Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 47b8aea..489916e 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -27,6 +27,23 @@ 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.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 +58,7 @@ 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;
@@ -49,6 +67,7 @@ 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;
@@ -75,26 +94,15 @@ 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 +129,8 @@ 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 +172,8 @@ 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 +219,8 @@ 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;
@@ -274,7 +285,8 @@ 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 +420,7 @@ 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 +448,7 @@ 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 +474,7 @@ 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 +513,7 @@ 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 +607,7 @@ 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 +682,7 @@ 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 +727,7 @@ 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 +776,7 @@ 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);
@@ -802,6 +814,7 @@ 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");
     }
   }
 
@@ -815,7 +828,7 @@ 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 +891,7 @@ 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 +1003,8 @@ 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 +1046,7 @@ 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 +1086,7 @@ 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 +1116,7 @@ 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 +1153,7 @@ 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 +1197,7 @@ 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 +1231,10 @@ 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 +1264,7 @@ 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 +1300,16 @@ 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<DBRefEntry> 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 +1318,7 @@ 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 +1330,7 @@ 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);
   }