 490       int repIndex = n % alignment.getHeight();
 491       SequenceI rep = alignment.getSequenceAt(repIndex);
 492       refseqs.put(ap.getViewName(), rep);
 493
 494       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 495       // todo refactor this to an alignment view controller
 496       av.setDisplayReferenceSeq(true);
 497       av.setColourByReferenceSeq(true);
 498       av.getAlignment().setSeqrep(rep);
 499
 500       n++;
 501     }
 502     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 503             ".jvp");
 504     try
 505     {
 506       new Jalview2XML(false).saveState(tfile);
 507     } catch (Throwable e)
 508     {
 509       Assert.fail("Didn't save the expanded view state", e);
 510     }
 511     Desktop.getInstance().closeAll_actionPerformed(null);
 512     if (Desktop.getAlignFrames() != null)
 513     {
 514       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 515     }
 516
 517     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 518             DataSourceType.FILE);
 519     afid = af.getViewport().getSequenceSetId();
 520
 521     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 522     {
 523       // check representative
 524       AlignmentI alignment = ap.getAlignment();
 525       SequenceI rep = alignment.getSeqrep();
 526       Assert.assertNotNull(rep,
 527               "Couldn't restore sequence representative from project");
 528       // can't use a strong equals here, because by definition, the sequence IDs
 529       // will be different.
 530       // could set vamsas session save/restore flag to preserve IDs across
 531       // load/saves.
 532       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 533               rep.toString(),
 534               "Representative wasn't the same when recovered.");
 535       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 536               "Display reference sequence view setting not set.");
 537       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 538               "Colour By Reference Seq view setting not set.");
 539     }
 540   }
 541
 542   @Test(groups = { "Functional" })
 543   public void testIsVersionStringLaterThan()
 544   {
 545     /*
 546      * No version / development / test / autobuild is leniently assumed to be
 547      * compatible
 548      */
 549     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 550     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 551     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 552     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 553             "Development Build"));
 554     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 555             "DEVELOPMENT BUILD"));
 556     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 557             "Development Build"));
 558     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 559     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 560     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 561     assertTrue(
 562             Jalview2XML.isVersionStringLaterThan(null, "Automated Build"));
 563     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 564             "Automated Build"));
 565     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 566             "AUTOMATED BUILD"));
 567
 568     /*
 569      * same version returns true i.e. compatible
 570      */
 571     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 572     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 573     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 574     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 575     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 576
 577     /*
 578      * later version returns true
 579      */
 580     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 581     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 582     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 583     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 584     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 585
 586     /*
 587      * earlier version returns false
 588      */
 589     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 590     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 591     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 592     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 593     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 594   }
 595
 596   /**
 597    * Test save and reload of a project with a different sequence group (and
 598    * representative sequence) in each view.
 599    *
 600    * @throws Exception
 601    */
 602   @Test(groups = { "Functional" })
 603   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 604   {
 605     Desktop.getInstance().closeAll_actionPerformed(null);
 606     // Jalview.setSynchronous(true);
 607     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 608             "examples/uniref50.fa", DataSourceType.FILE);
 609     assertNotNull(af, "Didn't read in the example file correctly.");
 610     String afid = af.getViewport().getSequenceSetId();
 611     // make a second view of the alignment
 612     af.newView_actionPerformed(null);
 613
 614     /*
 615      * remember representative and hidden sequences marked
 616      * on each panel
 617      */
 618     Map<String, SequenceI> repSeqs = new HashMap<>();
 619     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 620
 621     /*
 622      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 623      * as reference sequence for itself and the preceding sequence
 624      */
 625     int n = 1;
 626     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 627     {
 628       AlignViewportI av = ap.getAlignViewport();
 629       AlignmentI alignment = ap.getAlignment();
 630       int repIndex = n % alignment.getHeight();
 631       // ensure at least one preceding sequence i.e. index >= 1
 632       repIndex = Math.max(repIndex, 1);
 633       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 634       repSeqs.put(ap.getViewName(), repSeq);
 635       List<String> hiddenNames = new ArrayList<>();
 636       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 637
 638       /*
 639        * have rep sequence represent itself and the one before it
 640        * this hides the group (except for the rep seq)
 641        */
 642       SequenceGroup sg = new SequenceGroup();
 643       sg.addSequence(repSeq, false);
 644       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 645       sg.addSequence(precedingSeq, false);
 646       sg.setSeqrep(repSeq);
 647       assertTrue(sg.getSequences().contains(repSeq));
 648       assertTrue(sg.getSequences().contains(precedingSeq));
 649       av.setSelectionGroup(sg);
 650       assertSame(repSeq, sg.getSeqrep());
 651
 652       /*
 653        * represent group with sequence adds to a map of hidden rep sequences
 654        * (it does not create a group on the alignment)
 655        */
 656       ((AlignmentViewport) av).hideSequences(repSeq, true);
 657       assertSame(repSeq, sg.getSeqrep());
 658       assertTrue(sg.getSequences().contains(repSeq));
 659       assertTrue(sg.getSequences().contains(precedingSeq));
 660       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 661       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 662               .getHiddenRepSequences();
 663       assertNotNull(hiddenRepSeqsMap);
 664       assertEquals(1, hiddenRepSeqsMap.size());
 665       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 666       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 667       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 668       hiddenNames.add(precedingSeq.getName());
 669
 670       n++;
 671     }
 672     File tfile = File.createTempFile("testStoreAndRecoverGroupReps",
 673             ".jvp");
 674     try
 675     {
 676       new Jalview2XML(false).saveState(tfile);
 677     } catch (Throwable e)
 678     {
 679       Assert.fail("Didn't save the expanded view state", e);
 680     }
 681     Desktop.getInstance().closeAll_actionPerformed(null);
 682     if (Desktop.getAlignFrames() != null)
 683     {
 684       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 685     }
 686
 687     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 688             DataSourceType.FILE);
 689     afid = af.getViewport().getSequenceSetId();
 690
 691     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 692     {
 693       String viewName = ap.getViewName();
 694       AlignViewportI av = ap.getAlignViewport();
 695       AlignmentI alignment = ap.getAlignment();
 696       List<SequenceGroup> groups = alignment.getGroups();
 697       assertNotNull(groups);
 698       assertTrue(groups.isEmpty(), "Alignment has groups");
 699       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 700               .getHiddenRepSequences();
 701       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 702       assertEquals(1, hiddenRepSeqsMap.size());
 703       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 704               hiddenRepSeqsMap.keySet().iterator().next()
 705                       .getDisplayId(true));
 706
 707       /*
 708        * verify hidden sequences in restored panel
 709        */
 710       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 711       HiddenSequences hs = alignment.getHiddenSequences();
 712       assertEquals(hidden.size(), hs.getSize(),
 713               "wrong number of restored hidden sequences in "
 714                       + ap.getViewName());
 715     }
 716   }
 717
 718   /**
 719    * Test save and reload of PDBEntry in Jalview project
 720    *
 721    * @throws Exception
 722    */
 723   @Test(groups = { "Functional" })
 724   public void testStoreAndRecoverPDBEntry() throws Exception
 725   {
 726     Desktop.getInstance().closeAll_actionPerformed(null);
 727     String exampleFile = "examples/3W5V.pdb";
 728     // Jalview.setSynchronous(true);
 729     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 730             DataSourceType.FILE);
 731     assertNotNull(af, "Didn't read in the example file correctly.");
 732     String afid = af.getViewport().getSequenceSetId();
 733
 734     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 735     System.out.println();
 736     AlignmentViewPanel ap = alignPanels[0];
 737     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 738     String testFile = tfileBase + exampleFile;
 739     AlignmentI alignment = ap.getAlignment();
 740     System.out.println("blah");
 741     SequenceI[] seqs = alignment.getSequencesArray();
 742     Assert.assertNotNull(seqs[0]);
 743     Assert.assertNotNull(seqs[1]);
 744     Assert.assertNotNull(seqs[2]);
 745     Assert.assertNotNull(seqs[3]);
 746     Assert.assertNotNull(seqs[0].getDatasetSequence());
 747     Assert.assertNotNull(seqs[1].getDatasetSequence());
 748     Assert.assertNotNull(seqs[2].getDatasetSequence());
 749     Assert.assertNotNull(seqs[3].getDatasetSequence());
 750     PDBEntry[] pdbEntries = new PDBEntry[4];
 751     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 752     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 753     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 754     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 755     Assert.assertEquals(
 756             seqs[0].getDatasetSequence().getAllPDBEntries().get(0),
 757             pdbEntries[0]);
 758     Assert.assertEquals(
 759             seqs[1].getDatasetSequence().getAllPDBEntries().get(0),
 760             pdbEntries[1]);
 761     Assert.assertEquals(
 762             seqs[2].getDatasetSequence().getAllPDBEntries().get(0),
 763             pdbEntries[2]);
 764     Assert.assertEquals(
 765             seqs[3].getDatasetSequence().getAllPDBEntries().get(0),
 766             pdbEntries[3]);
 767
 768     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 769     try
 770     {
 771       new Jalview2XML(false).saveState(tfile);
 772     } catch (Throwable e)
 773     {
 774       Assert.fail("Didn't save the state", e);
 775     }
 776     Desktop.getInstance().closeAll_actionPerformed(null);
 777     if (Desktop.getAlignFrames() != null)
 778     {
 779       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 780     }
 781
 782     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 783             tfile.getAbsolutePath(), DataSourceType.FILE);
 784     String rfid = restoredFrame.getViewport().getSequenceSetId();
 785     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 786     AlignmentViewPanel rap = rAlignPanels[0];
 787     AlignmentI rAlignment = rap.getAlignment();
 788     System.out.println("blah");
 789     SequenceI[] rseqs = rAlignment.getSequencesArray();
 790     Assert.assertNotNull(rseqs[0]);
 791     Assert.assertNotNull(rseqs[1]);
 792     Assert.assertNotNull(rseqs[2]);
 793     Assert.assertNotNull(rseqs[3]);
 794     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 795     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 796     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 797     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 798
 799     // The Asserts below are expected to fail until the PDB chainCode is
 800     // recoverable from a Jalview projects
 801     for (int chain = 0; chain < 4; chain++)
 802     {
 803       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 804               .get(0);
 805       PDBEntry expected = pdbEntries[chain];
 806       Assert.assertEquals(recov.getId(), expected.getId(),
 807               "Mismatch PDB ID");
 808       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 809               "Mismatch PDB ID");
 810       Assert.assertEquals(recov.getType(), expected.getType(),
 811               "Mismatch PDBEntry 'Type'");
 812       Assert.assertNotNull(recov.getFile(),
 813               "Recovered PDBEntry should have a non-null file entry");
 814     }
 815   }
 816
 817   /**
 818    * Configure an alignment and a sub-group each with distinct colour schemes,
 819    * Conservation and PID thresholds, and confirm these are restored from the
 820    * saved project.
 821    *
 822    * @throws IOException
 823    */
 824   @Test(groups = { "Functional" })
 825   public void testStoreAndRecoverColourThresholds() throws IOException
 826   {
 827     Desktop.getInstance().closeAll_actionPerformed(null);
 828     // Jalview.setSynchronous(true);
 829     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 830             "examples/uniref50.fa", DataSourceType.FILE);
 831
 832     AlignViewport av = af.getViewport();
 833     AlignmentI al = av.getAlignment();
 834
 835     /*
 836      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 837      */
 838     av.setColourAppliesToAllGroups(false);
 839     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 840     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 841     af.abovePIDThreshold_actionPerformed(true);
 842     SliderPanel sp = SliderPanel.getSliderPanel();
 843     assertFalse(sp.isForConservation());
 844     sp.valueChanged(10);
 845     af.conservationMenuItem_actionPerformed(true);
 846     sp = SliderPanel.getSliderPanel();
 847     assertTrue(sp.isForConservation());
 848     sp.valueChanged(20);
 849     ResidueShaderI rs = av.getResidueShading();
 850     assertEquals(rs.getThreshold(), 10);
 851     assertTrue(rs.conservationApplied());
 852     assertEquals(rs.getConservationInc(), 20);
 853
 854     /*
 855      * create a group with Strand colouring, 30% Conservation
 856      * and 40% PID threshold
 857      */
 858     SequenceGroup sg = new SequenceGroup();
 859     sg.addSequence(al.getSequenceAt(0), false);
 860     sg.setStartRes(15);
 861     sg.setEndRes(25);
 862     av.setSelectionGroup(sg);
 863     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 864     popupMenu.changeColour_actionPerformed(
 865             JalviewColourScheme.Strand.toString());
 866     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 867     assertEquals(al.getGroups().size(), 1);
 868     assertSame(al.getGroups().get(0), sg);
 869     popupMenu.conservationMenuItem_actionPerformed(true);
 870     sp = SliderPanel.getSliderPanel();
 871     assertTrue(sp.isForConservation());
 872     sp.valueChanged(30);
 873     popupMenu.abovePIDColour_actionPerformed(true);
 874     sp = SliderPanel.getSliderPanel();
 875     assertFalse(sp.isForConservation());
 876     sp.valueChanged(40);
 877     assertTrue(sg.getGroupColourScheme().conservationApplied());
 878     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 879     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 880
 881     /*
 882      * save project, close windows, reload project, verify
 883      */
 884     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 885             ".jvp");
 886     tfile.deleteOnExit();
 887     new Jalview2XML(false).saveState(tfile);
 888     Desktop.getInstance().closeAll_actionPerformed(null);
 889     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 890             DataSourceType.FILE);
 891     Assert.assertNotNull(af, "Failed to reload project");
 892
 893     /*
 894      * verify alignment (background) colouring
 895      */
 896     rs = af.getViewport().getResidueShading();
 897     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 898     assertEquals(rs.getThreshold(), 10);
 899     assertTrue(rs.conservationApplied());
 900     assertEquals(rs.getConservationInc(), 20);
 901
 902     /*
 903      * verify group colouring
 904      */
 905     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 906     rs = af.getViewport().getAlignment().getGroups().get(0)
 907             .getGroupColourScheme();
 908     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 909     assertEquals(rs.getThreshold(), 40);
 910     assertTrue(rs.conservationApplied());
 911     assertEquals(rs.getConservationInc(), 30);
 912   }
 913
 914   /**
 915    * Test save and reload of feature colour schemes and filter settings
 916    *
 917    * @throws IOException
 918    */
 919   @Test(groups = { "Functional" })
 920   public void testSaveLoadFeatureColoursAndFilters() throws IOException
 921   {
 922     // Jalview.setSynchronous(true);
 923     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 924             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 925     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 926
 927     /*
 928      * add some features to the sequence
 929      */
 930     int score = 1;
 931     addFeatures(seq1, "type1", score++);
 932     addFeatures(seq1, "type2", score++);
 933     addFeatures(seq1, "type3", score++);
 934     addFeatures(seq1, "type4", score++);
 935     addFeatures(seq1, "type5", score++);
 936
 937     /*
 938      * set colour schemes for features
 939      */
 940     FeatureRenderer fr = af.getFeatureRenderer();
 941     fr.findAllFeatures(true);
 942
 943     // type1: red
 944     fr.setColour("type1", new FeatureColour(Color.red));
 945
 946     // type2: by label
 947     FeatureColourI byLabel = new FeatureColour();
 948     byLabel.setColourByLabel(true);
 949     fr.setColour("type2", byLabel);
 950
 951     // type3: by score above threshold
 952     FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
 953             Color.BLUE, null, 1, 10);
 954     byScore.setAboveThreshold(true);
 955     byScore.setThreshold(2f);
 956     fr.setColour("type3", byScore);
 957
 958     // type4: by attribute AF
 959     FeatureColourI byAF = new FeatureColour();
 960     byAF.setColourByLabel(true);
 961     byAF.setAttributeName("AF");
 962     fr.setColour("type4", byAF);
 963
 964     // type5: by attribute CSQ:PolyPhen below threshold
 965     FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
 966             Color.BLUE, null, 1, 10);
 967     byPolyPhen.setBelowThreshold(true);
 968     byPolyPhen.setThreshold(3f);
 969     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 970     fr.setColour("type5", byPolyPhen);
 971
 972     /*
 973      * set filters for feature types
 974      */
 975
 976     // filter type1 features by (label contains "x")
 977     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 978     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 979     fr.setFeatureFilter("type1", filterByX);
 980
 981     // filter type2 features by (score <= 2.4 and score > 1.1)
 982     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 983     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 984     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 985     fr.setFeatureFilter("type2", filterByScore);
 986
 987     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 988     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 989     filterByXY
 990             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 991     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 992             "PolyPhen"));
 993     fr.setFeatureFilter("type3", filterByXY);
 994
 995     /*
 996      * save as Jalview project
 997      */
 998     File tfile = File.createTempFile("JalviewTest", ".jvp");
 999     tfile.deleteOnExit();
1000     String filePath = tfile.getAbsolutePath();
1001     af.saveAlignment(filePath, FileFormat.Jalview);
1002     assertTrue(af.isSaveAlignmentSuccessful(),
1003             "Failed to store as a project.");
1004
1005     /*
1006      * close current alignment and load the saved project
1007      */
1008     af.closeMenuItem_actionPerformed(true);
1009     af = null;
1010     af = new FileLoader().LoadFileWaitTillLoaded(filePath,
1011             DataSourceType.FILE);
1012     assertNotNull(af, "Failed to import new project");
1013
1014     /*
1015      * verify restored feature colour schemes and filters
1016      */
1017     fr = af.getFeatureRenderer();
1018     FeatureColourI fc = fr.getFeatureStyle("type1");
1019     assertTrue(fc.isSimpleColour());
1020     assertEquals(fc.getColour(), Color.red);
1021     fc = fr.getFeatureStyle("type2");
1022     assertTrue(fc.isColourByLabel());
1023     fc = fr.getFeatureStyle("type3");
1024     assertTrue(fc.isGraduatedColour());
1025     assertNull(fc.getAttributeName());
1026     assertTrue(fc.isAboveThreshold());
1027     assertEquals(fc.getThreshold(), 2f);
1028     fc = fr.getFeatureStyle("type4");
1029     assertTrue(fc.isColourByLabel());
1030     assertTrue(fc.isColourByAttribute());
1031     assertEquals(fc.getAttributeName(), new String[] { "AF" });
1032     fc = fr.getFeatureStyle("type5");
1033     assertTrue(fc.isGraduatedColour());
1034     assertTrue(fc.isColourByAttribute());
1035     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1036     assertTrue(fc.isBelowThreshold());
1037     assertEquals(fc.getThreshold(), 3f);
1038
1039     assertEquals(fr.getFeatureFilter("type1").toStableString(),
1040             "Label Contains x");
1041     assertEquals(fr.getFeatureFilter("type2").toStableString(),
1042             "(Score LE 2.4) AND (Score GT 1.1)");
1043     assertEquals(fr.getFeatureFilter("type3").toStableString(),
1044             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
1045   }
1046
1047   private void addFeature(SequenceI seq, String featureType, int score)
1048   {
1049     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1050             score, "grp");
1051     sf.setValue("AF", score);
1052     sf.setValue("CSQ", new HashMap<String, String>()
1053     {
1054       {
1055         put("PolyPhen", Integer.toString(score));
1056       }
1057     });
1058     seq.addSequenceFeature(sf);
1059   }
1060
1061   /**
1062    * Adds two features of the given type to the given sequence, also setting the
1063    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1064    *
1065    * @param seq
1066    * @param featureType
1067    * @param score
1068    */
1069   private void addFeatures(SequenceI seq, String featureType, int score)
1070   {
1071     addFeature(seq, featureType, score++);
1072     addFeature(seq, featureType, score);
1073   }
1074
1075   /**
1076    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1077    * view (JAL-3171) this test ensures we can import and merge those views
1078    */
1079   @Test(groups = { "Functional" })
1080   public void testMergeDatasetsforViews() throws IOException
1081   {
1082     // simple project - two views on one alignment
1083     // Jalview.setSynchronous(true);
1084     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1085             "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
1086     assertNotNull(af);
1087     assertTrue(af.getAlignPanels().size() > 1);
1088     verifyDs(af);
1089   }
1090
1091   /**
1092    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1093    * view (JAL-3171) this test ensures we can import and merge those views This
1094    * is a more complex project
1095    */
1096   @Test(groups = { "Functional" })
1097   public void testMergeDatasetsforManyViews() throws IOException
1098   {
1099     Desktop.getInstance().closeAll_actionPerformed(null);
1100
1101     // complex project - one dataset, several views on several alignments
1102     // Jalview.setSynchronous(true);
1103     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1104             "examples/testdata/projects/manyViews.jvp",
1105             DataSourceType.FILE);
1106     assertNotNull(af);
1107
1108     AlignmentI ds = null;
1109     for (AlignFrame alignFrame : Desktop.getAlignFrames())
1110     {
1111       if (ds == null)
1112       {
1113         ds = verifyDs(alignFrame);
1114       }
1115       else
1116       {
1117         // check that this frame's dataset matches the last
1118         assertTrue(ds == verifyDs(alignFrame));
1119       }
1120     }
1121   }
1122
1123   private AlignmentI verifyDs(AlignFrame af)
1124   {
1125     AlignmentI ds = null;
1126     for (AlignmentViewPanel ap : af.getAlignPanels())
1127     {
1128       if (ds == null)
1129       {
1130         ds = ap.getAlignment().getDataset();
1131       }
1132       else
1133       {
1134         assertTrue(ap.getAlignment().getDataset() == ds,
1135                 "Dataset was not the same for imported 2.10.5 project with several alignment views");
1136       }
1137     }
1138     return ds;
1139   }
1140
1141   @Test(groups = "Functional")
1142   public void testPcaViewAssociation() throws IOException
1143   {
1144     Desktop.getInstance().closeAll_actionPerformed(null);
1145     // Jalview.setSynchronous(true);
1146     final String PCAVIEWNAME = "With PCA";
1147     // create a new tempfile
1148     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
1149
1150     {
1151       String exampleFile = "examples/uniref50.fa";
1152       AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
1153               DataSourceType.FILE);
1154       assertNotNull(af, "Didn't read in the example file correctly.");
1155       AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
1156       AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
1157       // create another for good measure
1158       af.newView("Not the PCA View", true);
1159       PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
1160               new SimilarityParams(true, true, true, false));
1161       // we're in the test exec thread, so we can just run synchronously here
1162       pcaPanel.run();
1163
1164       // now switch the linked view
1165       pcaPanel.selectAssociatedView(newview);
1166
1167       assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
1168               "PCA should be associated with 'With PCA' view: test is broken");
1169
1170       // now save and reload project
1171       Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
1172       tempfile.delete();
1173       jv2xml.saveState(tempfile);
1174       assertTrue(jv2xml.errorMessage == null,
1175               "Failed to save dummy project with PCA: test broken");
1176     }
1177
1178     // load again.
1179     Desktop.getInstance().closeAll_actionPerformed(null);
1180     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
1181             tempfile.getCanonicalPath(), DataSourceType.FILE);
1182     JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
1183     // PCA and the tabbed alignment view should be the only two windows on the
1184     // desktop
1185     assertEquals(frames.length, 2,
1186             "PCA and the tabbed alignment view should be the only two windows on the desktop");
1187     PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
1188
1189     AlignmentViewPanel restoredNewView = null;
1190     for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
1191     {
1192       if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
1193       {
1194         restoredNewView = alignpanel;
1195       }
1196     }
1197     assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
1198     assertTrue(
1199             restoredNewView.getAlignViewport() == pcaPanel
1200                     .getAlignViewport(),
1201             "Didn't restore correct view association for the PCA view");
1202   }
1203 }