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.datamodel.AlignmentAnnotation;
  36 import jalview.datamodel.AlignmentI;
  37 import jalview.datamodel.HiddenMarkovModel;
  38 import jalview.datamodel.HiddenSequences;
  39 import jalview.datamodel.Mapping;
  40 import jalview.datamodel.PDBEntry;
  41 import jalview.datamodel.PDBEntry.Type;
  42 import jalview.datamodel.SequenceCollectionI;
  43 import jalview.datamodel.SequenceFeature;
  44 import jalview.datamodel.SequenceGroup;
  45 import jalview.datamodel.SequenceI;
  46 import jalview.datamodel.features.FeatureMatcher;
  47 import jalview.datamodel.features.FeatureMatcherSet;
  48 import jalview.datamodel.features.FeatureMatcherSetI;
  49 import jalview.gui.AlignFrame;
  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.util.matcher.Condition;
  73 import jalview.viewmodel.AlignmentViewport;
  74
  75 import java.awt.Color;
  76 import java.io.File;
  77 import java.io.IOException;
  78 import java.util.ArrayList;
  79 import java.util.HashMap;
  80 import java.util.List;
  81 import java.util.Map;
  82
  83 import javax.swing.JInternalFrame;
  84
  85 import org.testng.Assert;
  86 import org.testng.AssertJUnit;
  87 import org.testng.annotations.BeforeClass;
  88 import org.testng.annotations.Test;
  89
  90 import junit.extensions.PA;
  91
  92 @Test(singleThreaded = true)
  93 public class Jalview2xmlTests extends Jalview2xmlBase
  94 {
  95
  96   @Override
  97   @BeforeClass(alwaysRun = true)
  98   public void setUpJvOptionPane()
  99   {
 100     JvOptionPane.setInteractiveMode(false);
 101     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
 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     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 111             DataSourceType.FILE);
 112     assertNotNull(af, "Didn't read input file " + inFile);
 113     int olddsann = countDsAnn(af.getViewport());
 114     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 115     af.changeColour_actionPerformed(
 116             JalviewColourScheme.RNAHelices.toString());
 117     assertTrue(
 118             af.getViewport()
 119                     .getGlobalColourScheme() instanceof RNAHelicesColour,
 120             "Couldn't apply RNA helices colourscheme");
 121     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 122             "Failed to store as a project.");
 123     af.closeMenuItem_actionPerformed(true);
 124     af = null;
 125     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 126             DataSourceType.FILE);
 127     assertNotNull(af, "Failed to import new project");
 128     int newdsann = countDsAnn(af.getViewport());
 129     assertEquals(olddsann, newdsann,
 130             "Differing numbers of dataset sequence annotation\nOriginally "
 131                     + olddsann + " and now " + newdsann);
 132     System.out.println(
 133             "Read in same number of annotations as originally present ("
 134                     + olddsann + ")");
 135     assertTrue(
 136
 137             af.getViewport()
 138                     .getGlobalColourScheme() instanceof RNAHelicesColour,
 139             "RNA helices colourscheme was not applied on import.");
 140   }
 141
 142   @Test(groups = { "Functional" })
 143   public void testTCoffeeScores() throws Exception
 144   {
 145     String inFile = "examples/uniref50.fa",
 146             inAnnot = "examples/uniref50.score_ascii";
 147     String tfile = File.createTempFile("JalviewTest", ".jvp")
 148             .getAbsolutePath();
 149     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 150             DataSourceType.FILE);
 151     assertNotNull(af, "Didn't read input file " + inFile);
 152     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 153     AlignViewport viewport = af.getViewport();
 154     assertSame(viewport.getGlobalColourScheme().getClass(),
 155             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 156     assertNotNull(
 157             ColourSchemeProperty.getColourScheme(viewport,
 158                     viewport.getAlignment(),
 159                     viewport.getGlobalColourScheme()
 160                             .getSchemeName()),
 161             "Recognise T-Coffee score from string");
 162
 163     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 164             "Failed to store as a project.");
 165     af.closeMenuItem_actionPerformed(true);
 166     af = null;
 167     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 168             DataSourceType.FILE);
 169     assertNotNull(af, "Failed to import new project");
 170     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 171             TCoffeeColourScheme.class,
 172             "Didn't set T-coffee colourscheme for imported project.");
 173     System.out.println(
 174             "T-Coffee score shading successfully recovered from project.");
 175   }
 176
 177   @Test(groups = { "Functional" })
 178   public void testColourByAnnotScores() throws Exception
 179   {
 180     String inFile = "examples/uniref50.fa",
 181             inAnnot = "examples/testdata/uniref50_iupred.jva";
 182     String tfile = File.createTempFile("JalviewTest", ".jvp")
 183             .getAbsolutePath();
 184     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 185             DataSourceType.FILE);
 186     assertNotNull(af, "Didn't read input file " + inFile);
 187     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 188     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 189             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 190     assertTrue(
 191
 192             aa != null && aa.length > 0,
 193             "Didn't find any IUPred annotation to use to shade alignment.");
 194     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 195             AnnotationColourGradient.ABOVE_THRESHOLD);
 196     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null,
 197             AnnotationColourGradient.BELOW_THRESHOLD);
 198     cs.setSeqAssociated(true);
 199     gcs.setSeqAssociated(true);
 200     af.changeColour(cs);
 201     SequenceGroup sg = new SequenceGroup();
 202     sg.setStartRes(57);
 203     sg.setEndRes(92);
 204     sg.cs.setColourScheme(gcs);
 205     af.getViewport().getAlignment().addGroup(sg);
 206     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 207     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 208     af.alignPanel.alignmentChanged();
 209     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 210             "Failed to store as a project.");
 211     af.closeMenuItem_actionPerformed(true);
 212     af = null;
 213     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
 214             DataSourceType.FILE);
 215     assertNotNull(af, "Failed to import new project");
 216
 217     // check for group and alignment colourschemes
 218
 219     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 220     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0)
 221             .getColourScheme();
 222     assertNotNull(_rcs, "Didn't recover global colourscheme");
 223     assertTrue(_rcs instanceof AnnotationColourGradient,
 224             "Didn't recover annotation colour global scheme");
 225     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 226     assertTrue(__rcs.isSeqAssociated(),
 227             "Annotation colourscheme wasn't sequence associated");
 228
 229     boolean diffseqcols = false, diffgseqcols = false;
 230     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 231     for (int p = 0, pSize = af.getViewport().getAlignment()
 232             .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
 233     {
 234       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 235               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 236       {
 237         diffseqcols = true;
 238       }
 239     }
 240     assertTrue(diffseqcols, "Got Different sequence colours");
 241     System.out.println(
 242             "Per sequence colourscheme (Background) successfully applied and recovered.");
 243
 244     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 245     assertTrue(_rgcs instanceof AnnotationColourGradient,
 246             "Didn't recover annotation colour group colourscheme");
 247     __rcs = (AnnotationColourGradient) _rgcs;
 248     assertTrue(__rcs.isSeqAssociated(),
 249             "Group Annotation colourscheme wasn't sequence associated");
 250
 251     for (int p = 0, pSize = af.getViewport().getAlignment()
 252             .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
 253     {
 254       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
 255               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
 256                       0f))
 257       {
 258         diffgseqcols = true;
 259       }
 260     }
 261     assertTrue(diffgseqcols, "Got Different group sequence colours");
 262     System.out.println(
 263             "Per sequence (Group) colourscheme successfully applied and recovered.");
 264   }
 265
 266   @Test(groups = { "Functional" })
 267   public void gatherViewsHere() throws Exception
 268   {
 269     int origCount = Desktop.getAlignFrames() == null ? 0
 270             : Desktop.getAlignFrames().length;
 271     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 272             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 273     assertNotNull(af, "Didn't read in the example file correctly.");
 274     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 275             "Didn't gather the views in the example file.");
 276
 277   }
 278
 279   /**
 280    * Test for JAL-2223 - multiple mappings in View Mapping report
 281    *
 282    * @throws Exception
 283    */
 284   @Test(groups = { "Functional" })
 285   public void noDuplicatePdbMappingsMade() throws Exception
 286   {
 287     StructureImportSettings.setProcessSecondaryStructure(true);
 288     StructureImportSettings.setVisibleChainAnnotation(true);
 289     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 290             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 291     assertNotNull(af, "Didn't read in the example file correctly.");
 292
 293     // locate Jmol viewer
 294     // count number of PDB mappings the structure selection manager holds -
 295     String pdbFile = af.getCurrentView().getStructureSelectionManager()
 296             .findFileForPDBId("1A70");
 297     assertEquals(
 298             af.getCurrentView().getStructureSelectionManager()
 299                     .getMapping(pdbFile).length,
 300             2, "Expected only two mappings for 1A70");
 301
 302   }
 303
 304   @Test(groups = { "Functional" })
 305   public void viewRefPdbAnnotation() throws Exception
 306   {
 307     StructureImportSettings.setProcessSecondaryStructure(true);
 308     StructureImportSettings.setVisibleChainAnnotation(true);
 309     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 310             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 311     assertNotNull(af, "Didn't read in the example file correctly.");
 312     AlignmentViewPanel sps = null;
 313     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 314     {
 315       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 316       {
 317         sps = ap;
 318         break;
 319       }
 320     }
 321     assertNotNull(sps, "Couldn't find the structure view");
 322     AlignmentAnnotation refan = null;
 323     for (AlignmentAnnotation ra : sps.getAlignment()
 324             .getAlignmentAnnotation())
 325     {
 326       if (ra.graph != 0)
 327       {
 328         refan = ra;
 329         break;
 330       }
 331     }
 332     assertNotNull(refan, "Annotation secondary structure not found.");
 333     SequenceI sq = sps.getAlignment().findName("1A70|");
 334     assertNotNull(sq, "Couldn't find 1a70 null chain");
 335     // compare the manually added temperature factor annotation
 336     // to the track automatically transferred from the pdb structure on load
 337     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 338             "1a70 has no annotation");
 339     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 340     {
 341       AlignmentAnnotation alaa;
 342       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 343       alaa.adjustForAlignment();
 344       if (ala.graph == refan.graph)
 345       {
 346         for (int p = 0; p < ala.annotations.length; p++)
 347         {
 348           sq.findPosition(p);
 349           try
 350           {
 351             assertTrue((alaa.annotations[p] == null
 352                     && refan.annotations[p] == null)
 353                     || alaa.annotations[p].value == refan.annotations[p].value,
 354                     "Mismatch at alignment position " + p);
 355           } catch (NullPointerException q)
 356           {
 357             Assert.fail("Mismatch of alignment annotations at position " + p
 358                     + " Ref seq ann: " + refan.annotations[p]
 359                     + " alignment " + alaa.annotations[p]);
 360           }
 361         }
 362       }
 363     }
 364
 365   }
 366
 367   @Test(groups = { "Functional" })
 368   public void testCopyViewSettings() throws Exception
 369   {
 370     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 371             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 372     assertNotNull(af, "Didn't read in the example file correctly.");
 373     AlignmentViewPanel sps = null, groups = null;
 374     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 375     {
 376       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 377       {
 378         sps = ap;
 379       }
 380       if (ap.getViewName().contains("MAFFT"))
 381       {
 382         groups = ap;
 383       }
 384     }
 385     assertNotNull(sps, "Couldn't find the structure view");
 386     assertNotNull(groups, "Couldn't find the MAFFT view");
 387
 388     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 389     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 390     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 391
 392     groups.getAlignViewport().setViewStyle(structureStyle);
 393     AssertJUnit.assertFalse(
 394             groupStyle.sameStyle(groups.getAlignViewport().getViewStyle()));
 395     Assert.assertTrue(structureStyle
 396             .sameStyle(groups.getAlignViewport().getViewStyle()));
 397
 398   }
 399
 400   /**
 401    * test store and recovery of expanded views
 402    *
 403    * @throws Exception
 404    */
 405   @Test(groups = { "Functional" }, enabled = true)
 406   public void testStoreAndRecoverExpandedviews() throws Exception
 407   {
 408     Desktop.instance.closeAll_actionPerformed(null);
 409
 410     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 411             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 412     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 413     String afid = af.getViewport().getSequenceSetId();
 414
 415     // check FileLoader returned a reference to the one alignFrame that is
 416     // actually on the Desktop
 417     assertSame(af, Desktop.getAlignFrameFor(af.getViewport()),
 418             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 419
 420     Desktop.explodeViews(af);
 421
 422     int oldviews = Desktop.getAlignFrames().length;
 423     Assert.assertEquals(Desktop.getAlignFrames().length,
 424             Desktop.getAlignmentPanels(afid).length);
 425     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 426     try
 427     {
 428       new Jalview2XML(false).saveState(tfile);
 429     } catch (Error e)
 430     {
 431       Assert.fail("Didn't save the expanded view state", e);
 432     } catch (Exception e)
 433     {
 434       Assert.fail("Didn't save the expanded view state", e);
 435     }
 436     Desktop.instance.closeAll_actionPerformed(null);
 437     if (Desktop.getAlignFrames() != null)
 438     {
 439       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 440     }
 441     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 442             DataSourceType.FILE);
 443     Assert.assertNotNull(af);
 444     Assert.assertEquals(Desktop.getAlignFrames().length,
 445             Desktop.getAlignmentPanels(
 446                     af.getViewport().getSequenceSetId()).length);
 447     Assert.assertEquals(
 448             Desktop.getAlignmentPanels(
 449                     af.getViewport().getSequenceSetId()).length,
 450             oldviews);
 451   }
 452
 453   /**
 454    * Test save and reload of a project with a different representative sequence
 455    * in each view.
 456    *
 457    * @throws Exception
 458    */
 459   @Test(groups = { "Functional" })
 460   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 461   {
 462     Desktop.instance.closeAll_actionPerformed(null);
 463     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 464             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 465     assertNotNull(af, "Didn't read in the example file correctly.");
 466     String afid = af.getViewport().getSequenceSetId();
 467
 468     // remember reference sequence for each panel
 469     Map<String, SequenceI> refseqs = new HashMap<>();
 470
 471     /*
 472      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 473      * as reference sequence for itself and the preceding sequence
 474      */
 475     int n = 1;
 476     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 477     {
 478       AlignViewportI av = ap.getAlignViewport();
 479       AlignmentI alignment = ap.getAlignment();
 480       int repIndex = n % alignment.getHeight();
 481       SequenceI rep = alignment.getSequenceAt(repIndex);
 482       refseqs.put(ap.getViewName(), rep);
 483
 484       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 485       // todo refactor this to an alignment view controller
 486       av.setDisplayReferenceSeq(true);
 487       av.setColourByReferenceSeq(true);
 488       av.getAlignment().setSeqrep(rep);
 489
 490       n++;
 491     }
 492     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 493             ".jvp");
 494     try
 495     {
 496       new Jalview2XML(false).saveState(tfile);
 497     } catch (Throwable e)
 498     {
 499       Assert.fail("Didn't save the expanded view state", e);
 500     }
 501     Desktop.instance.closeAll_actionPerformed(null);
 502     if (Desktop.getAlignFrames() != null)
 503     {
 504       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 505     }
 506
 507     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 508             DataSourceType.FILE);
 509     afid = af.getViewport().getSequenceSetId();
 510
 511     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 512     {
 513       // check representative
 514       AlignmentI alignment = ap.getAlignment();
 515       SequenceI rep = alignment.getSeqrep();
 516       Assert.assertNotNull(rep,
 517               "Couldn't restore sequence representative from project");
 518       // can't use a strong equals here, because by definition, the sequence IDs
 519       // will be different.
 520       // could set vamsas session save/restore flag to preserve IDs across
 521       // load/saves.
 522       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 523               rep.toString(),
 524               "Representative wasn't the same when recovered.");
 525       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 526               "Display reference sequence view setting not set.");
 527       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 528               "Colour By Reference Seq view setting not set.");
 529     }
 530   }
 531
 532   @Test(groups = { "Functional" })
 533   public void testIsVersionStringLaterThan()
 534   {
 535     /*
 536      * No version / development / test / autobuild is leniently assumed to be
 537      * compatible
 538      */
 539     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 540     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 541     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 542     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 543             "Development Build"));
 544     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 545             "DEVELOPMENT BUILD"));
 546     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 547             "Development Build"));
 548     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 549     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 550     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 551     assertTrue(
 552             Jalview2XML.isVersionStringLaterThan(null, "Automated Build"));
 553     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 554             "Automated Build"));
 555     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 556             "AUTOMATED BUILD"));
 557
 558     /*
 559      * same version returns true i.e. compatible
 560      */
 561     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 562     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 563     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 564     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 565     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 566
 567     /*
 568      * later version returns true
 569      */
 570     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 571     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 572     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 573     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 574     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 575
 576     /*
 577      * earlier version returns false
 578      */
 579     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 580     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 581     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 582     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 583     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 584   }
 585
 586   /**
 587    * Test save and reload of a project with a different sequence group (and
 588    * representative sequence) in each view.
 589    *
 590    * @throws Exception
 591    */
 592   @Test(groups = { "Functional" })
 593   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 594   {
 595     Desktop.instance.closeAll_actionPerformed(null);
 596     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 597             "examples/uniref50.fa", DataSourceType.FILE);
 598     assertNotNull(af, "Didn't read in the example file correctly.");
 599     String afid = af.getViewport().getSequenceSetId();
 600     // make a second view of the alignment
 601     af.newView_actionPerformed(null);
 602
 603     /*
 604      * remember representative and hidden sequences marked
 605      * on each panel
 606      */
 607     Map<String, SequenceI> repSeqs = new HashMap<>();
 608     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 609
 610     /*
 611      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 612      * as reference sequence for itself and the preceding sequence
 613      */
 614     int n = 1;
 615     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 616     {
 617       AlignViewportI av = ap.getAlignViewport();
 618       AlignmentI alignment = ap.getAlignment();
 619       int repIndex = n % alignment.getHeight();
 620       // ensure at least one preceding sequence i.e. index >= 1
 621       repIndex = Math.max(repIndex, 1);
 622       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 623       repSeqs.put(ap.getViewName(), repSeq);
 624       List<String> hiddenNames = new ArrayList<>();
 625       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 626
 627       /*
 628        * have rep sequence represent itself and the one before it
 629        * this hides the group (except for the rep seq)
 630        */
 631       SequenceGroup sg = new SequenceGroup();
 632       sg.addSequence(repSeq, false);
 633       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 634       sg.addSequence(precedingSeq, false);
 635       sg.setSeqrep(repSeq);
 636       assertTrue(sg.getSequences().contains(repSeq));
 637       assertTrue(sg.getSequences().contains(precedingSeq));
 638       av.setSelectionGroup(sg);
 639       assertSame(repSeq, sg.getSeqrep());
 640
 641       /*
 642        * represent group with sequence adds to a map of hidden rep sequences
 643        * (it does not create a group on the alignment)
 644        */
 645       ((AlignmentViewport) av).hideSequences(repSeq, true);
 646       assertSame(repSeq, sg.getSeqrep());
 647       assertTrue(sg.getSequences().contains(repSeq));
 648       assertTrue(sg.getSequences().contains(precedingSeq));
 649       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 650       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 651               .getHiddenRepSequences();
 652       assertNotNull(hiddenRepSeqsMap);
 653       assertEquals(1, hiddenRepSeqsMap.size());
 654       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 655       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 656       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 657       hiddenNames.add(precedingSeq.getName());
 658
 659       n++;
 660     }
 661     File tfile = File.createTempFile("testStoreAndRecoverGroupReps",
 662             ".jvp");
 663     try
 664     {
 665       new Jalview2XML(false).saveState(tfile);
 666     } catch (Throwable e)
 667     {
 668       Assert.fail("Didn't save the expanded view state", e);
 669     }
 670     Desktop.instance.closeAll_actionPerformed(null);
 671     if (Desktop.getAlignFrames() != null)
 672     {
 673       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 674     }
 675
 676     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 677             DataSourceType.FILE);
 678     afid = af.getViewport().getSequenceSetId();
 679
 680     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 681     {
 682       String viewName = ap.getViewName();
 683       AlignViewportI av = ap.getAlignViewport();
 684       AlignmentI alignment = ap.getAlignment();
 685       List<SequenceGroup> groups = alignment.getGroups();
 686       assertNotNull(groups);
 687       assertTrue(groups.isEmpty(), "Alignment has groups");
 688       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 689               .getHiddenRepSequences();
 690       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 691       assertEquals(1, hiddenRepSeqsMap.size());
 692       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 693               hiddenRepSeqsMap.keySet().iterator().next()
 694                       .getDisplayId(true));
 695
 696       /*
 697        * verify hidden sequences in restored panel
 698        */
 699       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 700       HiddenSequences hs = alignment.getHiddenSequences();
 701       assertEquals(hidden.size(), hs.getSize(),
 702               "wrong number of restored hidden sequences in "
 703                       + ap.getViewName());
 704     }
 705   }
 706
 707   /**
 708    * Test save and reload of PDBEntry in Jalview project
 709    *
 710    * @throws Exception
 711    */
 712   @Test(groups = { "Functional" })
 713   public void testStoreAndRecoverPDBEntry() throws Exception
 714   {
 715     Desktop.instance.closeAll_actionPerformed(null);
 716     String exampleFile = "examples/3W5V.pdb";
 717     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 718             DataSourceType.FILE);
 719     assertNotNull(af, "Didn't read in the example file correctly.");
 720     String afid = af.getViewport().getSequenceSetId();
 721
 722     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 723     System.out.println();
 724     AlignmentViewPanel ap = alignPanels[0];
 725     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 726     String testFile = tfileBase + exampleFile;
 727     AlignmentI alignment = ap.getAlignment();
 728     System.out.println("blah");
 729     SequenceI[] seqs = alignment.getSequencesArray();
 730     Assert.assertNotNull(seqs[0]);
 731     Assert.assertNotNull(seqs[1]);
 732     Assert.assertNotNull(seqs[2]);
 733     Assert.assertNotNull(seqs[3]);
 734     Assert.assertNotNull(seqs[0].getDatasetSequence());
 735     Assert.assertNotNull(seqs[1].getDatasetSequence());
 736     Assert.assertNotNull(seqs[2].getDatasetSequence());
 737     Assert.assertNotNull(seqs[3].getDatasetSequence());
 738     PDBEntry[] pdbEntries = new PDBEntry[4];
 739     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 740     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 741     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 742     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 743     Assert.assertEquals(
 744             seqs[0].getDatasetSequence().getAllPDBEntries().get(0),
 745             pdbEntries[0]);
 746     Assert.assertEquals(
 747             seqs[1].getDatasetSequence().getAllPDBEntries().get(0),
 748             pdbEntries[1]);
 749     Assert.assertEquals(
 750             seqs[2].getDatasetSequence().getAllPDBEntries().get(0),
 751             pdbEntries[2]);
 752     Assert.assertEquals(
 753             seqs[3].getDatasetSequence().getAllPDBEntries().get(0),
 754             pdbEntries[3]);
 755
 756     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 757     try
 758     {
 759       new Jalview2XML(false).saveState(tfile);
 760     } catch (Throwable e)
 761     {
 762       Assert.fail("Didn't save the state", e);
 763     }
 764     Desktop.instance.closeAll_actionPerformed(null);
 765     if (Desktop.getAlignFrames() != null)
 766     {
 767       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 768     }
 769
 770     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 771             tfile.getAbsolutePath(), DataSourceType.FILE);
 772     String rfid = restoredFrame.getViewport().getSequenceSetId();
 773     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 774     AlignmentViewPanel rap = rAlignPanels[0];
 775     AlignmentI rAlignment = rap.getAlignment();
 776     System.out.println("blah");
 777     SequenceI[] rseqs = rAlignment.getSequencesArray();
 778     Assert.assertNotNull(rseqs[0]);
 779     Assert.assertNotNull(rseqs[1]);
 780     Assert.assertNotNull(rseqs[2]);
 781     Assert.assertNotNull(rseqs[3]);
 782     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 783     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 784     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 785     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 786
 787     // The Asserts below are expected to fail until the PDB chainCode is
 788     // recoverable from a Jalview projects
 789     for (int chain = 0; chain < 4; chain++)
 790     {
 791       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 792               .get(0);
 793       PDBEntry expected = pdbEntries[chain];
 794       Assert.assertEquals(recov.getId(), expected.getId(),
 795               "Mismatch PDB ID");
 796       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 797               "Mismatch PDB ID");
 798       Assert.assertEquals(recov.getType(), expected.getType(),
 799               "Mismatch PDBEntry 'Type'");
 800       Assert.assertNotNull(recov.getFile(),
 801               "Recovered PDBEntry should have a non-null file entry");
 802     }
 803   }
 804
 805   /**
 806    * Configure an alignment and a sub-group each with distinct colour schemes,
 807    * Conservation and PID thresholds, and confirm these are restored from the
 808    * saved project.
 809    *
 810    * @throws IOException
 811    */
 812   @Test(groups = { "Functional" })
 813   public void testStoreAndRecoverColourThresholds() throws IOException
 814   {
 815     Desktop.instance.closeAll_actionPerformed(null);
 816     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 817             "examples/uniref50.fa", DataSourceType.FILE);
 818
 819     AlignViewportI av = af.getViewport();
 820     AlignmentI al = av.getAlignment();
 821
 822     /*
 823      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 824      */
 825     av.setColourAppliesToAllGroups(false);
 826     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 827     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 828     af.abovePIDThreshold_actionPerformed(true);
 829     SliderPanel sp = SliderPanel.getSliderPanel();
 830     assertFalse(sp.isForConservation());
 831     sp.valueChanged(10);
 832     af.conservationMenuItem_actionPerformed(true);
 833     sp = SliderPanel.getSliderPanel();
 834     assertTrue(sp.isForConservation());
 835     sp.valueChanged(20);
 836     ResidueShaderI rs = av.getResidueShading();
 837     assertEquals(rs.getThreshold(), 10);
 838     assertTrue(rs.conservationApplied());
 839     assertEquals(rs.getConservationInc(), 20);
 840
 841     /*
 842      * create a group with Strand colouring, 30% Conservation
 843      * and 40% PID threshold
 844      */
 845     SequenceGroup sg = new SequenceGroup();
 846     sg.addSequence(al.getSequenceAt(0), false);
 847     sg.setStartRes(15);
 848     sg.setEndRes(25);
 849     av.setSelectionGroup(sg);
 850     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 851     popupMenu.changeColour_actionPerformed(
 852             JalviewColourScheme.Strand.toString());
 853     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 854     assertEquals(al.getGroups().size(), 1);
 855     assertSame(al.getGroups().get(0), sg);
 856     popupMenu.conservationMenuItem_actionPerformed(true);
 857     sp = SliderPanel.getSliderPanel();
 858     assertTrue(sp.isForConservation());
 859     sp.valueChanged(30);
 860     popupMenu.abovePIDColour_actionPerformed(true);
 861     sp = SliderPanel.getSliderPanel();
 862     assertFalse(sp.isForConservation());
 863     sp.valueChanged(40);
 864     assertTrue(sg.getGroupColourScheme().conservationApplied());
 865     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 866     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 867
 868     /*
 869      * save project, close windows, reload project, verify
 870      */
 871     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 872             ".jvp");
 873     tfile.deleteOnExit();
 874     new Jalview2XML(false).saveState(tfile);
 875     Desktop.instance.closeAll_actionPerformed(null);
 876     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 877             DataSourceType.FILE);
 878     Assert.assertNotNull(af, "Failed to reload project");
 879
 880     /*
 881      * verify alignment (background) colouring
 882      */
 883     rs = af.getViewport().getResidueShading();
 884     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 885     assertEquals(rs.getThreshold(), 10);
 886     assertTrue(rs.conservationApplied());
 887     assertEquals(rs.getConservationInc(), 20);
 888
 889     /*
 890      * verify group colouring
 891      */
 892     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 893     rs = af.getViewport().getAlignment().getGroups().get(0)
 894             .getGroupColourScheme();
 895     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 896     assertEquals(rs.getThreshold(), 40);
 897     assertTrue(rs.conservationApplied());
 898     assertEquals(rs.getConservationInc(), 30);
 899   }
 900
 901   /**
 902    * Test save and reload of feature colour schemes and filter settings
 903    *
 904    * @throws IOException
 905    */
 906   @Test(groups = { "Functional" })
 907   public void testStoreAndRecoverFeatureColoursAndFilters()
 908           throws IOException
 909   {
 910     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 911             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 912     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 913
 914     /*
 915      * add some features to the sequence
 916      */
 917     int score = 1;
 918     addFeatures(seq1, "type1", score++);
 919     addFeatures(seq1, "type2", score++);
 920     addFeatures(seq1, "type3", score++);
 921     addFeatures(seq1, "type4", score++);
 922     addFeatures(seq1, "type5", score++);
 923
 924     /*
 925      * set colour schemes for features
 926      */
 927     FeatureRenderer fr = af.getFeatureRenderer();
 928     fr.findAllFeatures(true);
 929
 930     // type1: red
 931     fr.setColour("type1", new FeatureColour(Color.red));
 932
 933     // type2: by label
 934     FeatureColourI byLabel = new FeatureColour();
 935     byLabel.setColourByLabel(true);
 936     fr.setColour("type2", byLabel);
 937
 938     // type3: by score above threshold
 939     FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
 940             Color.BLUE, null, 1, 10);
 941     byScore.setAboveThreshold(true);
 942     byScore.setThreshold(2f);
 943     fr.setColour("type3", byScore);
 944
 945     // type4: by attribute AF
 946     FeatureColourI byAF = new FeatureColour();
 947     byAF.setColourByLabel(true);
 948     byAF.setAttributeName("AF");
 949     fr.setColour("type4", byAF);
 950
 951     // type5: by attribute CSQ:PolyPhen below threshold
 952     FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
 953             Color.BLUE, null, 1, 10);
 954     byPolyPhen.setBelowThreshold(true);
 955     byPolyPhen.setThreshold(3f);
 956     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 957     fr.setColour("type5", byPolyPhen);
 958
 959     /*
 960      * set filters for feature types
 961      */
 962
 963     // filter type1 features by (label contains "x")
 964     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 965     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 966     fr.setFeatureFilter("type1", filterByX);
 967
 968     // filter type2 features by (score <= 2.4 and score > 1.1)
 969     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 970     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 971     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 972     fr.setFeatureFilter("type2", filterByScore);
 973
 974     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 975     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 976     filterByXY
 977             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 978     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 979             "PolyPhen"));
 980     fr.setFeatureFilter("type3", filterByXY);
 981
 982     /*
 983      * save as Jalview project
 984      */
 985     File tfile = File.createTempFile("JalviewTest", ".jvp");
 986     tfile.deleteOnExit();
 987     String filePath = tfile.getAbsolutePath();
 988     assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
 989             "Failed to store as a project.");
 990
 991     /*
 992      * close current alignment and load the saved project
 993      */
 994     af.closeMenuItem_actionPerformed(true);
 995     af = null;
 996     af = new FileLoader().LoadFileWaitTillLoaded(filePath,
 997             DataSourceType.FILE);
 998     assertNotNull(af, "Failed to import new project");
 999
1000     /*
1001      * verify restored feature colour schemes and filters
1002      */
1003     fr = af.getFeatureRenderer();
1004     FeatureColourI fc = fr.getFeatureStyle("type1");
1005     assertTrue(fc.isSimpleColour());
1006     assertEquals(fc.getColour(), Color.red);
1007     fc = fr.getFeatureStyle("type2");
1008     assertTrue(fc.isColourByLabel());
1009     fc = fr.getFeatureStyle("type3");
1010     assertTrue(fc.isGraduatedColour());
1011     assertNull(fc.getAttributeName());
1012     assertTrue(fc.isAboveThreshold());
1013     assertEquals(fc.getThreshold(), 2f);
1014     fc = fr.getFeatureStyle("type4");
1015     assertTrue(fc.isColourByLabel());
1016     assertTrue(fc.isColourByAttribute());
1017     assertEquals(fc.getAttributeName(), new String[] { "AF" });
1018     fc = fr.getFeatureStyle("type5");
1019     assertTrue(fc.isGraduatedColour());
1020     assertTrue(fc.isColourByAttribute());
1021     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1022     assertTrue(fc.isBelowThreshold());
1023     assertEquals(fc.getThreshold(), 3f);
1024
1025     assertEquals(fr.getFeatureFilter("type1").toStableString(),
1026             "Label Contains x");
1027     assertEquals(fr.getFeatureFilter("type2").toStableString(),
1028             "(Score LE 2.4) AND (Score GT 1.1)");
1029     assertEquals(fr.getFeatureFilter("type3").toStableString(),
1030             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
1031   }
1032
1033   private void addFeature(SequenceI seq, String featureType, int score)
1034   {
1035     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1036             score, "grp");
1037     sf.setValue("AF", score);
1038     sf.setValue("CSQ", new HashMap<String, String>()
1039     {
1040       {
1041         put("PolyPhen", Integer.toString(score));
1042       }
1043     });
1044     seq.addSequenceFeature(sf);
1045   }
1046
1047   /**
1048    * Adds two features of the given type to the given sequence, also setting the
1049    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1050    *
1051    * @param seq
1052    * @param featureType
1053    * @param score
1054    */
1055   private void addFeatures(SequenceI seq, String featureType, int score)
1056   {
1057     addFeature(seq, featureType, score++);
1058     addFeature(seq, featureType, score);
1059   }
1060
1061   /**
1062    * Load an HMM profile to an alignment, and confirm it is correctly restored
1063    * when reloaded from project
1064    *
1065    * @throws IOException
1066    */
1067   @Test(groups = { "Functional" })
1068   public void testStoreAndRecoverHmmProfile() throws IOException
1069   {
1070     Desktop.instance.closeAll_actionPerformed(null);
1071     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
1072             "examples/uniref50.fa", DataSourceType.FILE);
1073
1074     AlignViewportI av = af.getViewport();
1075     AlignmentI al = av.getAlignment();
1076
1077     /*
1078      * mimic drag and drop of hmm file on to alignment
1079      */
1080     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
1081             "examples/uniref50.hmm", DataSourceType.FILE);
1082     al.insertSequenceAt(0,
1083             af2.getViewport().getAlignment().getSequenceAt(0));
1084
1085     /*
1086      * check it loaded in
1087      */
1088     SequenceI hmmSeq = al.getSequenceAt(0);
1089     assertTrue(hmmSeq.hasHMMProfile());
1090     HiddenMarkovModel hmm = hmmSeq.getHMM();
1091     assertSame(hmm.getConsensusSequence(), hmmSeq);
1092
1093     /*
1094      * save project, close windows, reload project, verify
1095      */
1096     File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
1097             ".jvp");
1098     tfile.deleteOnExit();
1099     new Jalview2XML(false).saveState(tfile);
1100     Desktop.instance.closeAll_actionPerformed(null);
1101     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
1102             DataSourceType.FILE);
1103     Assert.assertNotNull(af, "Failed to reload project");
1104
1105     hmmSeq = al.getSequenceAt(0);
1106     assertTrue(hmmSeq.hasHMMProfile());
1107     assertSame(hmm.getConsensusSequence(), hmmSeq);
1108     Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
1109             "mapToHmmConsensus");
1110     assertNotNull(mapToHmmConsensus);
1111     assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
1112   }
1113
1114   /**
1115    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1116    * view (JAL-3171) this test ensures we can import and merge those views
1117    */
1118   @Test(groups = { "Functional" })
1119   public void testMergeDatasetsforViews() throws IOException
1120   {
1121     // simple project - two views on one alignment
1122     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1123             "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
1124     assertNotNull(af);
1125     assertTrue(af.getAlignPanels().size() > 1);
1126     verifyDs(af);
1127   }
1128
1129   /**
1130    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
1131    * view (JAL-3171) this test ensures we can import and merge those views This
1132    * is a more complex project
1133    */
1134   @Test(groups = { "Functional" })
1135   public void testMergeDatasetsforManyViews() throws IOException
1136   {
1137     Desktop.instance.closeAll_actionPerformed(null);
1138
1139     // complex project - one dataset, several views on several alignments
1140     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
1141             "examples/testdata/projects/manyViews.jvp",
1142             DataSourceType.FILE);
1143     assertNotNull(af);
1144
1145     AlignmentI ds = null;
1146     for (AlignFrame alignFrame : Desktop.getAlignFrames())
1147     {
1148       if (ds == null)
1149       {
1150         ds = verifyDs(alignFrame);
1151       }
1152       else
1153       {
1154         // check that this frame's dataset matches the last
1155         assertTrue(ds == verifyDs(alignFrame));
1156       }
1157     }
1158   }
1159
1160   private AlignmentI verifyDs(AlignFrame af)
1161   {
1162     AlignmentI ds = null;
1163     for (AlignmentViewPanel ap : af.getAlignPanels())
1164     {
1165       if (ds == null)
1166       {
1167         ds = ap.getAlignment().getDataset();
1168       }
1169       else
1170       {
1171         assertTrue(ap.getAlignment().getDataset() == ds,
1172                 "Dataset was not the same for imported 2.10.5 project with several alignment views");
1173       }
1174     }
1175     return ds;
1176   }
1177
1178   @Test(groups = "Functional")
1179   public void testPcaViewAssociation() throws IOException
1180   {
1181     Desktop.instance.closeAll_actionPerformed(null);
1182     final String PCAVIEWNAME = "With PCA";
1183     // create a new tempfile
1184     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
1185
1186     {
1187       String exampleFile = "examples/uniref50.fa";
1188       AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
1189               DataSourceType.FILE);
1190       assertNotNull(af, "Didn't read in the example file correctly.");
1191       AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
1192       AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
1193       // create another for good measure
1194       af.newView("Not the PCA View", true);
1195       PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
1196               new SimilarityParams(true, true, true, false));
1197       // we're in the test exec thread, so we can just run synchronously here
1198       pcaPanel.run();
1199
1200       // now switch the linked view
1201       pcaPanel.selectAssociatedView(newview);
1202
1203       assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
1204               "PCA should be associated with 'With PCA' view: test is broken");
1205
1206       // now save and reload project
1207       Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
1208       tempfile.delete();
1209       jv2xml.saveState(tempfile);
1210       assertTrue(jv2xml.errorMessage == null,
1211               "Failed to save dummy project with PCA: test broken");
1212     }
1213
1214     // load again.
1215     Desktop.instance.closeAll_actionPerformed(null);
1216     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
1217             tempfile.getCanonicalPath(), DataSourceType.FILE);
1218     JInternalFrame[] frames = Desktop.instance.getAllFrames();
1219     // PCA and the tabbed alignment view should be the only two windows on the
1220     // desktop
1221     assertEquals(frames.length, 2,
1222             "PCA and the tabbed alignment view should be the only two windows on the desktop");
1223     PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
1224
1225     AlignmentViewPanel restoredNewView = null;
1226     for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
1227     {
1228       if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
1229       {
1230         restoredNewView = alignpanel;
1231       }
1232     }
1233     assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
1234     assertTrue(
1235             restoredNewView.getAlignViewport() == pcaPanel
1236                     .getAlignViewport(),
1237             "Didn't restore correct view association for the PCA view");
1238   }
1239 }