/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureImportSettings;
import jalview.viewmodel.AlignmentViewport;
import java.io.File;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class Jalview2xmlTests
{
/**
* @throws java.lang.Exception
*/
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
jalview.bin.Jalview.main(new String[] { "-props",
"test/jalview/io/testProps.jvprops" });
jalview.bin.Cache.setProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
Cache.date_format.format(Date.from(Instant.now().plusSeconds(
3600))));
}
/**
* @throws java.lang.Exception
*/
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
}
int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
int numdsann = 0;
for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
{
if (sq.getAnnotation() != null)
{
for (AlignmentAnnotation dssa : sq.getAnnotation())
{
if (dssa.isValidStruc())
{
numdsann++;
}
}
}
}
return numdsann;
}
@Test(groups = { "Functional" })
public void testRNAStructureRecovery() throws Exception
{
String inFile = "examples/RF00031_folded.stk";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
af.rnahelicesColour_actionPerformed(null);
assertTrue(
"Couldn't apply RNA helices colourscheme",
af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, "Jalview"));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
FormatAdapter.FILE);
assertTrue("Failed to import new project", af != null);
int newdsann = countDsAnn(af.getViewport());
assertTrue(
"Differing numbers of dataset sequence annotation\nOriginally "
+ olddsann + " and now " + newdsann,
olddsann == newdsann);
System.out
.println("Read in same number of annotations as originally present ("
+ olddsann + ")");
assertTrue(
"RNA helices colourscheme was not applied on import.",
af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
}
@Test(groups = { "Functional" })
public void testTCoffeeScores() throws Exception
{
String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
assertTrue(
"Didn't set T-coffee colourscheme",
af.getViewport().getGlobalColourScheme().getClass()
.equals(jalview.schemes.TCoffeeColourScheme.class));
assertTrue(
"Recognise T-Coffee score from string",
jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
.getAlignment(),
jalview.schemes.ColourSchemeProperty.getColourName(af
.getViewport().getGlobalColourScheme())) != null);
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, "Jalview"));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
FormatAdapter.FILE);
assertTrue("Failed to import new project", af != null);
assertTrue(
"Didn't set T-coffee colourscheme for imported project.",
af.getViewport().getGlobalColourScheme().getClass()
.equals(jalview.schemes.TCoffeeColourScheme.class));
System.out
.println("T-Coffee score shading successfully recovered from project.");
}
@Test(groups = { "Functional" })
public void testColourByAnnotScores() throws Exception
{
String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
AlignmentAnnotation[] aa = af.getViewport().getAlignment()
.getSequenceAt(0).getAnnotation("IUPredWS (Short)");
assertTrue(
"Didn't find any IUPred annotation to use to shade alignment.",
aa != null && aa.length > 0);
AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
cs.setSeqAssociated(true);
gcs.setSeqAssociated(true);
af.changeColour(cs);
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(57);
sg.setEndRes(92);
sg.cs = gcs;
af.getViewport().getAlignment().addGroup(sg);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, "Jalview"));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
FormatAdapter.FILE);
assertTrue("Failed to import new project", af != null);
// check for group and alignment colourschemes
ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
.get(0).cs;
assertTrue("Didn't recover global colourscheme", _rcs != null);
assertTrue("Didn't recover annotation colour global scheme",
_rcs instanceof AnnotationColourGradient);
AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
assertTrue("Annotation colourscheme wasn't sequence associated",
__rcs.isSeqAssociated());
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5]))
{
diffseqcols = true;
}
}
assertTrue("Got Different sequence colours", diffseqcols);
System.out
.println("Per sequence colourscheme (Background) successfully applied and recovered.");
assertTrue("Didn't recover group colourscheme", _rgcs != null);
assertTrue("Didn't recover annotation colour group colourscheme",
_rgcs instanceof AnnotationColourGradient);
__rcs = (AnnotationColourGradient) _rgcs;
assertTrue("Group Annotation colourscheme wasn't sequence associated",
__rcs.isSeqAssociated());
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
.findColour(sqs[2].getCharAt(p), p, sqs[2]))
{
diffgseqcols = true;
}
}
assertTrue("Got Different group sequence colours", diffgseqcols);
System.out
.println("Per sequence (Group) colourscheme successfully applied and recovered.");
}
@Test(groups = { "Functional" })
public void gatherViewsHere() throws Exception
{
int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
.getAlignFrames().length;
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
assertTrue("Didn't gather the views in the example file.",
Desktop.getAlignFrames().length == 1 + origCount);
}
@Test(groups = { "Functional" })
public void viewRefPdbAnnotation() throws Exception
{
// TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
// StructureImportSettings
// .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
StructureImportSettings.setProcessSecondaryStructure(true);
StructureImportSettings.setVisibleChainAnnotation(true);
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
AlignmentViewPanel sps = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
{
if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
{
sps = ap;
break;
}
}
assertTrue("Couldn't find the structure view", sps != null);
SequenceI sq = sps.getAlignment().findName("1A70|");
AlignmentAnnotation refan = null;
for (AlignmentAnnotation ra : sps.getAlignment()
.getAlignmentAnnotation())
{
if (ra.graph != 0)
{
refan = ra;
break;
}
}
assertTrue("Annotation secondary structure not found.", refan != null);
assertTrue("Couldn't find 1a70 null chain", sq != null);
// compare the manually added temperature factor annotation
// to the track automatically transferred from the pdb structure on load
for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
{
AlignmentAnnotation alaa;
sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
alaa.adjustForAlignment();
if (ala.graph == refan.graph)
{
for (int p = 0; p < ala.annotations.length; p++)
{
sq.findPosition(p);
try
{
assertTrue(
"Mismatch at alignment position " + p,
(alaa.annotations[p] == null && refan.annotations[p] == null)
|| alaa.annotations[p].value == refan.annotations[p].value);
} catch (NullPointerException q)
{
Assert.fail("Mismatch of alignment annotations at position "
+ p + " Ref seq ann: " + refan.annotations[p]
+ " alignment " + alaa.annotations[p]);
}
}
}
}
}
@Test(groups = { "Functional" })
public void testCopyViewSettings() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
AlignmentViewPanel sps = null, groups = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
{
if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
{
sps = ap;
}
if (ap.getViewName().contains("MAFFT"))
{
groups = ap;
}
}
assertTrue("Couldn't find the structure view", sps != null);
assertTrue("Couldn't find the MAFFT view", groups != null);
ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
groups.getAlignViewport().setViewStyle(structureStyle);
AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
.getViewStyle()));
Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
.getViewStyle()));
}
/**
* test store and recovery of expanded views
*
* @throws Exception
*/
@Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
Assert.assertEquals(Desktop.getAlignFrames().length, 1);
String afid = af.getViewport().getSequenceSetId();
// check FileLoader returned a reference to the one alignFrame that is
// actually on the Desktop
assertTrue(
"Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
af == Desktop.getAlignFrameFor(af.getViewport()));
Desktop.explodeViews(af);
int oldviews = Desktop.getAlignFrames().length;
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(afid).length);
File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
} catch (Error e)
{
Assert.fail("Didn't save the expanded view state", e);
} catch (Exception e)
{
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
tfile.getAbsolutePath(), FormatAdapter.FILE);
Assert.assertNotNull(af);
Assert.assertEquals(
Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(
oldviews,
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
}
/**
* Test save and reload of a project with a different representative sequence
* in each view.
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testStoreAndRecoverReferenceSeqSettings() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
String afid = af.getViewport().getSequenceSetId();
// remember reference sequence for each panel
Map refseqs = new HashMap();
/*
* mark sequence 2, 3, 4.. in panels 1, 2, 3...
* as reference sequence for itself and the preceding sequence
*/
int n = 1;
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
{
AlignViewportI av = ap.getAlignViewport();
AlignmentI alignment = ap.getAlignment();
int repIndex = n % alignment.getHeight();
SequenceI rep = alignment.getSequenceAt(repIndex);
refseqs.put(ap.getViewName(), rep);
// code from mark/unmark sequence as reference in jalview.gui.PopupMenu
// todo refactor this to an alignment view controller
av.setDisplayReferenceSeq(true);
av.setColourByReferenceSeq(true);
av.getAlignment().setSeqrep(rep);
n++;
}
File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
} catch (Throwable e)
{
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(
tfile.getAbsolutePath(), FormatAdapter.FILE);
afid = af.getViewport().getSequenceSetId();
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
{
// check representative
AlignmentI alignment = ap.getAlignment();
SequenceI rep = alignment.getSeqrep();
Assert.assertNotNull(rep,
"Couldn't restore sequence representative from project");
// can't use a strong equals here, because by definition, the sequence IDs
// will be different.
// could set vamsas session save/restore flag to preserve IDs across
// load/saves.
Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
rep.toString(),
"Representative wasn't the same when recovered.");
Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
"Display reference sequence view setting not set.");
Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
"Colour By Reference Seq view setting not set.");
}
}
@Test(groups = { "Functional" })
public void testIsVersionStringLaterThan()
{
/*
* No version / development / test / autobuild is leniently assumed to be
* compatible
*/
assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null,
"Development Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null,
"DEVELOPMENT BUILD"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
"Development Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
assertTrue(Jalview2XML
.isVersionStringLaterThan(null, "Automated Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
"Automated Build"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
"AUTOMATED BUILD"));
/*
* same version returns true i.e. compatible
*/
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
/*
* later version returns true
*/
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
/*
* earlier version returns false
*/
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
}
/**
* Test save and reload of a project with a different sequence group (and
* representative sequence) in each view.
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testStoreAndRecoverGroupRepSeqs() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", FormatAdapter.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
String afid = af.getViewport().getSequenceSetId();
// make a second view of the alignment
af.newView_actionPerformed(null);
/*
* remember representative and hidden sequences marked
* on each panel
*/
Map repSeqs = new HashMap();
Map> hiddenSeqNames = new HashMap>();
/*
* mark sequence 2, 3, 4.. in panels 1, 2, 3...
* as reference sequence for itself and the preceding sequence
*/
int n = 1;
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
{
AlignViewportI av = ap.getAlignViewport();
AlignmentI alignment = ap.getAlignment();
int repIndex = n % alignment.getHeight();
// ensure at least one preceding sequence i.e. index >= 1
repIndex = Math.max(repIndex, 1);
SequenceI repSeq = alignment.getSequenceAt(repIndex);
repSeqs.put(ap.getViewName(), repSeq);
List hiddenNames = new ArrayList();
hiddenSeqNames.put(ap.getViewName(), hiddenNames);
/*
* have rep sequence represent itself and the one before it
* this hides the group (except for the rep seq)
*/
SequenceGroup sg = new SequenceGroup();
sg.addSequence(repSeq, false);
SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
sg.addSequence(precedingSeq, false);
sg.setSeqrep(repSeq);
assertTrue(sg.getSequences().contains(repSeq));
assertTrue(sg.getSequences().contains(precedingSeq));
av.setSelectionGroup(sg);
assertSame(repSeq, sg.getSeqrep());
/*
* represent group with sequence adds to a map of hidden rep sequences
* (it does not create a group on the alignment)
*/
((AlignmentViewport) av).hideSequences(repSeq, true);
assertSame(repSeq, sg.getSeqrep());
assertTrue(sg.getSequences().contains(repSeq));
assertTrue(sg.getSequences().contains(precedingSeq));
assertTrue("alignment has groups", alignment.getGroups().isEmpty());
Map hiddenRepSeqsMap = av.getHiddenRepSequences();
assertNotNull(hiddenRepSeqsMap);
assertEquals(1, hiddenRepSeqsMap.size());
assertSame(sg, hiddenRepSeqsMap.get(repSeq));
assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
hiddenNames.add(precedingSeq.getName());
n++;
}
File tfile = File
.createTempFile("testStoreAndRecoverGroupReps",
".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
} catch (Throwable e)
{
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(
tfile.getAbsolutePath(), FormatAdapter.FILE);
afid = af.getViewport().getSequenceSetId();
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
{
String viewName = ap.getViewName();
AlignViewportI av = ap.getAlignViewport();
AlignmentI alignment = ap.getAlignment();
List groups = alignment.getGroups();
assertNotNull(groups);
assertTrue("Alignment has groups", groups.isEmpty());
Map hiddenRepSeqsMap = av
.getHiddenRepSequences();
assertNotNull("No hidden represented sequences", hiddenRepSeqsMap);
assertEquals(1, hiddenRepSeqsMap.size());
assertEquals(repSeqs.get(viewName).getDisplayId(true),
hiddenRepSeqsMap.keySet().iterator().next()
.getDisplayId(true));
/*
* verify hidden sequences in restored panel
*/
List hidden = hiddenSeqNames.get(ap.getViewName());
HiddenSequences hs = alignment.getHiddenSequences();
assertEquals(
"wrong number of restored hidden sequences in "
+ ap.getViewName(),
hidden.size(), hs.getSize());
}
}
}