X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=f0fbfc4be423995c23b4f7031af445d35176cc20;hb=158e0595615ae4bfb13554f41f03b570642f6bb2;hp=47b8aeae5d1e768c80dc98847b39d77cfcc5d971;hpb=6398c0217546a4d6943f63f670c2684c7c7274be;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 47b8aea..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; @@ -41,6 +57,7 @@ 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; @@ -75,26 +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) @@ -121,7 +128,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase af.getViewport() .getGlobalColourScheme() instanceof RNAHelicesColour, "Couldn't apply RNA helices colourscheme"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -163,7 +171,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getSchemeName()), "Recognise T-Coffee score from string"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -209,7 +218,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -274,9 +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."); - } /** @@ -408,7 +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); @@ -436,7 +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); @@ -462,7 +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."); @@ -501,7 +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); @@ -595,7 +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."); @@ -670,7 +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); @@ -715,7 +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); @@ -764,7 +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); @@ -815,7 +825,7 @@ 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); @@ -878,7 +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"); @@ -990,7 +1000,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase File tfile = File.createTempFile("JalviewTest", ".jvp"); tfile.deleteOnExit(); String filePath = tfile.getAbsolutePath(); - assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), + af.saveAlignment(filePath, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); /* @@ -1032,7 +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) @@ -1072,7 +1083,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testStoreAndRecoverHmmProfile() throws IOException { - Desktop.instance.closeAll_actionPerformed(null); + Desktop.getInstance().closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); @@ -1102,7 +1113,7 @@ 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"); @@ -1139,7 +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( @@ -1183,7 +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"); @@ -1217,10 +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, @@ -1250,7 +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); @@ -1286,16 +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 = rpep.getDBRefs(); - 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); @@ -1304,7 +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()); @@ -1316,7 +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); }