test/jalview/io/Jalview2xmlTests.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertFalse;
  25 import static org.testng.Assert.assertNotNull;
  26 import static org.testng.Assert.assertNull;
  27 import static org.testng.Assert.assertSame;
  28 import static org.testng.Assert.assertTrue;
  29
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.AlignmentViewPanel;
  32 import jalview.api.FeatureColourI;
  33 import jalview.api.ViewStyleI;
  34 import jalview.datamodel.AlignmentAnnotation;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.HiddenMarkovModel;
  37 import jalview.datamodel.HiddenSequences;
  38 import jalview.datamodel.Mapping;
  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.AlignmentPanel;
  50 import jalview.gui.Desktop;
  51 import jalview.gui.FeatureRenderer;
  52 import jalview.gui.Jalview2XML;
  53 import jalview.gui.JvOptionPane;
  54 import jalview.gui.PopupMenu;
  55 import jalview.gui.SliderPanel;
  56 import jalview.renderer.ResidueShaderI;
  57 import jalview.schemes.AnnotationColourGradient;
  58 import jalview.schemes.BuriedColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.ColourSchemeProperty;
  61 import jalview.schemes.FeatureColour;
  62 import jalview.schemes.JalviewColourScheme;
  63 import jalview.schemes.RNAHelicesColour;
  64 import jalview.schemes.StrandColourScheme;
  65 import jalview.schemes.TCoffeeColourScheme;
  66 import jalview.structure.StructureImportSettings;
  67 import jalview.util.matcher.Condition;
  68 import jalview.viewmodel.AlignmentViewport;
  69
  70 import java.awt.Color;
  71 import java.io.File;
  72 import java.io.IOException;
  73 import java.util.ArrayList;
  74 import java.util.HashMap;
  75 import java.util.List;
  76 import java.util.Map;
  77
  78 import org.testng.Assert;
  79 import org.testng.AssertJUnit;
  80 import org.testng.annotations.BeforeClass;
  81 import org.testng.annotations.Test;
  82
  83 import junit.extensions.PA;
  84
  85 @Test(singleThreaded = true)
  86 public class Jalview2xmlTests extends Jalview2xmlBase
  87 {
  88
  89   @Override
  90   @BeforeClass(alwaysRun = true)
  91   public void setUpJvOptionPane()
  92   {
  93     JvOptionPane.setInteractiveMode(false);
  94     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  95   }
  96
  97   @Test(groups = { "Functional" })
  98   public void testRNAStructureRecovery() throws Exception
  99   {
 100     String inFile = "examples/RF00031_folded.stk";
 101     String tfile = File.createTempFile("JalviewTest", ".jvp")
 102             .getAbsolutePath();
 103     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 104             DataSourceType.FILE);
 105     assertNotNull(af, "Didn't read input file " + inFile);
 106     int olddsann = countDsAnn(af.getViewport());
 107     assertTrue(olddsann > 0, "Didn't find any dataset annotations");
 108     af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
 109             .toString());
 110     assertTrue(
 111             af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 112             "Couldn't apply RNA helices colourscheme");
 113     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 114             "Failed to store as a project.");
 115     af.closeMenuItem_actionPerformed(true);
 116     af = null;
 117     af = new FileLoader()
 118             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 119     assertNotNull(af, "Failed to import new project");
 120     int newdsann = countDsAnn(af.getViewport());
 121     assertEquals(olddsann, newdsann,
 122             "Differing numbers of dataset sequence annotation\nOriginally "
 123                     + olddsann + " and now " + newdsann);
 124     System.out
 125             .println("Read in same number of annotations as originally present ("
 126                     + olddsann + ")");
 127     assertTrue(
 128
 129     af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
 130             "RNA helices colourscheme was not applied on import.");
 131   }
 132
 133   @Test(groups = { "Functional" })
 134   public void testTCoffeeScores() throws Exception
 135   {
 136     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
 137     String tfile = File.createTempFile("JalviewTest", ".jvp")
 138             .getAbsolutePath();
 139     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 140             DataSourceType.FILE);
 141     assertNotNull(af, "Didn't read input file " + inFile);
 142     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 143     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 144             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
 145     assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
 146             .getAlignment(), af.getViewport().getGlobalColourScheme()
 147             .getSchemeName()), "Recognise T-Coffee score from string");
 148
 149     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 150             "Failed to store as a project.");
 151     af.closeMenuItem_actionPerformed(true);
 152     af = null;
 153     af = new FileLoader()
 154             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 155     assertNotNull(af, "Failed to import new project");
 156     assertSame(af.getViewport().getGlobalColourScheme().getClass(),
 157             TCoffeeColourScheme.class,
 158             "Didn't set T-coffee colourscheme for imported project.");
 159     System.out
 160             .println("T-Coffee score shading successfully recovered from project.");
 161   }
 162
 163   @Test(groups = { "Functional" })
 164   public void testColourByAnnotScores() throws Exception
 165   {
 166     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
 167     String tfile = File.createTempFile("JalviewTest", ".jvp")
 168             .getAbsolutePath();
 169     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
 170             DataSourceType.FILE);
 171     assertNotNull(af, "Didn't read input file " + inFile);
 172     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
 173     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
 174             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
 175     assertTrue(
 176
 177     aa != null && aa.length > 0,
 178             "Didn't find any IUPred annotation to use to shade alignment.");
 179     AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
 180             AnnotationColourGradient.ABOVE_THRESHOLD);
 181     AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
 182             null, AnnotationColourGradient.BELOW_THRESHOLD);
 183     cs.setSeqAssociated(true);
 184     gcs.setSeqAssociated(true);
 185     af.changeColour(cs);
 186     SequenceGroup sg = new SequenceGroup();
 187     sg.setStartRes(57);
 188     sg.setEndRes(92);
 189     sg.cs.setColourScheme(gcs);
 190     af.getViewport().getAlignment().addGroup(sg);
 191     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
 192     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
 193     af.alignPanel.alignmentChanged();
 194     assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
 195             "Failed to store as a project.");
 196     af.closeMenuItem_actionPerformed(true);
 197     af = null;
 198     af = new FileLoader()
 199             .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
 200     assertNotNull(af, "Failed to import new project");
 201
 202     // check for group and alignment colourschemes
 203
 204     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
 205     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
 206             .get(0).getColourScheme();
 207     assertNotNull(_rcs, "Didn't recover global colourscheme");
 208     assertTrue(_rcs instanceof AnnotationColourGradient,
 209             "Didn't recover annotation colour global scheme");
 210     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
 211     assertTrue(__rcs.isSeqAssociated(),
 212             "Annotation colourscheme wasn't sequence associated");
 213
 214     boolean diffseqcols = false, diffgseqcols = false;
 215     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
 216     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 217             && (!diffseqcols || !diffgseqcols); p++)
 218     {
 219       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
 220               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
 221       {
 222         diffseqcols = true;
 223       }
 224     }
 225     assertTrue(diffseqcols, "Got Different sequence colours");
 226     System.out
 227             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 228
 229     assertNotNull(_rgcs, "Didn't recover group colourscheme");
 230     assertTrue(_rgcs instanceof AnnotationColourGradient,
 231             "Didn't recover annotation colour group colourscheme");
 232     __rcs = (AnnotationColourGradient) _rgcs;
 233     assertTrue(__rcs.isSeqAssociated(),
 234             "Group Annotation colourscheme wasn't sequence associated");
 235
 236     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
 237             && (!diffseqcols || !diffgseqcols); p++)
 238     {
 239       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
 240               .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
 241       {
 242         diffgseqcols = true;
 243       }
 244     }
 245     assertTrue(diffgseqcols, "Got Different group sequence colours");
 246     System.out
 247             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
 248   }
 249
 250   @Test(groups = { "Functional" })
 251   public void gatherViewsHere() throws Exception
 252   {
 253     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
 254             .getAlignFrames().length;
 255     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 256             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 257     assertNotNull(af, "Didn't read in the example file correctly.");
 258     assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
 259             "Didn't gather the views in the example file.");
 260
 261   }
 262
 263   @Test(groups = { "Functional" })
 264   public void viewRefPdbAnnotation() throws Exception
 265   {
 266     StructureImportSettings.setProcessSecondaryStructure(true);
 267     StructureImportSettings.setVisibleChainAnnotation(true);
 268     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 269             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 270     assertNotNull(af, "Didn't read in the example file correctly.");
 271     AlignmentViewPanel sps = null;
 272     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 273     {
 274       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 275       {
 276         sps = ap;
 277         break;
 278       }
 279     }
 280     assertNotNull(sps, "Couldn't find the structure view");
 281     AlignmentAnnotation refan = null;
 282     for (AlignmentAnnotation ra : sps.getAlignment()
 283             .getAlignmentAnnotation())
 284     {
 285       if (ra.graph != 0)
 286       {
 287         refan = ra;
 288         break;
 289       }
 290     }
 291     assertNotNull(refan, "Annotation secondary structure not found.");
 292     SequenceI sq = sps.getAlignment().findName("1A70|");
 293     assertNotNull(sq, "Couldn't find 1a70 null chain");
 294     // compare the manually added temperature factor annotation
 295     // to the track automatically transferred from the pdb structure on load
 296     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 297             "1a70 has no annotation");
 298     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 299     {
 300       AlignmentAnnotation alaa;
 301       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 302       alaa.adjustForAlignment();
 303       if (ala.graph == refan.graph)
 304       {
 305         for (int p = 0; p < ala.annotations.length; p++)
 306         {
 307           sq.findPosition(p);
 308           try
 309           {
 310             assertTrue(
 311                     (alaa.annotations[p] == null && refan.annotations[p] == null)
 312                             || alaa.annotations[p].value == refan.annotations[p].value,
 313                     "Mismatch at alignment position " + p);
 314           } catch (NullPointerException q)
 315           {
 316             Assert.fail("Mismatch of alignment annotations at position "
 317                     + p + " Ref seq ann: " + refan.annotations[p]
 318                     + " alignment " + alaa.annotations[p]);
 319           }
 320         }
 321       }
 322     }
 323
 324   }
 325
 326   @Test(groups = { "Functional" })
 327   public void testCopyViewSettings() throws Exception
 328   {
 329     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 330             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 331     assertNotNull(af, "Didn't read in the example file correctly.");
 332     AlignmentViewPanel sps = null, groups = null;
 333     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 334     {
 335       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 336       {
 337         sps = ap;
 338       }
 339       if (ap.getViewName().contains("MAFFT"))
 340       {
 341         groups = ap;
 342       }
 343     }
 344     assertNotNull(sps, "Couldn't find the structure view");
 345     assertNotNull(groups, "Couldn't find the MAFFT view");
 346
 347     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 348     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 349     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 350
 351     groups.getAlignViewport().setViewStyle(structureStyle);
 352     AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
 353             .getViewStyle()));
 354     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
 355             .getViewStyle()));
 356
 357   }
 358
 359   /**
 360    * test store and recovery of expanded views
 361    *
 362    * @throws Exception
 363    */
 364   @Test(groups = { "Functional" }, enabled = true)
 365   public void testStoreAndRecoverExpandedviews() throws Exception
 366   {
 367     Desktop.instance.closeAll_actionPerformed(null);
 368
 369     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 370             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 371     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 372     String afid = af.getViewport().getSequenceSetId();
 373
 374     // check FileLoader returned a reference to the one alignFrame that is
 375     // actually on the Desktop
 376     assertSame(
 377             af,
 378             Desktop.getAlignFrameFor(af.getViewport()),
 379             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 380
 381     Desktop.explodeViews(af);
 382
 383     int oldviews = Desktop.getAlignFrames().length;
 384     Assert.assertEquals(Desktop.getAlignFrames().length,
 385             Desktop.getAlignmentPanels(afid).length);
 386     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 387     try
 388     {
 389       new Jalview2XML(false).saveState(tfile);
 390     } catch (Error e)
 391     {
 392       Assert.fail("Didn't save the expanded view state", e);
 393     } catch (Exception e)
 394     {
 395       Assert.fail("Didn't save the expanded view state", e);
 396     }
 397     Desktop.instance.closeAll_actionPerformed(null);
 398     if (Desktop.getAlignFrames() != null)
 399     {
 400       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 401     }
 402     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 403             DataSourceType.FILE);
 404     Assert.assertNotNull(af);
 405     Assert.assertEquals(
 406             Desktop.getAlignFrames().length,
 407             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
 408     Assert.assertEquals(
 409             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
 410             oldviews);
 411   }
 412
 413   /**
 414    * Test save and reload of a project with a different representative sequence
 415    * in each view.
 416    *
 417    * @throws Exception
 418    */
 419   @Test(groups = { "Functional" })
 420   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 421   {
 422     Desktop.instance.closeAll_actionPerformed(null);
 423     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 424             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 425     assertNotNull(af, "Didn't read in the example file correctly.");
 426     String afid = af.getViewport().getSequenceSetId();
 427
 428     // remember reference sequence for each panel
 429     Map<String, SequenceI> refseqs = new HashMap<>();
 430
 431     /*
 432      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 433      * as reference sequence for itself and the preceding sequence
 434      */
 435     int n = 1;
 436     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 437     {
 438       AlignViewportI av = ap.getAlignViewport();
 439       AlignmentI alignment = ap.getAlignment();
 440       int repIndex = n % alignment.getHeight();
 441       SequenceI rep = alignment.getSequenceAt(repIndex);
 442       refseqs.put(ap.getViewName(), rep);
 443
 444       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 445       // todo refactor this to an alignment view controller
 446       av.setDisplayReferenceSeq(true);
 447       av.setColourByReferenceSeq(true);
 448       av.getAlignment().setSeqrep(rep);
 449
 450       n++;
 451     }
 452     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 453             ".jvp");
 454     try
 455     {
 456       new Jalview2XML(false).saveState(tfile);
 457     } catch (Throwable e)
 458     {
 459       Assert.fail("Didn't save the expanded view state", e);
 460     }
 461     Desktop.instance.closeAll_actionPerformed(null);
 462     if (Desktop.getAlignFrames() != null)
 463     {
 464       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 465     }
 466
 467     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 468             DataSourceType.FILE);
 469     afid = af.getViewport().getSequenceSetId();
 470
 471     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 472     {
 473       // check representative
 474       AlignmentI alignment = ap.getAlignment();
 475       SequenceI rep = alignment.getSeqrep();
 476       Assert.assertNotNull(rep,
 477               "Couldn't restore sequence representative from project");
 478       // can't use a strong equals here, because by definition, the sequence IDs
 479       // will be different.
 480       // could set vamsas session save/restore flag to preserve IDs across
 481       // load/saves.
 482       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 483               rep.toString(),
 484               "Representative wasn't the same when recovered.");
 485       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 486               "Display reference sequence view setting not set.");
 487       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 488               "Colour By Reference Seq view setting not set.");
 489     }
 490   }
 491
 492   @Test(groups = { "Functional" })
 493   public void testIsVersionStringLaterThan()
 494   {
 495     /*
 496      * No version / development / test / autobuild is leniently assumed to be
 497      * compatible
 498      */
 499     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 500     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 501     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 502     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 503             "Development Build"));
 504     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 505             "DEVELOPMENT BUILD"));
 506     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 507             "Development Build"));
 508     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 509     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 510     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 511     assertTrue(Jalview2XML
 512             .isVersionStringLaterThan(null, "Automated Build"));
 513     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 514             "Automated Build"));
 515     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 516             "AUTOMATED BUILD"));
 517
 518     /*
 519      * same version returns true i.e. compatible
 520      */
 521     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 522     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 523     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 524     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 525     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 526
 527     /*
 528      * later version returns true
 529      */
 530     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 531     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 532     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 533     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 534     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 535
 536     /*
 537      * earlier version returns false
 538      */
 539     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 540     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 541     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 542     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 543     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 544   }
 545
 546   /**
 547    * Test save and reload of a project with a different sequence group (and
 548    * representative sequence) in each view.
 549    *
 550    * @throws Exception
 551    */
 552   @Test(groups = { "Functional" })
 553   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 554   {
 555     Desktop.instance.closeAll_actionPerformed(null);
 556     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 557             "examples/uniref50.fa", DataSourceType.FILE);
 558     assertNotNull(af, "Didn't read in the example file correctly.");
 559     String afid = af.getViewport().getSequenceSetId();
 560     // make a second view of the alignment
 561     af.newView_actionPerformed(null);
 562
 563     /*
 564      * remember representative and hidden sequences marked
 565      * on each panel
 566      */
 567     Map<String, SequenceI> repSeqs = new HashMap<>();
 568     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 569
 570     /*
 571      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 572      * as reference sequence for itself and the preceding sequence
 573      */
 574     int n = 1;
 575     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 576     {
 577       AlignViewportI av = ap.getAlignViewport();
 578       AlignmentI alignment = ap.getAlignment();
 579       int repIndex = n % alignment.getHeight();
 580       // ensure at least one preceding sequence i.e. index >= 1
 581       repIndex = Math.max(repIndex, 1);
 582       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 583       repSeqs.put(ap.getViewName(), repSeq);
 584       List<String> hiddenNames = new ArrayList<>();
 585       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 586
 587       /*
 588        * have rep sequence represent itself and the one before it
 589        * this hides the group (except for the rep seq)
 590        */
 591       SequenceGroup sg = new SequenceGroup();
 592       sg.addSequence(repSeq, false);
 593       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 594       sg.addSequence(precedingSeq, false);
 595       sg.setSeqrep(repSeq);
 596       assertTrue(sg.getSequences().contains(repSeq));
 597       assertTrue(sg.getSequences().contains(precedingSeq));
 598       av.setSelectionGroup(sg);
 599       assertSame(repSeq, sg.getSeqrep());
 600
 601       /*
 602        * represent group with sequence adds to a map of hidden rep sequences
 603        * (it does not create a group on the alignment)
 604        */
 605       ((AlignmentViewport) av).hideSequences(repSeq, true);
 606       assertSame(repSeq, sg.getSeqrep());
 607       assertTrue(sg.getSequences().contains(repSeq));
 608       assertTrue(sg.getSequences().contains(precedingSeq));
 609       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 610       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 611               .getHiddenRepSequences();
 612       assertNotNull(hiddenRepSeqsMap);
 613       assertEquals(1, hiddenRepSeqsMap.size());
 614       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 615       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 616       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 617       hiddenNames.add(precedingSeq.getName());
 618
 619       n++;
 620     }
 621     File tfile = File
 622             .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
 623     try
 624     {
 625       new Jalview2XML(false).saveState(tfile);
 626     } catch (Throwable e)
 627     {
 628       Assert.fail("Didn't save the expanded view state", e);
 629     }
 630     Desktop.instance.closeAll_actionPerformed(null);
 631     if (Desktop.getAlignFrames() != null)
 632     {
 633       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 634     }
 635
 636     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 637             DataSourceType.FILE);
 638     afid = af.getViewport().getSequenceSetId();
 639
 640     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 641     {
 642       String viewName = ap.getViewName();
 643       AlignViewportI av = ap.getAlignViewport();
 644       AlignmentI alignment = ap.getAlignment();
 645       List<SequenceGroup> groups = alignment.getGroups();
 646       assertNotNull(groups);
 647       assertTrue(groups.isEmpty(), "Alignment has groups");
 648       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 649               .getHiddenRepSequences();
 650       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 651       assertEquals(1, hiddenRepSeqsMap.size());
 652       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 653               hiddenRepSeqsMap.keySet().iterator().next()
 654                       .getDisplayId(true));
 655
 656       /*
 657        * verify hidden sequences in restored panel
 658        */
 659       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 660       HiddenSequences hs = alignment.getHiddenSequences();
 661       assertEquals(
 662               hidden.size(),
 663               hs.getSize(),
 664               "wrong number of restored hidden sequences in "
 665                       + ap.getViewName());
 666     }
 667   }
 668
 669   /**
 670    * Test save and reload of PDBEntry in Jalview project
 671    *
 672    * @throws Exception
 673    */
 674   @Test(groups = { "Functional" })
 675   public void testStoreAndRecoverPDBEntry() throws Exception
 676   {
 677     Desktop.instance.closeAll_actionPerformed(null);
 678     String exampleFile = "examples/3W5V.pdb";
 679     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 680             DataSourceType.FILE);
 681     assertNotNull(af, "Didn't read in the example file correctly.");
 682     String afid = af.getViewport().getSequenceSetId();
 683
 684     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 685     System.out.println();
 686     AlignmentViewPanel ap = alignPanels[0];
 687     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 688     String testFile = tfileBase + exampleFile;
 689     AlignmentI alignment = ap.getAlignment();
 690     System.out.println("blah");
 691     SequenceI[] seqs = alignment.getSequencesArray();
 692     Assert.assertNotNull(seqs[0]);
 693     Assert.assertNotNull(seqs[1]);
 694     Assert.assertNotNull(seqs[2]);
 695     Assert.assertNotNull(seqs[3]);
 696     Assert.assertNotNull(seqs[0].getDatasetSequence());
 697     Assert.assertNotNull(seqs[1].getDatasetSequence());
 698     Assert.assertNotNull(seqs[2].getDatasetSequence());
 699     Assert.assertNotNull(seqs[3].getDatasetSequence());
 700     PDBEntry[] pdbEntries = new PDBEntry[4];
 701     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 702     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 703     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 704     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 705     Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
 706             .get(0), pdbEntries[0]);
 707     Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
 708             .get(0), pdbEntries[1]);
 709     Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
 710             .get(0), pdbEntries[2]);
 711     Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
 712             .get(0), pdbEntries[3]);
 713
 714     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 715     try
 716     {
 717       new Jalview2XML(false).saveState(tfile);
 718     } catch (Throwable e)
 719     {
 720       Assert.fail("Didn't save the state", e);
 721     }
 722     Desktop.instance.closeAll_actionPerformed(null);
 723     if (Desktop.getAlignFrames() != null)
 724     {
 725       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 726     }
 727
 728     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 729             tfile.getAbsolutePath(), DataSourceType.FILE);
 730     String rfid = restoredFrame.getViewport().getSequenceSetId();
 731     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 732     AlignmentViewPanel rap = rAlignPanels[0];
 733     AlignmentI rAlignment = rap.getAlignment();
 734     System.out.println("blah");
 735     SequenceI[] rseqs = rAlignment.getSequencesArray();
 736     Assert.assertNotNull(rseqs[0]);
 737     Assert.assertNotNull(rseqs[1]);
 738     Assert.assertNotNull(rseqs[2]);
 739     Assert.assertNotNull(rseqs[3]);
 740     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 741     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 742     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 743     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 744
 745     // The Asserts below are expected to fail until the PDB chainCode is
 746     // recoverable from a Jalview projects
 747     for (int chain = 0; chain < 4; chain++)
 748     {
 749       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 750               .get(0);
 751       PDBEntry expected = pdbEntries[chain];
 752       Assert.assertEquals(recov.getId(), expected.getId(),
 753               "Mismatch PDB ID");
 754       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 755               "Mismatch PDB ID");
 756       Assert.assertEquals(recov.getType(), expected.getType(),
 757               "Mismatch PDBEntry 'Type'");
 758       Assert.assertNotNull(recov.getFile(),
 759               "Recovered PDBEntry should have a non-null file entry");
 760     }
 761   }
 762
 763   /**
 764    * Configure an alignment and a sub-group each with distinct colour schemes,
 765    * Conservation and PID thresholds, and confirm these are restored from the
 766    * saved project.
 767    *
 768    * @throws IOException
 769    */
 770   @Test(groups = { "Functional" })
 771   public void testStoreAndRecoverColourThresholds() throws IOException
 772   {
 773     Desktop.instance.closeAll_actionPerformed(null);
 774     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 775             "examples/uniref50.fa", DataSourceType.FILE);
 776
 777     AlignViewportI av = af.getViewport();
 778     AlignmentI al = av.getAlignment();
 779
 780     /*
 781      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 782      */
 783     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 784     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 785     af.abovePIDThreshold_actionPerformed(true);
 786     SliderPanel sp = SliderPanel.getSliderPanel();
 787     assertFalse(sp.isForConservation());
 788     sp.valueChanged(10);
 789     af.conservationMenuItem_actionPerformed(true);
 790     sp = SliderPanel.getSliderPanel();
 791     assertTrue(sp.isForConservation());
 792     sp.valueChanged(20);
 793     ResidueShaderI rs = av.getResidueShading();
 794     assertEquals(rs.getThreshold(), 10);
 795     assertTrue(rs.conservationApplied());
 796     assertEquals(rs.getConservationInc(), 20);
 797
 798     /*
 799      * create a group with Strand colouring, 30% Conservation
 800      * and 40% PID threshold
 801      */
 802     SequenceGroup sg = new SequenceGroup();
 803     sg.addSequence(al.getSequenceAt(0), false);
 804     sg.setStartRes(15);
 805     sg.setEndRes(25);
 806     av.setSelectionGroup(sg);
 807     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 808     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
 809             .toString());
 810     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 811     assertEquals(al.getGroups().size(), 1);
 812     assertSame(al.getGroups().get(0), sg);
 813     popupMenu.conservationMenuItem_actionPerformed(true);
 814     sp = SliderPanel.getSliderPanel();
 815     assertTrue(sp.isForConservation());
 816     sp.valueChanged(30);
 817     popupMenu.abovePIDColour_actionPerformed(true);
 818     sp = SliderPanel.getSliderPanel();
 819     assertFalse(sp.isForConservation());
 820     sp.valueChanged(40);
 821     assertTrue(sg.getGroupColourScheme().conservationApplied());
 822     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 823     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 824
 825     /*
 826      * save project, close windows, reload project, verify
 827      */
 828     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 829             ".jvp");
 830     tfile.deleteOnExit();
 831     new Jalview2XML(false).saveState(tfile);
 832     Desktop.instance.closeAll_actionPerformed(null);
 833     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 834             DataSourceType.FILE);
 835     Assert.assertNotNull(af, "Failed to reload project");
 836
 837     /*
 838      * verify alignment (background) colouring
 839      */
 840     rs = af.getViewport().getResidueShading();
 841     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 842     assertEquals(rs.getThreshold(), 10);
 843     assertTrue(rs.conservationApplied());
 844     assertEquals(rs.getConservationInc(), 20);
 845
 846     /*
 847      * verify group colouring
 848      */
 849     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 850     rs = af.getViewport().getAlignment().getGroups().get(0)
 851             .getGroupColourScheme();
 852     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 853     assertEquals(rs.getThreshold(), 40);
 854     assertTrue(rs.conservationApplied());
 855     assertEquals(rs.getConservationInc(), 30);
 856   }
 857
 858   /**
 859    * Test save and reload of feature colour schemes and filter settings
 860    *
 861    * @throws IOException
 862    */
 863   @Test(groups = { "Functional" })
 864   public void testStoreAndRecoverFeatureColoursAndFilters()
 865           throws IOException
 866   {
 867     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 868             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 869     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 870
 871     /*
 872      * add some features to the sequence
 873      */
 874     int score = 1;
 875     addFeatures(seq1, "type1", score++);
 876     addFeatures(seq1, "type2", score++);
 877     addFeatures(seq1, "type3", score++);
 878     addFeatures(seq1, "type4", score++);
 879     addFeatures(seq1, "type5", score++);
 880
 881     /*
 882      * set colour schemes for features
 883      */
 884     FeatureRenderer fr = af.getFeatureRenderer();
 885     fr.findAllFeatures(true);
 886
 887     // type1: red
 888     fr.setColour("type1", new FeatureColour(Color.red));
 889
 890     // type2: by label
 891     FeatureColourI byLabel = new FeatureColour();
 892     byLabel.setColourByLabel(true);
 893     fr.setColour("type2", byLabel);
 894
 895     // type3: by score above threshold
 896     FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
 897             10);
 898     byScore.setAboveThreshold(true);
 899     byScore.setThreshold(2f);
 900     fr.setColour("type3", byScore);
 901
 902     // type4: by attribute AF
 903     FeatureColourI byAF = new FeatureColour();
 904     byAF.setColourByLabel(true);
 905     byAF.setAttributeName("AF");
 906     fr.setColour("type4", byAF);
 907
 908     // type5: by attribute CSQ:PolyPhen below threshold
 909     FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
 910             1, 10);
 911     byPolyPhen.setBelowThreshold(true);
 912     byPolyPhen.setThreshold(3f);
 913     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 914     fr.setColour("type5", byPolyPhen);
 915
 916     /*
 917      * set filters for feature types
 918      */
 919
 920     // filter type1 features by (label contains "x")
 921     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 922     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 923     fr.setFeatureFilter("type1", filterByX);
 924
 925     // filter type2 features by (score <= 2.4 and score > 1.1)
 926     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 927     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 928     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 929     fr.setFeatureFilter("type2", filterByScore);
 930
 931     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 932     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 933     filterByXY
 934             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 935     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 936             "PolyPhen"));
 937     fr.setFeatureFilter("type3", filterByXY);
 938
 939     /*
 940      * save as Jalview project
 941      */
 942     File tfile = File.createTempFile("JalviewTest", ".jvp");
 943     tfile.deleteOnExit();
 944     String filePath = tfile.getAbsolutePath();
 945     assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
 946             "Failed to store as a project.");
 947
 948     /*
 949      * close current alignment and load the saved project
 950      */
 951     af.closeMenuItem_actionPerformed(true);
 952     af = null;
 953     af = new FileLoader()
 954             .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
 955     assertNotNull(af, "Failed to import new project");
 956
 957     /*
 958      * verify restored feature colour schemes and filters
 959      */
 960     fr = af.getFeatureRenderer();
 961     FeatureColourI fc = fr.getFeatureStyle("type1");
 962     assertTrue(fc.isSimpleColour());
 963     assertEquals(fc.getColour(), Color.red);
 964     fc = fr.getFeatureStyle("type2");
 965     assertTrue(fc.isColourByLabel());
 966     fc = fr.getFeatureStyle("type3");
 967     assertTrue(fc.isGraduatedColour());
 968     assertNull(fc.getAttributeName());
 969     assertTrue(fc.isAboveThreshold());
 970     assertEquals(fc.getThreshold(), 2f);
 971     fc = fr.getFeatureStyle("type4");
 972     assertTrue(fc.isColourByLabel());
 973     assertTrue(fc.isColourByAttribute());
 974     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 975     fc = fr.getFeatureStyle("type5");
 976     assertTrue(fc.isGraduatedColour());
 977     assertTrue(fc.isColourByAttribute());
 978     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
 979     assertTrue(fc.isBelowThreshold());
 980     assertEquals(fc.getThreshold(), 3f);
 981
 982     assertEquals(fr.getFeatureFilter("type1").toStableString(),
 983             "Label Contains x");
 984     assertEquals(fr.getFeatureFilter("type2").toStableString(),
 985             "(Score LE 2.4) AND (Score GT 1.1)");
 986     assertEquals(fr.getFeatureFilter("type3").toStableString(),
 987             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
 988   }
 989
 990   private void addFeature(SequenceI seq, String featureType, int score)
 991   {
 992     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
 993             score, "grp");
 994     sf.setValue("AF", score);
 995     sf.setValue("CSQ", new HashMap<String, String>()
 996     {
 997       {
 998         put("PolyPhen", Integer.toString(score));
 999       }
1000     });
1001     seq.addSequenceFeature(sf);
1002   }
1003
1004   /**
1005    * Adds two features of the given type to the given sequence, also setting the
1006    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1007    *
1008    * @param seq
1009    * @param featureType
1010    * @param score
1011    */
1012   private void addFeatures(SequenceI seq, String featureType, int score)
1013   {
1014     addFeature(seq, featureType, score++);
1015     addFeature(seq, featureType, score);
1016   }
1017
1018   /**
1019    * Load an HMM profile to an alignment, and confirm it is correctly restored
1020    * when reloaded from project
1021    *
1022    * @throws IOException
1023    */
1024   @Test(groups = { "Functional" })
1025   public void testStoreAndRecoverHmmProfile() throws IOException
1026   {
1027     Desktop.instance.closeAll_actionPerformed(null);
1028     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
1029             "examples/uniref50.fa", DataSourceType.FILE);
1030
1031     AlignViewportI av = af.getViewport();
1032     AlignmentI al = av.getAlignment();
1033
1034     /*
1035      * mimic drag and drop of hmm file on to alignment
1036      */
1037     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
1038             "examples/uniref50.hmm", DataSourceType.FILE);
1039     al.insertSequenceAt(0,
1040             af2.getViewport().getAlignment().getSequenceAt(0));
1041
1042     /*
1043      * check it loaded in
1044      */
1045     SequenceI hmmSeq = al.getSequenceAt(0);
1046     assertTrue(hmmSeq.hasHMMProfile());
1047     HiddenMarkovModel hmm = hmmSeq.getHMM();
1048     assertSame(hmm.getConsensusSequence(), hmmSeq);
1049
1050     /*
1051      * save project, close windows, reload project, verify
1052      */
1053     File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
1054             ".jvp");
1055     tfile.deleteOnExit();
1056     new Jalview2XML(false).saveState(tfile);
1057     Desktop.instance.closeAll_actionPerformed(null);
1058     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
1059             DataSourceType.FILE);
1060     Assert.assertNotNull(af, "Failed to reload project");
1061
1062     hmmSeq = al.getSequenceAt(0);
1063     assertTrue(hmmSeq.hasHMMProfile());
1064     assertSame(hmm.getConsensusSequence(), hmmSeq);
1065     Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
1066             "mapToHmmConsensus");
1067     assertNotNull(mapToHmmConsensus);
1068     assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
1069   }
1070 }