+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
-import static org.junit.Assert.*;
+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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.viewmodel.AlignmentViewport;
import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
-public class Jalview2xmlTests
+@Test(singleThreaded = true)
+public class Jalview2xmlTests extends Jalview2xmlBase
{
- /**
- * @throws java.lang.Exception
- */
- @BeforeClass
- public static void setUpBeforeClass() throws Exception
+ @Test(groups = { "Functional" })
+ public void testRNAStructureRecovery() throws Exception
{
- jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+ String inFile = "examples/RF00031_folded.stk";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ FormatAdapter.FILE);
+ assertNotNull("Didn't read input file " + inFile, af);
+ 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 FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+ assertNotNull("Failed to import new project", af);
+ 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);
}
- /**
- * @throws java.lang.Exception
- */
- @AfterClass
- public static void tearDownAfterClass() throws Exception
+ @Test(groups = { "Functional" })
+ public void testTCoffeeScores() throws Exception
{
- jalview.gui.Desktop.instance.quit();
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ FormatAdapter.FILE);
+ assertNotNull("Didn't read input file " + inFile, af);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ assertSame("Didn't set T-coffee colourscheme", af.getViewport()
+ .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
+ assertNotNull("Recognise T-Coffee score from string",
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
+ .getAlignment(), ColourSchemeProperty.getColourName(af
+ .getViewport().getGlobalColourScheme())));
+
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+ assertNotNull("Failed to import new project", af);
+ assertSame("Didn't set T-coffee colourscheme for imported project.", af
+ .getViewport().getGlobalColourScheme().getClass(),
+ TCoffeeColourScheme.class);
+ System.out
+ .println("T-Coffee score shading successfully recovered from project.");
}
- public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+
+ @Test(groups = { "Functional" })
+ public void testColourByAnnotScores() throws Exception
{
- int numdsann=0;
- for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
- if (sq.getAnnotation() != null)
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ FormatAdapter.FILE);
+ assertNotNull("Didn't read input file " + inFile, af);
+ 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 AnnotationColourGradient(aa[0], null,
+ AnnotationColourGradient.ABOVE_THRESHOLD);
+ AnnotationColourGradient gcs = new 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 FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+ assertNotNull("Failed to import new project", af);
+
+ // check for group and alignment colourschemes
+
+ ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+ ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+ .get(0).cs;
+ assertNotNull("Didn't recover global colourscheme", _rcs);
+ 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]))
{
- for (AlignmentAnnotation dssa : sq.getAnnotation())
+ diffseqcols = true;
+ }
+ }
+ assertTrue("Got Different sequence colours", diffseqcols);
+ System.out
+ .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+ assertNotNull("Didn't recover group colourscheme", _rgcs);
+ 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 FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ assertTrue("Didn't gather the views in the example file.",
+ Desktop.getAlignFrames().length == 1 + origCount);
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void viewRefPdbAnnotation() throws Exception
+ {
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ AlignmentViewPanel sps = null;
+ for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+ {
+ if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ {
+ sps = ap;
+ break;
+ }
+ }
+ assertNotNull("Couldn't find the structure view", sps);
+ AlignmentAnnotation refan = null;
+ for (AlignmentAnnotation ra : sps.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ra.graph != 0)
+ {
+ refan = ra;
+ break;
+ }
+ }
+ assertNotNull("Annotation secondary structure not found.", refan);
+ SequenceI sq = sps.getAlignment().findName("1A70|");
+ assertNotNull("Couldn't find 1a70 null chain", sq);
+ // compare the manually added temperature factor annotation
+ // to the track automatically transferred from the pdb structure on load
+ assertNotNull("1a70 has no annotation", sq.getDatasetSequence()
+ .getAnnotation());
+ 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++)
{
- if (dssa.isValidStruc())
+ sq.findPosition(p);
+ try
{
- numdsann++;
+ 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]);
}
}
}
}
- return numdsann;
+
}
- @Test
- public void testRNAStructureRecovery() throws Exception
+
+ @Test(groups = { "Functional" })
+ public void testCopyViewSettings() 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);
- 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+")");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ 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;
+ }
+ }
+ assertNotNull("Couldn't find the structure view", sps);
+ assertNotNull("Couldn't find the MAFFT view", groups);
+
+ 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
- public void testTCoffeeScores() throws Exception
+
+ /**
+ * test store and recovery of expanded views
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverExpandedviews() 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));
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ 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(
- "Recognise T-Coffee score from string",
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(),
- jalview.schemes.ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())) != null);
+ "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+ af == Desktop.getAlignFrameFor(af.getViewport()));
- 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.");
+ 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 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);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ String afid = af.getViewport().getSequenceSetId();
+
+ // remember reference sequence for each panel
+ Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+
+ /*
+ * 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);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ 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<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+
+ /*
+ * 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<String> hiddenNames = new ArrayList<String>();
+ 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<SequenceI, SequenceCollectionI> 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<SequenceGroup> groups = alignment.getGroups();
+ assertNotNull(groups);
+ assertTrue("Alignment has groups", groups.isEmpty());
+ Map<SequenceI, SequenceCollectionI> 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<String> hidden = hiddenSeqNames.get(ap.getViewName());
+ HiddenSequences hs = alignment.getHiddenSequences();
+ assertEquals(
+ "wrong number of restored hidden sequences in "
+ + ap.getViewName(), hidden.size(), hs.getSize());
+ }
+ }
+
+ /**
+ * Test save and reload of PDBEntry in Jalview project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverPDBEntry() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String exampleFile = "examples/3W5V.pdb";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ FormatAdapter.FILE);
+ assertNotNull("Didn't read in the example file correctly.", af);
+ String afid = af.getViewport().getSequenceSetId();
+
+ AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+ System.out.println();
+ AlignmentViewPanel ap = alignPanels[0];
+ String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+ String testFile = tfileBase + exampleFile;
+ AlignmentI alignment = ap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] seqs = alignment.getSequencesArray();
+ Assert.assertNotNull(seqs[0]);
+ Assert.assertNotNull(seqs[1]);
+ Assert.assertNotNull(seqs[2]);
+ Assert.assertNotNull(seqs[3]);
+ Assert.assertNotNull(seqs[0].getDatasetSequence());
+ Assert.assertNotNull(seqs[1].getDatasetSequence());
+ Assert.assertNotNull(seqs[2].getDatasetSequence());
+ Assert.assertNotNull(seqs[3].getDatasetSequence());
+ PDBEntry[] pdbEntries = new PDBEntry[4];
+ pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
+ pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
+ pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
+ pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
+ Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[0]);
+ Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[1]);
+ Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[2]);
+ Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0), pdbEntries[3]);
+
+ File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ String rfid = restoredFrame.getViewport().getSequenceSetId();
+ AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+ AlignmentViewPanel rap = rAlignPanels[0];
+ AlignmentI rAlignment = rap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] rseqs = rAlignment.getSequencesArray();
+ Assert.assertNotNull(rseqs[0]);
+ Assert.assertNotNull(rseqs[1]);
+ Assert.assertNotNull(rseqs[2]);
+ Assert.assertNotNull(rseqs[3]);
+ Assert.assertNotNull(rseqs[0].getDatasetSequence());
+ Assert.assertNotNull(rseqs[1].getDatasetSequence());
+ Assert.assertNotNull(rseqs[2].getDatasetSequence());
+ Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+ // The Asserts below are expected to fail until the PDB chainCode is
+ // recoverable from a Jalview projects
+ for (int chain = 0; chain < 4; chain++)
+ {
+ PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
+ .get(0);
+ PDBEntry expected = pdbEntries[chain];
+ Assert.assertEquals(recov.getId(), expected.getId(),
+ "Mismatch PDB ID");
+ Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
+ "Mismatch PDB ID");
+ Assert.assertEquals(recov.getType(), expected.getType(),
+ "Mismatch PDBEntry 'Type'");
+ Assert.assertNotNull(recov.getFile(),
+ "Recovered PDBEntry should have a non-null file entry");
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff