X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=3281db198ec1c814f4d6c25701f0a79e170d09af;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=75626e963b2bbdc96fe878093a190d70316c7dea;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 75626e9..3281db1 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,47 +20,65 @@ */ package jalview.io; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; +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.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.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; +@Test(singleThreaded = true) 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/jalview/io/testProps.jvprops" }); + jalview.bin.Jalview.main(new String[] { "-props", + "test/jalview/io/testProps.jvprops" }); } /** * @throws java.lang.Exception */ - @AfterClass + @AfterClass(alwaysRun = true) public static void tearDownAfterClass() throws Exception { jalview.gui.Desktop.instance.closeAll_actionPerformed(null); - } - public int countDsAnn(jalview.viewmodel.AlignmentViewport avp) + int countDsAnn(jalview.viewmodel.AlignmentViewport avp) { int numdsann = 0; for (SequenceI sq : avp.getAlignment().getDataset().getSequences()) @@ -79,14 +97,14 @@ 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); + inFile, DataSourceType.FILE); assertTrue("Didn't read input file " + inFile, af != null); int olddsann = countDsAnn(af.getViewport()); assertTrue("Didn't find any dataset annotations", olddsann > 0); @@ -95,11 +113,11 @@ public class Jalview2xmlTests "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.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); + DataSourceType.FILE); assertTrue("Failed to import new project", af != null); int newdsann = countDsAnn(af.getViewport()); assertTrue( @@ -114,16 +132,16 @@ public class Jalview2xmlTests 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); + inFile, DataSourceType.FILE); assertTrue("Didn't read input file " + inFile, af != null); - af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); assertTrue( "Didn't set T-coffee colourscheme", af.getViewport().getGlobalColourScheme().getClass() @@ -136,11 +154,11 @@ public class Jalview2xmlTests .getViewport().getGlobalColourScheme())) != null); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); + DataSourceType.FILE); assertTrue("Failed to import new project", af != null); assertTrue( "Didn't set T-coffee colourscheme for imported project.", @@ -150,16 +168,16 @@ public class Jalview2xmlTests .println("T-Coffee score shading successfully recovered from project."); } - @Test + @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); + inFile, DataSourceType.FILE); assertTrue("Didn't read input file " + inFile, af != null); - af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); AlignmentAnnotation[] aa = af.getViewport().getAlignment() .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); assertTrue( @@ -181,11 +199,11 @@ public class Jalview2xmlTests sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); + DataSourceType.FILE); assertTrue("Failed to import new project", af != null); // check for group and alignment colourschemes @@ -236,24 +254,28 @@ public class Jalview2xmlTests .println("Per sequence (Group) colourscheme successfully applied and recovered."); } - @Test + @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { - int origCount = Desktop.getAlignframes() == null ? 0 : Desktop - .getAlignframes().length; + int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop + .getAlignFrames().length; AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.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); + Desktop.getAlignFrames().length == 1 + origCount); } - @Test + @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); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); assertTrue("Didn't read in the example file correctly.", af != null); AlignmentViewPanel sps = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) @@ -267,7 +289,8 @@ public class Jalview2xmlTests assertTrue("Couldn't find the structure view", sps != null); SequenceI sq = sps.getAlignment().findName("1A70|"); AlignmentAnnotation refan = null; - for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation()) + for (AlignmentAnnotation ra : sps.getAlignment() + .getAlignmentAnnotation()) { if (ra.graph != 0) { @@ -275,7 +298,7 @@ public class Jalview2xmlTests break; } } - assertTrue("Annotation secondary structure not found.",refan!=null); + 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 @@ -289,21 +312,371 @@ public class Jalview2xmlTests for (int p = 0; p < ala.annotations.length; p++) { sq.findPosition(p); - try { + try + { assertTrue( "Mismatch at alignment position " + p, - (alaa.annotations[p] == null && refan.annotations[p] == null) + (alaa.annotations[p] == null && refan.annotations[p] == null) || alaa.annotations[p].value == refan.annotations[p].value); - } - catch (NullPointerException q) + } catch (NullPointerException q) { - fail("Mismatch of alignment annotations at position " + p - + " Ref seq ann: " + refan.annotations[p] + 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", DataSourceType.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 = true) + public void testStoreAndRecoverExpandedviews() throws Exception + { + AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.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(), DataSourceType.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", DataSourceType.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(), 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); + 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(), 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 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()); } - } }