test/jalview/io/Jalview2xmlTests.java

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