X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=f0fbfc4be423995c23b4f7031af445d35176cc20;hb=7d602d0e4b439e56af3e4551ed71f181a8025534;hp=0609ee532db92bb6a3c2d7a5ea986dc8110c3842;hpb=fe350265127bd31fd149b2a4b23e51d2d0bd9ef5;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 0609ee5..f0fbfc4 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -27,6 +27,22 @@ import static org.testng.Assert.assertNull; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +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 javax.swing.JInternalFrame; + +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -36,10 +52,12 @@ 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.Sequence.DBModList; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -48,7 +66,6 @@ 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.JvOptionPane; @@ -75,24 +92,16 @@ import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; -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 javax.swing.JInternalFrame; - -import org.testng.Assert; -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 { + @AfterMethod(alwaysRun = true) + public void tearDown() + { + Desktop.getInstance().closeAll_actionPerformed(null); + } @Override @BeforeClass(alwaysRun = true) @@ -152,7 +161,7 @@ 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( @@ -275,9 +284,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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, + assertEquals(Desktop.getAlignFrames().length, + 1 + origCount, "Didn't gather the views in the example file."); - } /** @@ -409,7 +418,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }, enabled = true) public void testStoreAndRecoverExpandedviews() throws Exception { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); @@ -437,7 +446,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.fail("Didn't save the expanded view state", e); } - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); if (Desktop.getAlignFrames() != null) { Assert.assertEquals(Desktop.getAlignFrames().length, 0); @@ -463,7 +472,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverReferenceSeqSettings() throws Exception { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().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."); @@ -502,7 +511,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.fail("Didn't save the expanded view state", e); } - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); if (Desktop.getAlignFrames() != null) { Assert.assertEquals(Desktop.getAlignFrames().length, 0); @@ -596,7 +605,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverGroupRepSeqs() throws Exception { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); assertNotNull(af, "Didn't read in the example file correctly."); @@ -671,7 +680,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.fail("Didn't save the expanded view state", e); } - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); if (Desktop.getAlignFrames() != null) { Assert.assertEquals(Desktop.getAlignFrames().length, 0); @@ -716,7 +725,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverPDBEntry() throws Exception { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); String exampleFile = "examples/3W5V.pdb"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, DataSourceType.FILE); @@ -765,7 +774,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.fail("Didn't save the state", e); } - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); if (Desktop.getAlignFrames() != null) { Assert.assertEquals(Desktop.getAlignFrames().length, 0); @@ -816,11 +825,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverColourThresholds() throws IOException { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); - AlignViewport av = af.getViewport(); + AlignViewportI av = af.getViewport(); AlignmentI al = av.getAlignment(); /* @@ -879,7 +888,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase ".jvp"); tfile.deleteOnExit(); new Jalview2XML(false).saveState(tfile); - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af, "Failed to reload project"); @@ -1034,7 +1043,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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)"); + "(AF Contains X) OR (CSQ:PolyPhen NE 0)"); } private void addFeature(SequenceI seq, String featureType, int score) @@ -1066,6 +1075,59 @@ 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.getInstance().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.getInstance().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 */ @@ -1088,7 +1150,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testMergeDatasetsforManyViews() throws IOException { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); // complex project - one dataset, several views on several alignments AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( @@ -1132,7 +1194,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = "Functional") public void testPcaViewAssociation() throws IOException { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); final String PCAVIEWNAME = "With PCA"; // create a new tempfile File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp"); @@ -1166,10 +1228,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase } // load again. - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( tempfile.getCanonicalPath(), DataSourceType.FILE); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); + JInternalFrame[] frames = Desktop.getInstance().getAllFrames(); // PCA and the tabbed alignment view should be the only two windows on the // desktop assertEquals(frames.length, 2, @@ -1199,7 +1261,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverGeneLocus() throws Exception { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); @@ -1235,16 +1297,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.fail("Didn't save the state", e); } - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; SequenceI rpep = rap.getAlignment().getSequenceAt(0); + DBModList dbrefs = rpep.getDBRefs(); assertEquals(rpep.getName(), "P30419"); - DBRefEntry[] dbrefs = (DBRefEntry[]) rpep.getDBRefs().toArray(); - assertEquals(dbrefs.length, 3); - DBRefEntry dbRef = dbrefs[0]; + assertEquals(dbrefs.size(), 3); + DBRefEntry dbRef = dbrefs.get(0); assertFalse(dbRef instanceof GeneLocus); assertNull(dbRef.getMap()); assertEquals(dbRef, dbref1); @@ -1253,7 +1315,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase * restored dbrefs with mapping have a different 'map to' * sequence but otherwise match the original dbrefs */ - dbRef = dbrefs[1]; + dbRef = dbrefs.get(1); assertFalse(dbRef instanceof GeneLocus); assertTrue(dbRef.equalRef(dbref2)); assertNotNull(dbRef.getMap()); @@ -1265,7 +1327,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * GeneLocus map.to is null so can compare Mapping objects */ - dbRef = dbrefs[2]; + dbRef = dbrefs.get(2); assertTrue(dbRef instanceof GeneLocus); assertEquals(dbRef, dbref3); }