JAL-2164 fix failing test

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 39d2c89..3d53234 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -33,6 +33,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -42,6 +43,8 @@ import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -65,9 +68,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/RF00031_folded.stk";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     int olddsann = countDsAnn(af.getViewport());
     assertTrue("Didn't find any dataset annotations", olddsann > 0);
     af.rnahelicesColour_actionPerformed(null);
@@ -78,9 +81,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
     int newdsann = countDsAnn(af.getViewport());
     assertTrue(
             "Differing numbers of dataset sequence annotation\nOriginally "
@@ -100,32 +102,26 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
-    assertTrue(
-            "Didn't set T-coffee colourscheme",
-            af.getViewport().getGlobalColourScheme().getClass()
-                    .equals(jalview.schemes.TCoffeeColourScheme.class));
-    assertTrue(
-            "Recognise T-Coffee score from string",
+    assertSame("Didn't set T-coffee colourscheme", af.getViewport()
+            .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
+    assertNotNull("Recognise T-Coffee score from string",
             jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
-                    .getAlignment(),
-                    jalview.schemes.ColourSchemeProperty.getColourName(af
-                            .getViewport().getGlobalColourScheme())) != null);
+                    .getAlignment(), ColourSchemeProperty.getColourName(af
+                    .getViewport().getGlobalColourScheme())));
 
     assertTrue("Failed to store as a project.",
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
-    assertTrue(
-            "Didn't set T-coffee colourscheme for imported project.",
-            af.getViewport().getGlobalColourScheme().getClass()
-                    .equals(jalview.schemes.TCoffeeColourScheme.class));
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
+    assertSame("Didn't set T-coffee colourscheme for imported project.", af
+            .getViewport().getGlobalColourScheme().getClass(),
+            TCoffeeColourScheme.class);
     System.out
             .println("T-Coffee score shading successfully recovered from project.");
   }
@@ -136,19 +132,19 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
     assertTrue(
             "Didn't find any IUPred annotation to use to shade alignment.",
             aa != null && aa.length > 0);
-    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
-            aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
-    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
-            aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+    AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
+            AnnotationColourGradient.ABOVE_THRESHOLD);
+    AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
+            null, AnnotationColourGradient.BELOW_THRESHOLD);
     cs.setSeqAssociated(true);
     gcs.setSeqAssociated(true);
     af.changeColour(cs);
@@ -164,16 +160,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
 
     // check for group and alignment colourschemes
 
     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
             .get(0).cs;
-    assertTrue("Didn't recover global colourscheme", _rcs != null);
+    assertNotNull("Didn't recover global colourscheme", _rcs);
     assertTrue("Didn't recover annotation colour global scheme",
             _rcs instanceof AnnotationColourGradient);
     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
@@ -195,7 +190,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     System.out
             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 
-    assertTrue("Didn't recover group colourscheme", _rgcs != null);
+    assertNotNull("Didn't recover group colourscheme", _rgcs);
     assertTrue("Didn't recover annotation colour group colourscheme",
             _rgcs instanceof AnnotationColourGradient);
     __rcs = (AnnotationColourGradient) _rgcs;
@@ -221,9 +216,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
             .getAlignFrames().length;
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     assertTrue("Didn't gather the views in the example file.",
             Desktop.getAlignFrames().length == 1 + origCount);
 
@@ -232,14 +227,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
-    // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
-    // StructureImportSettings
-    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
     {
@@ -249,8 +241,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         break;
       }
     }
-    assertTrue("Couldn't find the structure view", sps != null);
-    SequenceI sq = sps.getAlignment().findName("1A70|");
+    assertNotNull("Couldn't find the structure view", sps);
     AlignmentAnnotation refan = null;
     for (AlignmentAnnotation ra : sps.getAlignment()
             .getAlignmentAnnotation())
@@ -261,10 +252,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         break;
       }
     }
-    assertTrue("Annotation secondary structure not found.", refan != null);
-    assertTrue("Couldn't find 1a70 null chain", sq != null);
+    assertNotNull("Annotation secondary structure not found.", refan);
+    SequenceI sq = sps.getAlignment().findName("1A70|");
+    assertNotNull("Couldn't find 1a70 null chain", sq);
     // compare the manually added temperature factor annotation
     // to the track automatically transferred from the pdb structure on load
+    assertNotNull("1a70 has no annotation", sq.getDatasetSequence()
+            .getAnnotation());
     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
     {
       AlignmentAnnotation alaa;
@@ -296,9 +290,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testCopyViewSettings() throws Exception
   {
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null, groups = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
     {
@@ -311,8 +305,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         groups = ap;
       }
     }
-    assertTrue("Couldn't find the structure view", sps != null);
-    assertTrue("Couldn't find the MAFFT view", groups != null);
+    assertNotNull("Couldn't find the structure view", sps);
+    assertNotNull("Couldn't find the MAFFT view", groups);
 
     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
@@ -336,9 +330,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.instance.closeAll_actionPerformed(null);
 
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
 
@@ -369,8 +362,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     Assert.assertNotNull(af);
     Assert.assertEquals(
             Desktop.getAlignFrames().length,
@@ -392,7 +385,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
 
     // remember reference sequence for each panel
@@ -434,8 +427,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
 
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     afid = af.getViewport().getSequenceSetId();
 
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
@@ -525,18 +518,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
     // make a second view of the alignment
     af.newView_actionPerformed(null);
-  
+
     /*
      * remember representative and hidden sequences marked 
      * on each panel
      */
     Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
     Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
-  
+
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
      * as reference sequence for itself and the preceding sequence
@@ -553,7 +546,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       repSeqs.put(ap.getViewName(), repSeq);
       List<String> hiddenNames = new ArrayList<String>();
       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
-  
+
       /*
        * have rep sequence represent itself and the one before it
        * this hides the group (except for the rep seq)
@@ -577,7 +570,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       assertTrue(sg.getSequences().contains(repSeq));
       assertTrue(sg.getSequences().contains(precedingSeq));
       assertTrue("alignment has groups", alignment.getGroups().isEmpty());
-      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av.getHiddenRepSequences();
+      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+              .getHiddenRepSequences();
       assertNotNull(hiddenRepSeqsMap);
       assertEquals(1, hiddenRepSeqsMap.size());
       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
@@ -588,8 +582,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       n++;
     }
     File tfile = File
-            .createTempFile("testStoreAndRecoverGroupReps",
-            ".jvp");
+            .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
     try
     {
       new Jalview2XML(false).saveState(tfile);
@@ -602,11 +595,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-  
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     afid = af.getViewport().getSequenceSetId();
-  
+
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
     {
       String viewName = ap.getViewName();
@@ -630,8 +623,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       HiddenSequences hs = alignment.getHiddenSequences();
       assertEquals(
               "wrong number of restored hidden sequences in "
-                      + ap.getViewName(),
-              hidden.size(), hs.getSize());
+                      + ap.getViewName(), hidden.size(), hs.getSize());
     }
   }
 
@@ -647,7 +639,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String exampleFile = "examples/3W5V.pdb";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
             FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
 
     AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
@@ -667,18 +659,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertNotNull(seqs[2].getDatasetSequence());
     Assert.assertNotNull(seqs[3].getDatasetSequence());
     PDBEntry[] pdbEntries = new PDBEntry[4];
-    pdbEntries[0] = new PDBEntry("3W5V", "A", null, testFile);
-    pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile);
-    pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile);
-    pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile);
-    Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries()
-            .get(0).equals(pdbEntries[0]));
-    Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries()
-            .get(0).equals(pdbEntries[1]));
-    Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries()
-            .get(0).equals(pdbEntries[2]));
-    Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries()
-            .get(0).equals(pdbEntries[3]));
+    pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
+    pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
+    pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
+    pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
+    Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[0]);
+    Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[1]);
+    Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[2]);
+    Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[3]);
 
     File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
     try