X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=e1bc3ae362bb048e2da0d233acf6ecae0f924b24;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=3c634fd5b8d14fb52b6485a97b7d52c2e5e25378;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 3c634fd..e1bc3ae 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -20,12 +20,20 @@ */ package jalview.io; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; @@ -33,8 +41,16 @@ import jalview.gui.Desktop; import jalview.gui.Jalview2XML; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; +import jalview.structure.StructureImportSettings; +import jalview.viewmodel.AlignmentViewport; import java.io.File; +import java.time.Instant; +import java.util.ArrayList; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import org.testng.Assert; import org.testng.AssertJUnit; @@ -42,6 +58,7 @@ import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +@Test(singleThreaded = true) public class Jalview2xmlTests { @@ -53,19 +70,21 @@ public class Jalview2xmlTests { jalview.bin.Jalview.main(new String[] { "-props", "test/jalview/io/testProps.jvprops" }); + jalview.bin.Cache.setProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", + Cache.date_format.format(Date.from(Instant.now().plusSeconds( + 3600)))); } /** * @throws java.lang.Exception */ - @AfterClass + @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()) @@ -257,10 +276,11 @@ public class Jalview2xmlTests @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()); + // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER + // StructureImportSettings + // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER); + StructureImportSettings.setProcessSecondaryStructure(true); + StructureImportSettings.setVisibleChainAnnotation(true); AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); assertTrue("Didn't read in the example file correctly.", af != null); @@ -351,37 +371,29 @@ public class Jalview2xmlTests } /** - * 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. + * test store and recovery of expanded views * * @throws Exception */ - @Test(groups = { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = true) public void testStoreAndRecoverExpandedviews() throws Exception { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); assertTrue("Didn't read in the example file correctly.", af != null); + Assert.assertEquals(Desktop.getAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); - { - 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); - // } + + // check FileLoader returned a reference to the one alignFrame that is + // actually on the Desktop + assertTrue( + "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window", + af == Desktop.getAlignFrameFor(af.getViewport())); + + Desktop.explodeViews(af); + int oldviews = Desktop.getAlignFrames().length; Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels(afid).length); @@ -412,4 +424,258 @@ public class Jalview2xmlTests Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); } + /** + * Test save and reload of a project with a different representative sequence + * in each view. + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverReferenceSeqSettings() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + assertTrue("Didn't read in the example file correctly.", af != null); + String afid = af.getViewport().getSequenceSetId(); + + // remember reference sequence for each panel + Map refseqs = new HashMap(); + + /* + * mark sequence 2, 3, 4.. in panels 1, 2, 3... + * as reference sequence for itself and the preceding sequence + */ + int n = 1; + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + int repIndex = n % alignment.getHeight(); + SequenceI rep = alignment.getSequenceAt(repIndex); + refseqs.put(ap.getViewName(), rep); + + // code from mark/unmark sequence as reference in jalview.gui.PopupMenu + // todo refactor this to an alignment view controller + av.setDisplayReferenceSeq(true); + av.setColourByReferenceSeq(true); + av.getAlignment().setSeqrep(rep); + + n++; + } + File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the expanded view state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + + af = new FileLoader().LoadFileWaitTillLoaded( + tfile.getAbsolutePath(), FormatAdapter.FILE); + afid = af.getViewport().getSequenceSetId(); + + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + // check representative + AlignmentI alignment = ap.getAlignment(); + SequenceI rep = alignment.getSeqrep(); + Assert.assertNotNull(rep, + "Couldn't restore sequence representative from project"); + // can't use a strong equals here, because by definition, the sequence IDs + // will be different. + // could set vamsas session save/restore flag to preserve IDs across + // load/saves. + Assert.assertEquals(refseqs.get(ap.getViewName()).toString(), + rep.toString(), + "Representative wasn't the same when recovered."); + Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(), + "Display reference sequence view setting not set."); + Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(), + "Colour By Reference Seq view setting not set."); + } + } + + @Test(groups = { "Functional" }) + public void testIsVersionStringLaterThan() + { + /* + * No version / development / test / autobuild is leniently assumed to be + * compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan(null, null)); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null)); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "DEVELOPMENT BUILD")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); + assertTrue(Jalview2XML + .isVersionStringLaterThan(null, "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "AUTOMATED BUILD")); + + /* + * same version returns true i.e. compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1")); + + /* + * later version returns true + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1")); + + /* + * earlier version returns false + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + } + + /** + * Test save and reload of a project with a different sequence group (and + * representative sequence) in each view. + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverGroupRepSeqs() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", FormatAdapter.FILE); + assertTrue("Didn't read in the example file correctly.", af != null); + String afid = af.getViewport().getSequenceSetId(); + // make a second view of the alignment + af.newView_actionPerformed(null); + + /* + * remember representative and hidden sequences marked + * on each panel + */ + Map repSeqs = new HashMap(); + Map> hiddenSeqNames = new HashMap>(); + + /* + * mark sequence 2, 3, 4.. in panels 1, 2, 3... + * as reference sequence for itself and the preceding sequence + */ + int n = 1; + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + int repIndex = n % alignment.getHeight(); + // ensure at least one preceding sequence i.e. index >= 1 + repIndex = Math.max(repIndex, 1); + SequenceI repSeq = alignment.getSequenceAt(repIndex); + repSeqs.put(ap.getViewName(), repSeq); + List hiddenNames = new ArrayList(); + hiddenSeqNames.put(ap.getViewName(), hiddenNames); + + /* + * have rep sequence represent itself and the one before it + * this hides the group (except for the rep seq) + */ + SequenceGroup sg = new SequenceGroup(); + sg.addSequence(repSeq, false); + SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1); + sg.addSequence(precedingSeq, false); + sg.setSeqrep(repSeq); + assertTrue(sg.getSequences().contains(repSeq)); + assertTrue(sg.getSequences().contains(precedingSeq)); + av.setSelectionGroup(sg); + assertSame(repSeq, sg.getSeqrep()); + + /* + * represent group with sequence adds to a map of hidden rep sequences + * (it does not create a group on the alignment) + */ + ((AlignmentViewport) av).hideSequences(repSeq, true); + assertSame(repSeq, sg.getSeqrep()); + assertTrue(sg.getSequences().contains(repSeq)); + assertTrue(sg.getSequences().contains(precedingSeq)); + assertTrue("alignment has groups", alignment.getGroups().isEmpty()); + Map hiddenRepSeqsMap = av.getHiddenRepSequences(); + assertNotNull(hiddenRepSeqsMap); + assertEquals(1, hiddenRepSeqsMap.size()); + assertSame(sg, hiddenRepSeqsMap.get(repSeq)); + assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq)); + assertFalse(alignment.getHiddenSequences().isHidden(repSeq)); + hiddenNames.add(precedingSeq.getName()); + + n++; + } + File tfile = File + .createTempFile("testStoreAndRecoverGroupReps", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the expanded view state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + + af = new FileLoader().LoadFileWaitTillLoaded( + tfile.getAbsolutePath(), FormatAdapter.FILE); + afid = af.getViewport().getSequenceSetId(); + + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + String viewName = ap.getViewName(); + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + List groups = alignment.getGroups(); + assertNotNull(groups); + assertTrue("Alignment has groups", groups.isEmpty()); + Map hiddenRepSeqsMap = av + .getHiddenRepSequences(); + assertNotNull("No hidden represented sequences", hiddenRepSeqsMap); + assertEquals(1, hiddenRepSeqsMap.size()); + assertEquals(repSeqs.get(viewName).getDisplayId(true), + hiddenRepSeqsMap.keySet().iterator().next() + .getDisplayId(true)); + + /* + * verify hidden sequences in restored panel + */ + List hidden = hiddenSeqNames.get(ap.getViewName()); + HiddenSequences hs = alignment.getHiddenSequences(); + assertEquals( + "wrong number of restored hidden sequences in " + + ap.getViewName(), + hidden.size(), hs.getSize()); + } + } }