JAL-2189 format tests

[jalview.git] / test / jalview / ext / jmol / JmolParserTest.java

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 8788609..fb092f6 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -31,6 +31,7 @@ import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.util.Vector;
 
@@ -93,6 +94,8 @@ public class JmolParserTest
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
     StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -162,7 +165,8 @@ public class JmolParserTest
 
   private void checkFirstAAIsAssoc(SequenceI sq)
   {
-    assertTrue("No secondary structure assigned for protein sequence.",
+    assertTrue("No secondary structure assigned for protein sequence for "
+            + sq.getName(),
             sq.getAnnotation() != null && sq.getAnnotation().length >= 1
                     && sq.getAnnotation()[0].hasIcons);
     assertTrue(
@@ -179,8 +183,7 @@ public class JmolParserTest
   public void testParse_missingResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false,
-            pastePDBDataWithChainBreak,
-            AppletFormatAdapter.PASTE);
+            pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
     JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
             AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
@@ -208,7 +211,7 @@ public class JmolParserTest
             AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
-  
+
     assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
     assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
     assertEquals("ALC", seqs.get(0).getSequenceAsString());