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.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.JvOptionPane;
  52 import jalview.gui.PopupMenu;
  53 import jalview.gui.SliderPanel;
  54 import jalview.io.DataSourceType;
  55 import jalview.io.FileFormat;
  56 import jalview.io.FileLoader;
  57 import jalview.io.Jalview2xmlBase;
  58 import jalview.renderer.ResidueShaderI;
  59 import jalview.schemes.AnnotationColourGradient;
  60 import jalview.schemes.BuriedColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.ColourSchemeProperty;
  63 import jalview.schemes.FeatureColour;
  64 import jalview.schemes.JalviewColourScheme;
  65 import jalview.schemes.RNAHelicesColour;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.structure.StructureImportSettings;
  69 import jalview.util.matcher.Condition;
  70 import jalview.viewmodel.AlignmentViewport;
  71
  72 import java.awt.Color;
  73 import java.io.File;
  74 import java.io.IOException;
  75 import java.util.ArrayList;
  76 import java.util.HashMap;
  77 import java.util.List;
  78 import java.util.Map;
  79
  80 import org.testng.Assert;
  81 import org.testng.AssertJUnit;
  82 import org.testng.annotations.BeforeClass;
  83 import org.testng.annotations.Test;
  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   /**
 264    * Test for JAL-2223 - multiple mappings in View Mapping report
 265    *
 266    * @throws Exception
 267    */
 268   @Test(groups = { "Functional" })
 269   public void noDuplicatePdbMappingsMade() throws Exception
 270   {
 271     StructureImportSettings.setProcessSecondaryStructure(true);
 272     StructureImportSettings.setVisibleChainAnnotation(true);
 273     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 274             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 275     assertNotNull(af, "Didn't read in the example file correctly.");
 276
 277     // locate Jmol viewer
 278     // count number of PDB mappings the structure selection manager holds -
 279     String pdbFile = af.getCurrentView().getStructureSelectionManager()
 280             .findFileForPDBId("1A70");
 281     assertEquals(
 282             af.getCurrentView().getStructureSelectionManager()
 283                     .getMapping(pdbFile).length,
 284             2, "Expected only two mappings for 1A70");
 285
 286   }
 287
 288   @Test(groups = { "Functional" })
 289   public void viewRefPdbAnnotation() throws Exception
 290   {
 291     StructureImportSettings.setProcessSecondaryStructure(true);
 292     StructureImportSettings.setVisibleChainAnnotation(true);
 293     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 294             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 295     assertNotNull(af, "Didn't read in the example file correctly.");
 296     AlignmentViewPanel sps = null;
 297     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 298     {
 299       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 300       {
 301         sps = ap;
 302         break;
 303       }
 304     }
 305     assertNotNull(sps, "Couldn't find the structure view");
 306     AlignmentAnnotation refan = null;
 307     for (AlignmentAnnotation ra : sps.getAlignment()
 308             .getAlignmentAnnotation())
 309     {
 310       if (ra.graph != 0)
 311       {
 312         refan = ra;
 313         break;
 314       }
 315     }
 316     assertNotNull(refan, "Annotation secondary structure not found.");
 317     SequenceI sq = sps.getAlignment().findName("1A70|");
 318     assertNotNull(sq, "Couldn't find 1a70 null chain");
 319     // compare the manually added temperature factor annotation
 320     // to the track automatically transferred from the pdb structure on load
 321     assertNotNull(sq.getDatasetSequence().getAnnotation(),
 322             "1a70 has no annotation");
 323     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
 324     {
 325       AlignmentAnnotation alaa;
 326       sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
 327       alaa.adjustForAlignment();
 328       if (ala.graph == refan.graph)
 329       {
 330         for (int p = 0; p < ala.annotations.length; p++)
 331         {
 332           sq.findPosition(p);
 333           try
 334           {
 335             assertTrue(
 336                     (alaa.annotations[p] == null && refan.annotations[p] == null)
 337                             || alaa.annotations[p].value == refan.annotations[p].value,
 338                     "Mismatch at alignment position " + p);
 339           } catch (NullPointerException q)
 340           {
 341             Assert.fail("Mismatch of alignment annotations at position "
 342                     + p + " Ref seq ann: " + refan.annotations[p]
 343                     + " alignment " + alaa.annotations[p]);
 344           }
 345         }
 346       }
 347     }
 348
 349   }
 350
 351   @Test(groups = { "Functional" })
 352   public void testCopyViewSettings() throws Exception
 353   {
 354     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 355             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 356     assertNotNull(af, "Didn't read in the example file correctly.");
 357     AlignmentViewPanel sps = null, groups = null;
 358     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
 359     {
 360       if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
 361       {
 362         sps = ap;
 363       }
 364       if (ap.getViewName().contains("MAFFT"))
 365       {
 366         groups = ap;
 367       }
 368     }
 369     assertNotNull(sps, "Couldn't find the structure view");
 370     assertNotNull(groups, "Couldn't find the MAFFT view");
 371
 372     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
 373     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
 374     AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
 375
 376     groups.getAlignViewport().setViewStyle(structureStyle);
 377     AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
 378             .getViewStyle()));
 379     Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
 380             .getViewStyle()));
 381
 382   }
 383
 384   /**
 385    * test store and recovery of expanded views
 386    *
 387    * @throws Exception
 388    */
 389   @Test(groups = { "Functional" }, enabled = true)
 390   public void testStoreAndRecoverExpandedviews() throws Exception
 391   {
 392     Desktop.instance.closeAll_actionPerformed(null);
 393
 394     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 395             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 396     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
 397     String afid = af.getViewport().getSequenceSetId();
 398
 399     // check FileLoader returned a reference to the one alignFrame that is
 400     // actually on the Desktop
 401     assertSame(
 402             af,
 403             Desktop.getAlignFrameFor(af.getViewport()),
 404             "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
 405
 406     Desktop.explodeViews(af);
 407
 408     int oldviews = Desktop.getAlignFrames().length;
 409     Assert.assertEquals(Desktop.getAlignFrames().length,
 410             Desktop.getAlignmentPanels(afid).length);
 411     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
 412     try
 413     {
 414       new Jalview2XML(false).saveState(tfile);
 415     } catch (Error e)
 416     {
 417       Assert.fail("Didn't save the expanded view state", e);
 418     } catch (Exception e)
 419     {
 420       Assert.fail("Didn't save the expanded view state", e);
 421     }
 422     Desktop.instance.closeAll_actionPerformed(null);
 423     if (Desktop.getAlignFrames() != null)
 424     {
 425       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 426     }
 427     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 428             DataSourceType.FILE);
 429     Assert.assertNotNull(af);
 430     Assert.assertEquals(
 431             Desktop.getAlignFrames().length,
 432             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
 433     Assert.assertEquals(
 434             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
 435             oldviews);
 436   }
 437
 438   /**
 439    * Test save and reload of a project with a different representative sequence
 440    * in each view.
 441    *
 442    * @throws Exception
 443    */
 444   @Test(groups = { "Functional" })
 445   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
 446   {
 447     Desktop.instance.closeAll_actionPerformed(null);
 448     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 449             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
 450     assertNotNull(af, "Didn't read in the example file correctly.");
 451     String afid = af.getViewport().getSequenceSetId();
 452
 453     // remember reference sequence for each panel
 454     Map<String, SequenceI> refseqs = new HashMap<>();
 455
 456     /*
 457      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 458      * as reference sequence for itself and the preceding sequence
 459      */
 460     int n = 1;
 461     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 462     {
 463       AlignViewportI av = ap.getAlignViewport();
 464       AlignmentI alignment = ap.getAlignment();
 465       int repIndex = n % alignment.getHeight();
 466       SequenceI rep = alignment.getSequenceAt(repIndex);
 467       refseqs.put(ap.getViewName(), rep);
 468
 469       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
 470       // todo refactor this to an alignment view controller
 471       av.setDisplayReferenceSeq(true);
 472       av.setColourByReferenceSeq(true);
 473       av.getAlignment().setSeqrep(rep);
 474
 475       n++;
 476     }
 477     File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
 478             ".jvp");
 479     try
 480     {
 481       new Jalview2XML(false).saveState(tfile);
 482     } catch (Throwable e)
 483     {
 484       Assert.fail("Didn't save the expanded view state", e);
 485     }
 486     Desktop.instance.closeAll_actionPerformed(null);
 487     if (Desktop.getAlignFrames() != null)
 488     {
 489       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 490     }
 491
 492     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 493             DataSourceType.FILE);
 494     afid = af.getViewport().getSequenceSetId();
 495
 496     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 497     {
 498       // check representative
 499       AlignmentI alignment = ap.getAlignment();
 500       SequenceI rep = alignment.getSeqrep();
 501       Assert.assertNotNull(rep,
 502               "Couldn't restore sequence representative from project");
 503       // can't use a strong equals here, because by definition, the sequence IDs
 504       // will be different.
 505       // could set vamsas session save/restore flag to preserve IDs across
 506       // load/saves.
 507       Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
 508               rep.toString(),
 509               "Representative wasn't the same when recovered.");
 510       Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
 511               "Display reference sequence view setting not set.");
 512       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
 513               "Colour By Reference Seq view setting not set.");
 514     }
 515   }
 516
 517   @Test(groups = { "Functional" })
 518   public void testIsVersionStringLaterThan()
 519   {
 520     /*
 521      * No version / development / test / autobuild is leniently assumed to be
 522      * compatible
 523      */
 524     assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
 525     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
 526     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
 527     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 528             "Development Build"));
 529     assertTrue(Jalview2XML.isVersionStringLaterThan(null,
 530             "DEVELOPMENT BUILD"));
 531     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 532             "Development Build"));
 533     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
 534     assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
 535     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
 536     assertTrue(Jalview2XML
 537             .isVersionStringLaterThan(null, "Automated Build"));
 538     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 539             "Automated Build"));
 540     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
 541             "AUTOMATED BUILD"));
 542
 543     /*
 544      * same version returns true i.e. compatible
 545      */
 546     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
 547     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
 548     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
 549     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
 550     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
 551
 552     /*
 553      * later version returns true
 554      */
 555     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
 556     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
 557     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
 558     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
 559     assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
 560
 561     /*
 562      * earlier version returns false
 563      */
 564     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
 565     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
 566     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
 567     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
 568     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
 569   }
 570
 571   /**
 572    * Test save and reload of a project with a different sequence group (and
 573    * representative sequence) in each view.
 574    *
 575    * @throws Exception
 576    */
 577   @Test(groups = { "Functional" })
 578   public void testStoreAndRecoverGroupRepSeqs() throws Exception
 579   {
 580     Desktop.instance.closeAll_actionPerformed(null);
 581     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 582             "examples/uniref50.fa", DataSourceType.FILE);
 583     assertNotNull(af, "Didn't read in the example file correctly.");
 584     String afid = af.getViewport().getSequenceSetId();
 585     // make a second view of the alignment
 586     af.newView_actionPerformed(null);
 587
 588     /*
 589      * remember representative and hidden sequences marked
 590      * on each panel
 591      */
 592     Map<String, SequenceI> repSeqs = new HashMap<>();
 593     Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 594
 595     /*
 596      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
 597      * as reference sequence for itself and the preceding sequence
 598      */
 599     int n = 1;
 600     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 601     {
 602       AlignViewportI av = ap.getAlignViewport();
 603       AlignmentI alignment = ap.getAlignment();
 604       int repIndex = n % alignment.getHeight();
 605       // ensure at least one preceding sequence i.e. index >= 1
 606       repIndex = Math.max(repIndex, 1);
 607       SequenceI repSeq = alignment.getSequenceAt(repIndex);
 608       repSeqs.put(ap.getViewName(), repSeq);
 609       List<String> hiddenNames = new ArrayList<>();
 610       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 611
 612       /*
 613        * have rep sequence represent itself and the one before it
 614        * this hides the group (except for the rep seq)
 615        */
 616       SequenceGroup sg = new SequenceGroup();
 617       sg.addSequence(repSeq, false);
 618       SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
 619       sg.addSequence(precedingSeq, false);
 620       sg.setSeqrep(repSeq);
 621       assertTrue(sg.getSequences().contains(repSeq));
 622       assertTrue(sg.getSequences().contains(precedingSeq));
 623       av.setSelectionGroup(sg);
 624       assertSame(repSeq, sg.getSeqrep());
 625
 626       /*
 627        * represent group with sequence adds to a map of hidden rep sequences
 628        * (it does not create a group on the alignment)
 629        */
 630       ((AlignmentViewport) av).hideSequences(repSeq, true);
 631       assertSame(repSeq, sg.getSeqrep());
 632       assertTrue(sg.getSequences().contains(repSeq));
 633       assertTrue(sg.getSequences().contains(precedingSeq));
 634       assertTrue(alignment.getGroups().isEmpty(), "alignment has groups");
 635       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 636               .getHiddenRepSequences();
 637       assertNotNull(hiddenRepSeqsMap);
 638       assertEquals(1, hiddenRepSeqsMap.size());
 639       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
 640       assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
 641       assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
 642       hiddenNames.add(precedingSeq.getName());
 643
 644       n++;
 645     }
 646     File tfile = File
 647             .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
 648     try
 649     {
 650       new Jalview2XML(false).saveState(tfile);
 651     } catch (Throwable e)
 652     {
 653       Assert.fail("Didn't save the expanded view state", e);
 654     }
 655     Desktop.instance.closeAll_actionPerformed(null);
 656     if (Desktop.getAlignFrames() != null)
 657     {
 658       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 659     }
 660
 661     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 662             DataSourceType.FILE);
 663     afid = af.getViewport().getSequenceSetId();
 664
 665     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
 666     {
 667       String viewName = ap.getViewName();
 668       AlignViewportI av = ap.getAlignViewport();
 669       AlignmentI alignment = ap.getAlignment();
 670       List<SequenceGroup> groups = alignment.getGroups();
 671       assertNotNull(groups);
 672       assertTrue(groups.isEmpty(), "Alignment has groups");
 673       Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
 674               .getHiddenRepSequences();
 675       assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
 676       assertEquals(1, hiddenRepSeqsMap.size());
 677       assertEquals(repSeqs.get(viewName).getDisplayId(true),
 678               hiddenRepSeqsMap.keySet().iterator().next()
 679                       .getDisplayId(true));
 680
 681       /*
 682        * verify hidden sequences in restored panel
 683        */
 684       List<String> hidden = hiddenSeqNames.get(ap.getViewName());
 685       HiddenSequences hs = alignment.getHiddenSequences();
 686       assertEquals(
 687               hidden.size(),
 688               hs.getSize(),
 689               "wrong number of restored hidden sequences in "
 690                       + ap.getViewName());
 691     }
 692   }
 693
 694   /**
 695    * Test save and reload of PDBEntry in Jalview project
 696    *
 697    * @throws Exception
 698    */
 699   @Test(groups = { "Functional" })
 700   public void testStoreAndRecoverPDBEntry() throws Exception
 701   {
 702     Desktop.instance.closeAll_actionPerformed(null);
 703     String exampleFile = "examples/3W5V.pdb";
 704     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
 705             DataSourceType.FILE);
 706     assertNotNull(af, "Didn't read in the example file correctly.");
 707     String afid = af.getViewport().getSequenceSetId();
 708
 709     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
 710     System.out.println();
 711     AlignmentViewPanel ap = alignPanels[0];
 712     String tfileBase = new File(".").getAbsolutePath().replace(".", "");
 713     String testFile = tfileBase + exampleFile;
 714     AlignmentI alignment = ap.getAlignment();
 715     System.out.println("blah");
 716     SequenceI[] seqs = alignment.getSequencesArray();
 717     Assert.assertNotNull(seqs[0]);
 718     Assert.assertNotNull(seqs[1]);
 719     Assert.assertNotNull(seqs[2]);
 720     Assert.assertNotNull(seqs[3]);
 721     Assert.assertNotNull(seqs[0].getDatasetSequence());
 722     Assert.assertNotNull(seqs[1].getDatasetSequence());
 723     Assert.assertNotNull(seqs[2].getDatasetSequence());
 724     Assert.assertNotNull(seqs[3].getDatasetSequence());
 725     PDBEntry[] pdbEntries = new PDBEntry[4];
 726     pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
 727     pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
 728     pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
 729     pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
 730     Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
 731             .get(0), pdbEntries[0]);
 732     Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
 733             .get(0), pdbEntries[1]);
 734     Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
 735             .get(0), pdbEntries[2]);
 736     Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
 737             .get(0), pdbEntries[3]);
 738
 739     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
 740     try
 741     {
 742       new Jalview2XML(false).saveState(tfile);
 743     } catch (Throwable e)
 744     {
 745       Assert.fail("Didn't save the state", e);
 746     }
 747     Desktop.instance.closeAll_actionPerformed(null);
 748     if (Desktop.getAlignFrames() != null)
 749     {
 750       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
 751     }
 752
 753     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
 754             tfile.getAbsolutePath(), DataSourceType.FILE);
 755     String rfid = restoredFrame.getViewport().getSequenceSetId();
 756     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
 757     AlignmentViewPanel rap = rAlignPanels[0];
 758     AlignmentI rAlignment = rap.getAlignment();
 759     System.out.println("blah");
 760     SequenceI[] rseqs = rAlignment.getSequencesArray();
 761     Assert.assertNotNull(rseqs[0]);
 762     Assert.assertNotNull(rseqs[1]);
 763     Assert.assertNotNull(rseqs[2]);
 764     Assert.assertNotNull(rseqs[3]);
 765     Assert.assertNotNull(rseqs[0].getDatasetSequence());
 766     Assert.assertNotNull(rseqs[1].getDatasetSequence());
 767     Assert.assertNotNull(rseqs[2].getDatasetSequence());
 768     Assert.assertNotNull(rseqs[3].getDatasetSequence());
 769
 770     // The Asserts below are expected to fail until the PDB chainCode is
 771     // recoverable from a Jalview projects
 772     for (int chain = 0; chain < 4; chain++)
 773     {
 774       PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
 775               .get(0);
 776       PDBEntry expected = pdbEntries[chain];
 777       Assert.assertEquals(recov.getId(), expected.getId(),
 778               "Mismatch PDB ID");
 779       Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
 780               "Mismatch PDB ID");
 781       Assert.assertEquals(recov.getType(), expected.getType(),
 782               "Mismatch PDBEntry 'Type'");
 783       Assert.assertNotNull(recov.getFile(),
 784               "Recovered PDBEntry should have a non-null file entry");
 785     }
 786   }
 787
 788   /**
 789    * Configure an alignment and a sub-group each with distinct colour schemes,
 790    * Conservation and PID thresholds, and confirm these are restored from the
 791    * saved project.
 792    *
 793    * @throws IOException
 794    */
 795   @Test(groups = { "Functional" })
 796   public void testStoreAndRecoverColourThresholds() throws IOException
 797   {
 798     Desktop.instance.closeAll_actionPerformed(null);
 799     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 800             "examples/uniref50.fa", DataSourceType.FILE);
 801
 802     AlignViewport av = af.getViewport();
 803     AlignmentI al = av.getAlignment();
 804
 805     /*
 806      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
 807      */
 808     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
 809     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
 810     af.abovePIDThreshold_actionPerformed(true);
 811     SliderPanel sp = SliderPanel.getSliderPanel();
 812     assertFalse(sp.isForConservation());
 813     sp.valueChanged(10);
 814     af.conservationMenuItem_actionPerformed(true);
 815     sp = SliderPanel.getSliderPanel();
 816     assertTrue(sp.isForConservation());
 817     sp.valueChanged(20);
 818     ResidueShaderI rs = av.getResidueShading();
 819     assertEquals(rs.getThreshold(), 10);
 820     assertTrue(rs.conservationApplied());
 821     assertEquals(rs.getConservationInc(), 20);
 822
 823     /*
 824      * create a group with Strand colouring, 30% Conservation
 825      * and 40% PID threshold
 826      */
 827     SequenceGroup sg = new SequenceGroup();
 828     sg.addSequence(al.getSequenceAt(0), false);
 829     sg.setStartRes(15);
 830     sg.setEndRes(25);
 831     av.setSelectionGroup(sg);
 832     PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
 833     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
 834             .toString());
 835     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
 836     assertEquals(al.getGroups().size(), 1);
 837     assertSame(al.getGroups().get(0), sg);
 838     popupMenu.conservationMenuItem_actionPerformed(true);
 839     sp = SliderPanel.getSliderPanel();
 840     assertTrue(sp.isForConservation());
 841     sp.valueChanged(30);
 842     popupMenu.abovePIDColour_actionPerformed(true);
 843     sp = SliderPanel.getSliderPanel();
 844     assertFalse(sp.isForConservation());
 845     sp.valueChanged(40);
 846     assertTrue(sg.getGroupColourScheme().conservationApplied());
 847     assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
 848     assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
 849
 850     /*
 851      * save project, close windows, reload project, verify
 852      */
 853     File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
 854             ".jvp");
 855     tfile.deleteOnExit();
 856     new Jalview2XML(false).saveState(tfile);
 857     Desktop.instance.closeAll_actionPerformed(null);
 858     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
 859             DataSourceType.FILE);
 860     Assert.assertNotNull(af, "Failed to reload project");
 861
 862     /*
 863      * verify alignment (background) colouring
 864      */
 865     rs = af.getViewport().getResidueShading();
 866     assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
 867     assertEquals(rs.getThreshold(), 10);
 868     assertTrue(rs.conservationApplied());
 869     assertEquals(rs.getConservationInc(), 20);
 870
 871     /*
 872      * verify group colouring
 873      */
 874     assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
 875     rs = af.getViewport().getAlignment().getGroups().get(0)
 876             .getGroupColourScheme();
 877     assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
 878     assertEquals(rs.getThreshold(), 40);
 879     assertTrue(rs.conservationApplied());
 880     assertEquals(rs.getConservationInc(), 30);
 881   }
 882
 883   /**
 884    * Test save and reload of feature colour schemes and filter settings
 885    *
 886    * @throws IOException
 887    */
 888   @Test(groups = { "Functional" })
 889   public void testSaveLoadFeatureColoursAndFilters() throws IOException
 890   {
 891     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
 892             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
 893     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
 894
 895     /*
 896      * add some features to the sequence
 897      */
 898     int score = 1;
 899     addFeatures(seq1, "type1", score++);
 900     addFeatures(seq1, "type2", score++);
 901     addFeatures(seq1, "type3", score++);
 902     addFeatures(seq1, "type4", score++);
 903     addFeatures(seq1, "type5", score++);
 904
 905     /*
 906      * set colour schemes for features
 907      */
 908     FeatureRenderer fr = af.getFeatureRenderer();
 909     fr.findAllFeatures(true);
 910
 911     // type1: red
 912     fr.setColour("type1", new FeatureColour(Color.red));
 913
 914     // type2: by label
 915     FeatureColourI byLabel = new FeatureColour();
 916     byLabel.setColourByLabel(true);
 917     fr.setColour("type2", byLabel);
 918
 919     // type3: by score above threshold
 920     FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
 921             10);
 922     byScore.setAboveThreshold(true);
 923     byScore.setThreshold(2f);
 924     fr.setColour("type3", byScore);
 925
 926     // type4: by attribute AF
 927     FeatureColourI byAF = new FeatureColour();
 928     byAF.setColourByLabel(true);
 929     byAF.setAttributeName("AF");
 930     fr.setColour("type4", byAF);
 931
 932     // type5: by attribute CSQ:PolyPhen below threshold
 933     FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
 934             1, 10);
 935     byPolyPhen.setBelowThreshold(true);
 936     byPolyPhen.setThreshold(3f);
 937     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
 938     fr.setColour("type5", byPolyPhen);
 939
 940     /*
 941      * set filters for feature types
 942      */
 943
 944     // filter type1 features by (label contains "x")
 945     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
 946     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
 947     fr.setFeatureFilter("type1", filterByX);
 948
 949     // filter type2 features by (score <= 2.4 and score > 1.1)
 950     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
 951     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
 952     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
 953     fr.setFeatureFilter("type2", filterByScore);
 954
 955     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 956     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 957     filterByXY
 958             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 959     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 960             "PolyPhen"));
 961     fr.setFeatureFilter("type3", filterByXY);
 962
 963     /*
 964      * save as Jalview project
 965      */
 966     File tfile = File.createTempFile("JalviewTest", ".jvp");
 967     tfile.deleteOnExit();
 968     String filePath = tfile.getAbsolutePath();
 969     assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
 970             "Failed to store as a project.");
 971
 972     /*
 973      * close current alignment and load the saved project
 974      */
 975     af.closeMenuItem_actionPerformed(true);
 976     af = null;
 977     af = new FileLoader()
 978             .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
 979     assertNotNull(af, "Failed to import new project");
 980
 981     /*
 982      * verify restored feature colour schemes and filters
 983      */
 984     fr = af.getFeatureRenderer();
 985     FeatureColourI fc = fr.getFeatureStyle("type1");
 986     assertTrue(fc.isSimpleColour());
 987     assertEquals(fc.getColour(), Color.red);
 988     fc = fr.getFeatureStyle("type2");
 989     assertTrue(fc.isColourByLabel());
 990     fc = fr.getFeatureStyle("type3");
 991     assertTrue(fc.isGraduatedColour());
 992     assertNull(fc.getAttributeName());
 993     assertTrue(fc.isAboveThreshold());
 994     assertEquals(fc.getThreshold(), 2f);
 995     fc = fr.getFeatureStyle("type4");
 996     assertTrue(fc.isColourByLabel());
 997     assertTrue(fc.isColourByAttribute());
 998     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 999     fc = fr.getFeatureStyle("type5");
1000     assertTrue(fc.isGraduatedColour());
1001     assertTrue(fc.isColourByAttribute());
1002     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
1003     assertTrue(fc.isBelowThreshold());
1004     assertEquals(fc.getThreshold(), 3f);
1005
1006     assertEquals(fr.getFeatureFilter("type1").toStableString(),
1007             "Label Contains x");
1008     assertEquals(fr.getFeatureFilter("type2").toStableString(),
1009             "(Score LE 2.4) AND (Score GT 1.1)");
1010     assertEquals(fr.getFeatureFilter("type3").toStableString(),
1011             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
1012   }
1013
1014   private void addFeature(SequenceI seq, String featureType, int score)
1015   {
1016     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
1017             score, "grp");
1018     sf.setValue("AF", score);
1019     sf.setValue("CSQ", new HashMap<String, String>()
1020     {
1021       {
1022         put("PolyPhen", Integer.toString(score));
1023       }
1024     });
1025     seq.addSequenceFeature(sf);
1026   }
1027
1028   /**
1029    * Adds two features of the given type to the given sequence, also setting the
1030    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
1031    *
1032    * @param seq
1033    * @param featureType
1034    * @param score
1035    */
1036   private void addFeatures(SequenceI seq, String featureType, int score)
1037   {
1038     addFeature(seq, featureType, score++);
1039     addFeature(seq, featureType, score);
1040   }
1041 }