X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=79d622c6e068065de8cbf53c2c65a71b0bdadf9e;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=5f1256c56f2285d8a813dc3900c8c3cf58976620;hpb=cbeb7ad59d51b468c54ca3db2a2a7693060a2509;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 5f1256c..79d622c 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.Locale; +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 jalview.analysis.scoremodels.SimilarityParams; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -40,6 +56,7 @@ 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; @@ -51,7 +68,6 @@ 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; @@ -74,21 +90,7 @@ import jalview.structure.StructureImportSettings; import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; - -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 jalview.viewmodel.seqfeatures.FeatureRendererModel; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase @@ -119,7 +121,8 @@ 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; @@ -157,11 +160,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull( ColourSchemeProperty.getColourScheme(viewport, viewport.getAlignment(), - viewport.getGlobalColourScheme() - .getSchemeName()), + viewport.getGlobalColourScheme().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; @@ -207,7 +210,8 @@ 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; @@ -445,9 +449,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels( - af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -800,6 +803,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Mismatch PDBEntry 'Type'"); Assert.assertNotNull(recov.getFile(), "Recovered PDBEntry should have a non-null file entry"); + Assert.assertEquals( + recov.getFile().toLowerCase(Locale.ENGLISH) + .lastIndexOf("pdb"), + recov.getFile().length() - 3, + "Recovered PDBEntry file should have PDB suffix"); } } @@ -842,13 +850,16 @@ 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); @@ -924,7 +935,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * set colour schemes for features */ - FeatureRenderer fr = af.getFeatureRenderer(); + FeatureRendererModel fr = af.getFeatureRenderer(); fr.findAllFeatures(true); // type1: red @@ -985,7 +996,8 @@ 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."); /* @@ -1027,7 +1039,7 @@ 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) @@ -1197,7 +1209,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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); @@ -1229,15 +1241,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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); + 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); @@ -1246,7 +1258,7 @@ 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()); @@ -1258,7 +1270,7 @@ 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); }