X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=924dd37c2c266d1ed433130f74f88a3ff048b907;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3a695959babe15fdc42d0e874e5b52613a27a9dc;hpb=115b633239d47d2158d8e0fd1803fc0c2a15c676;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 3a69595..924dd37 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -1,15 +1,46 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.junit.Assert.*; +import static org.testng.AssertJUnit.assertTrue; + +import jalview.api.AlignmentViewPanel; +import jalview.api.ViewStyleI; +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; +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 java.io.File; -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; public class Jalview2xmlTests { @@ -17,10 +48,11 @@ public class Jalview2xmlTests /** * @throws java.lang.Exception */ - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"}); + jalview.bin.Jalview.main(new String[] { "-props", + "test/jalview/io/testProps.jvprops" }); } /** @@ -29,12 +61,15 @@ public class Jalview2xmlTests @AfterClass public static void tearDownAfterClass() throws Exception { - jalview.gui.Desktop.instance.quit(); + jalview.gui.Desktop.instance.closeAll_actionPerformed(null); + } + public int countDsAnn(jalview.viewmodel.AlignmentViewport avp) { - int numdsann=0; - for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) { + int numdsann = 0; + for (SequenceI sq : avp.getAlignment().getDataset().getSequences()) + { if (sq.getAnnotation() != null) { for (AlignmentAnnotation dssa : sq.getAnnotation()) @@ -48,35 +83,52 @@ public class Jalview2xmlTests } return numdsann; } - @Test + + @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); + 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")); + 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); + 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 + + @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); + 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() @@ -88,12 +140,276 @@ public class Jalview2xmlTests jalview.schemes.ColourSchemeProperty.getColourName(af .getViewport().getGlobalColourScheme())) != null); - assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview")); + 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); - 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."); + 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 + { + Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("ADD_SS_ANN", + Boolean.TRUE.toString()); + 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 - currently this is disabled + * since the Desktop.explodeViews method doesn't seem to result in the views + * being expanded to distinct align frames when executed programmatically. + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = false) + public void testStoreAndRecoverExpandedviews() 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); + String afid = af.getViewport().getSequenceSetId(); + { + final AlignFrame xaf = af; + af = null; + new Thread(new Runnable() + { + @Override + public void run() + { + Desktop.instance.explodeViews(xaf); + } + }).start(); + Thread.sleep(1000); + } + // int times = 0; + // while (++times < 5 && Desktop.getAlignFrames().length < ) + // { + // Thread.sleep(300); + // } + 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); } + }