+++ /dev/null
-/*
- * 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.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertSame;
-import static org.testng.Assert.assertTrue;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureColourI;
-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.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcher;
-import jalview.datamodel.features.FeatureMatcherSet;
-import jalview.datamodel.features.FeatureMatcherSetI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.Jalview2XML;
-import jalview.gui.JvOptionPane;
-import jalview.gui.PopupMenu;
-import jalview.gui.SliderPanel;
-import jalview.renderer.ResidueShaderI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.FeatureColour;
-import jalview.schemes.JalviewColourScheme;
-import jalview.schemes.RNAHelicesColour;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.util.matcher.Condition;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-@Test(singleThreaded = true)
-public class Jalview2xmlTests extends Jalview2xmlBase
-{
-
- @Override
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testRNAStructureRecovery() throws Exception
- {
- String inFile = "examples/RF00031_folded.stk";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read input file " + inFile);
- int olddsann = countDsAnn(af.getViewport());
- assertTrue(olddsann > 0, "Didn't find any dataset annotations");
- af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
- .toString());
- assertTrue(
- af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
- "Couldn't apply RNA helices colourscheme");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
- "Failed to store as a project.");
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
- assertNotNull(af, "Failed to import new project");
- int newdsann = countDsAnn(af.getViewport());
- assertEquals(olddsann, newdsann,
- "Differing numbers of dataset sequence annotation\nOriginally "
- + olddsann + " and now " + newdsann);
- System.out
- .println("Read in same number of annotations as originally present ("
- + olddsann + ")");
- assertTrue(
-
- af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour,
- "RNA helices colourscheme was not applied on import.");
- }
-
- @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 FileLoader().LoadFileWaitTillLoaded(inFile,
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read input file " + inFile);
- af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
- TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
- assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport()
- .getAlignment(), af.getViewport().getGlobalColourScheme()
- .getSchemeName()), "Recognise T-Coffee score from string");
-
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
- "Failed to store as a project.");
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
- assertNotNull(af, "Failed to import new project");
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
- TCoffeeColourScheme.class,
- "Didn't set T-coffee colourscheme for imported project.");
- 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 FileLoader().LoadFileWaitTillLoaded(inFile,
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read input file " + inFile);
- af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- AlignmentAnnotation[] aa = af.getViewport().getAlignment()
- .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
- assertTrue(
-
- aa != null && aa.length > 0,
- "Didn't find any IUPred annotation to use to shade alignment.");
- 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.setColourScheme(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(af.saveAlignment(tfile, FileFormat.Jalview),
- "Failed to store as a project.");
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
- assertNotNull(af, "Failed to import new project");
-
- // check for group and alignment colourschemes
-
- ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
- ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
- .get(0).getColourScheme();
- assertNotNull(_rcs, "Didn't recover global colourscheme");
- assertTrue(_rcs instanceof AnnotationColourGradient,
- "Didn't recover annotation colour global scheme");
- AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
- assertTrue(__rcs.isSeqAssociated(),
- "Annotation colourscheme wasn't sequence associated");
-
- 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], null, 0f) != _rcs
- .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
- {
- diffseqcols = true;
- }
- }
- assertTrue(diffseqcols, "Got Different sequence colours");
- System.out
- .println("Per sequence colourscheme (Background) successfully applied and recovered.");
-
- assertNotNull(_rgcs, "Didn't recover group colourscheme");
- assertTrue(_rgcs instanceof AnnotationColourGradient,
- "Didn't recover annotation colour group colourscheme");
- __rcs = (AnnotationColourGradient) _rgcs;
- assertTrue(__rcs.isSeqAssociated(),
- "Group Annotation colourscheme wasn't sequence associated");
-
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
- {
- if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
- .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
- {
- diffgseqcols = true;
- }
- }
- assertTrue(diffgseqcols, "Got Different group sequence colours");
- 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", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
- "Didn't gather the views in the example file.");
-
- }
-
- /**
- * Test for JAL-2223 - multiple mappings in View Mapping report
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void noDuplicatePdbMappingsMade() throws Exception
- {
- StructureImportSettings.setProcessSecondaryStructure(true);
- StructureImportSettings.setVisibleChainAnnotation(true);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
-
- // locate Jmol viewer
- // count number of PDB mappings the structure selection manager holds -
- String pdbFile = af.getCurrentView().getStructureSelectionManager()
- .findFileForPDBId("1A70");
- assertEquals(
- af.getCurrentView().getStructureSelectionManager()
- .getMapping(pdbFile).length,
- 2, "Expected only two mappings for 1A70");
-
- }
-
- @Test(groups = { "Functional" })
- public void viewRefPdbAnnotation() throws Exception
- {
- StructureImportSettings.setProcessSecondaryStructure(true);
- StructureImportSettings.setVisibleChainAnnotation(true);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- AlignmentViewPanel sps = null;
- for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
- {
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- break;
- }
- }
- assertNotNull(sps, "Couldn't find the structure view");
- AlignmentAnnotation refan = null;
- for (AlignmentAnnotation ra : sps.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ra.graph != 0)
- {
- refan = ra;
- break;
- }
- }
- assertNotNull(refan, "Annotation secondary structure not found.");
- SequenceI sq = sps.getAlignment().findName("1A70|");
- assertNotNull(sq, "Couldn't find 1a70 null chain");
- // compare the manually added temperature factor annotation
- // to the track automatically transferred from the pdb structure on load
- assertNotNull(sq.getDatasetSequence().getAnnotation(),
- "1a70 has no annotation");
- 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(
- (alaa.annotations[p] == null && refan.annotations[p] == null)
- || alaa.annotations[p].value == refan.annotations[p].value,
- "Mismatch at alignment position " + p);
- } 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 FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- 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(sps, "Couldn't find the structure view");
- assertNotNull(groups, "Couldn't find the MAFFT view");
-
- 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 FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", DataSourceType.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
- assertSame(
- af,
- Desktop.getAlignFrameFor(af.getViewport()),
- "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window");
-
- 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(),
- DataSourceType.FILE);
- Assert.assertNotNull(af);
- Assert.assertEquals(
- Desktop.getAlignFrames().length,
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
- oldviews);
- }
-
- /**
- * 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", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- String afid = af.getViewport().getSequenceSetId();
-
- // remember reference sequence for each panel
- Map<String, SequenceI> 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(),
- DataSourceType.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", DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- 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<>();
- Map<String, List<String>> 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<String> 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.getGroups().isEmpty(), "alignment has groups");
- 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(),
- DataSourceType.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(groups.isEmpty(), "Alignment has groups");
- Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
- .getHiddenRepSequences();
- assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences");
- 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(
- hidden.size(),
- hs.getSize(),
- "wrong number of restored hidden sequences in "
- + ap.getViewName());
- }
- }
-
- /**
- * 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,
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- 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(), DataSourceType.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");
- }
- }
-
- /**
- * Configure an alignment and a sub-group each with distinct colour schemes,
- * Conservation and PID thresholds, and confirm these are restored from the
- * saved project.
- *
- * @throws IOException
- */
- @Test(groups = { "Functional" })
- public void testStoreAndRecoverColourThresholds() throws IOException
- {
- Desktop.instance.closeAll_actionPerformed(null);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", DataSourceType.FILE);
-
- AlignViewport av = af.getViewport();
- AlignmentI al = av.getAlignment();
-
- /*
- * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
- */
- af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
- assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
- af.abovePIDThreshold_actionPerformed(true);
- SliderPanel sp = SliderPanel.getSliderPanel();
- assertFalse(sp.isForConservation());
- sp.valueChanged(10);
- af.conservationMenuItem_actionPerformed(true);
- sp = SliderPanel.getSliderPanel();
- assertTrue(sp.isForConservation());
- sp.valueChanged(20);
- ResidueShaderI rs = av.getResidueShading();
- assertEquals(rs.getThreshold(), 10);
- assertTrue(rs.conservationApplied());
- assertEquals(rs.getConservationInc(), 20);
-
- /*
- * create a group with Strand colouring, 30% Conservation
- * and 40% PID threshold
- */
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(al.getSequenceAt(0), false);
- sg.setStartRes(15);
- sg.setEndRes(25);
- av.setSelectionGroup(sg);
- PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
- popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
- .toString());
- assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
- assertEquals(al.getGroups().size(), 1);
- assertSame(al.getGroups().get(0), sg);
- popupMenu.conservationMenuItem_actionPerformed(true);
- sp = SliderPanel.getSliderPanel();
- assertTrue(sp.isForConservation());
- sp.valueChanged(30);
- popupMenu.abovePIDColour_actionPerformed(true);
- sp = SliderPanel.getSliderPanel();
- assertFalse(sp.isForConservation());
- sp.valueChanged(40);
- assertTrue(sg.getGroupColourScheme().conservationApplied());
- assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
- assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
-
- /*
- * save project, close windows, reload project, verify
- */
- File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
- ".jvp");
- tfile.deleteOnExit();
- new Jalview2XML(false).saveState(tfile);
- Desktop.instance.closeAll_actionPerformed(null);
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- DataSourceType.FILE);
- Assert.assertNotNull(af, "Failed to reload project");
-
- /*
- * verify alignment (background) colouring
- */
- rs = af.getViewport().getResidueShading();
- assertTrue(rs.getColourScheme() instanceof BuriedColourScheme);
- assertEquals(rs.getThreshold(), 10);
- assertTrue(rs.conservationApplied());
- assertEquals(rs.getConservationInc(), 20);
-
- /*
- * verify group colouring
- */
- assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1);
- rs = af.getViewport().getAlignment().getGroups().get(0)
- .getGroupColourScheme();
- assertTrue(rs.getColourScheme() instanceof StrandColourScheme);
- assertEquals(rs.getThreshold(), 40);
- assertTrue(rs.conservationApplied());
- assertEquals(rs.getConservationInc(), 30);
- }
-
- /**
- * Test save and reload of feature colour schemes and filter settings
- *
- * @throws IOException
- */
- @Test(groups = { "Functional" })
- public void testSaveLoadFeatureColoursAndFilters() throws IOException
- {
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
- SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
-
- /*
- * add some features to the sequence
- */
- int score = 1;
- addFeatures(seq1, "type1", score++);
- addFeatures(seq1, "type2", score++);
- addFeatures(seq1, "type3", score++);
- addFeatures(seq1, "type4", score++);
- addFeatures(seq1, "type5", score++);
-
- /*
- * set colour schemes for features
- */
- FeatureRenderer fr = af.getFeatureRenderer();
- fr.findAllFeatures(true);
-
- // type1: red
- fr.setColour("type1", new FeatureColour(Color.red));
-
- // type2: by label
- FeatureColourI byLabel = new FeatureColour();
- byLabel.setColourByLabel(true);
- fr.setColour("type2", byLabel);
-
- // type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
- byScore.setAboveThreshold(true);
- byScore.setThreshold(2f);
- fr.setColour("type3", byScore);
-
- // type4: by attribute AF
- FeatureColourI byAF = new FeatureColour();
- byAF.setColourByLabel(true);
- byAF.setAttributeName("AF");
- fr.setColour("type4", byAF);
-
- // type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
- byPolyPhen.setBelowThreshold(true);
- byPolyPhen.setThreshold(3f);
- byPolyPhen.setAttributeName("CSQ", "PolyPhen");
- fr.setColour("type5", byPolyPhen);
-
- /*
- * set filters for feature types
- */
-
- // filter type1 features by (label contains "x")
- FeatureMatcherSetI filterByX = new FeatureMatcherSet();
- filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
- fr.setFeatureFilter("type1", filterByX);
-
- // filter type2 features by (score <= 2.4 and score > 1.1)
- FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
- filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
- filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
- fr.setFeatureFilter("type2", filterByScore);
-
- // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
- FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
- filterByXY
- .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
- filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
- "PolyPhen"));
- fr.setFeatureFilter("type3", filterByXY);
-
- /*
- * save as Jalview project
- */
- File tfile = File.createTempFile("JalviewTest", ".jvp");
- tfile.deleteOnExit();
- String filePath = tfile.getAbsolutePath();
- assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
- "Failed to store as a project.");
-
- /*
- * close current alignment and load the saved project
- */
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new FileLoader()
- .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
- assertNotNull(af, "Failed to import new project");
-
- /*
- * verify restored feature colour schemes and filters
- */
- fr = af.getFeatureRenderer();
- FeatureColourI fc = fr.getFeatureStyle("type1");
- assertTrue(fc.isSimpleColour());
- assertEquals(fc.getColour(), Color.red);
- fc = fr.getFeatureStyle("type2");
- assertTrue(fc.isColourByLabel());
- fc = fr.getFeatureStyle("type3");
- assertTrue(fc.isGraduatedColour());
- assertNull(fc.getAttributeName());
- assertTrue(fc.isAboveThreshold());
- assertEquals(fc.getThreshold(), 2f);
- fc = fr.getFeatureStyle("type4");
- assertTrue(fc.isColourByLabel());
- assertTrue(fc.isColourByAttribute());
- assertEquals(fc.getAttributeName(), new String[] { "AF" });
- fc = fr.getFeatureStyle("type5");
- assertTrue(fc.isGraduatedColour());
- assertTrue(fc.isColourByAttribute());
- assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
- assertTrue(fc.isBelowThreshold());
- assertEquals(fc.getThreshold(), 3f);
-
- assertEquals(fr.getFeatureFilter("type1").toStableString(),
- "Label Contains x");
- assertEquals(fr.getFeatureFilter("type2").toStableString(),
- "(Score LE 2.4) AND (Score GT 1.1)");
- assertEquals(fr.getFeatureFilter("type3").toStableString(),
- "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
- }
-
- private void addFeature(SequenceI seq, String featureType, int score)
- {
- SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
- score, "grp");
- sf.setValue("AF", score);
- sf.setValue("CSQ", new HashMap<String, String>()
- {
- {
- put("PolyPhen", Integer.toString(score));
- }
- });
- seq.addSequenceFeature(sf);
- }
-
- /**
- * Adds two features of the given type to the given sequence, also setting the
- * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
- *
- * @param seq
- * @param featureType
- * @param score
- */
- private void addFeatures(SequenceI seq, String featureType, int score)
- {
- addFeature(seq, featureType, score++);
- addFeature(seq, featureType, score);
- }
-}
git://source.jalview.org / jalview.git / blobdiff