X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=47b8aeae5d1e768c80dc98847b39d77cfcc5d971;hb=ddc73338c0a046369b53151e8b3ebfba4d385df7;hp=1250748c853062c6f192d10508d956e708ed2e36;hpb=8aa94d348698138bb5c30715ef0aa15349f47fbb;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 1250748..47b8aea 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -34,7 +34,11 @@ import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; +import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.HiddenSequences; +import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceCollectionI; @@ -45,10 +49,8 @@ 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.JvOptionPane; import jalview.gui.PCAPanel; import jalview.gui.PopupMenu; @@ -68,8 +70,10 @@ import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.structure.StructureImportSettings; +import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.Color; import java.io.File; @@ -86,6 +90,8 @@ import org.testng.AssertJUnit; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import junit.extensions.PA; + @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase { @@ -147,7 +153,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase DataSourceType.FILE); assertNotNull(af, "Didn't read input file " + inFile); af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); - AlignViewport viewport = af.getViewport(); + AlignViewportI viewport = af.getViewport(); assertSame(viewport.getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); assertNotNull( @@ -164,7 +170,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); - assertSame(viewport.getGlobalColourScheme().getClass(), + assertSame(af.getViewport().getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme for imported project."); System.out.println( @@ -813,7 +819,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); - AlignViewport av = af.getViewport(); + AlignViewportI av = af.getViewport(); AlignmentI al = av.getAlignment(); /* @@ -838,13 +844,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * create a group with Strand colouring, 30% Conservation * and 40% PID threshold + * (notice menu action applies to selection group even if mouse click + * is at a sequence not in the group) */ 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 popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), + null); popupMenu.changeColour_actionPerformed( JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); @@ -920,7 +929,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * set colour schemes for features */ - FeatureRenderer fr = af.getFeatureRenderer(); + FeatureRendererModel fr = af.getFeatureRenderer(); fr.findAllFeatures(true); // type1: red @@ -1055,6 +1064,59 @@ public class Jalview2xmlTests extends Jalview2xmlBase } /** + * Load an HMM profile to an alignment, and confirm it is correctly restored + * when reloaded from project + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverHmmProfile() throws IOException + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + AlignViewportI av = af.getViewport(); + AlignmentI al = av.getAlignment(); + + /* + * mimic drag and drop of hmm file on to alignment + */ + AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.hmm", DataSourceType.FILE); + al.insertSequenceAt(0, + af2.getViewport().getAlignment().getSequenceAt(0)); + + /* + * check it loaded in + */ + SequenceI hmmSeq = al.getSequenceAt(0); + assertTrue(hmmSeq.hasHMMProfile()); + HiddenMarkovModel hmm = hmmSeq.getHMM(); + assertSame(hmm.getConsensusSequence(), hmmSeq); + + /* + * save project, close windows, reload project, verify + */ + File tfile = File.createTempFile("testStoreAndRecoverHmmProfile", + ".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"); + + hmmSeq = al.getSequenceAt(0); + assertTrue(hmmSeq.hasHMMProfile()); + assertSame(hmm.getConsensusSequence(), hmmSeq); + Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm, + "mapToHmmConsensus"); + assertNotNull(mapToHmmConsensus); + assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence()); + } + + /** * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each * view (JAL-3171) this test ensures we can import and merge those views */ @@ -1179,4 +1241,83 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getAlignViewport(), "Didn't restore correct view association for the PCA view"); } + + /** + * Test save and reload of DBRefEntry including GeneLocus in project + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverGeneLocus() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, + DataSourceType.PASTE); + assertNotNull(af, "Didn't read in the example file correctly."); + + AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; + SequenceI pep = ap.getAlignment().getSequenceAt(0); + SequenceI cds = ap.getAlignment().getSequenceAt(1); + + /* + * give 'protein' a dbref to self, a dbref with map to CDS, + * and a dbref with map to gene 'locus' + */ + DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null); + pep.addDBRef(dbref1); + Mapping cdsmap = new Mapping(cds, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); + DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap); + pep.addDBRef(dbref2); + Mapping locusmap = new Mapping(null, + new MapList(new int[] + { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3)); + DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap); + pep.addDBRef(dbref3); + + File tfile = File.createTempFile("testStoreAndRecoverGeneLocus", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + + new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; + SequenceI rpep = rap.getAlignment().getSequenceAt(0); + assertEquals(rpep.getName(), "P30419"); + DBRefEntry[] dbrefs = rpep.getDBRefs(); + assertEquals(dbrefs.length, 3); + DBRefEntry dbRef = dbrefs[0]; + assertFalse(dbRef instanceof GeneLocus); + assertNull(dbRef.getMap()); + assertEquals(dbRef, dbref1); + + /* + * restored dbrefs with mapping have a different 'map to' + * sequence but otherwise match the original dbrefs + */ + dbRef = dbrefs[1]; + assertFalse(dbRef instanceof GeneLocus); + assertTrue(dbRef.equalRef(dbref2)); + assertNotNull(dbRef.getMap()); + SequenceI rcds = rap.getAlignment().getSequenceAt(1); + assertSame(dbRef.getMap().getTo(), rcds); + // compare MapList but not map.to + assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap()); + + /* + * GeneLocus map.to is null so can compare Mapping objects + */ + dbRef = dbrefs[2]; + assertTrue(dbRef instanceof GeneLocus); + assertEquals(dbRef, dbref3); + } }