JAL-2157 JAL-1803 refactored Sequence.updatePDBIds, parse DBRefs with

[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 7ab058e..a014ef8 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -31,7 +31,6 @@ 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;
 
@@ -86,13 +85,14 @@ public class JmolParserTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+            Boolean.FALSE.toString());
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
     StructureImportSettings.setDefaultStructureFileFormat("PDB");
-    StructureImportSettings
-            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -114,8 +114,7 @@ public class JmolParserTest
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
               AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              jalview.io.AppletFormatAdapter.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -163,7 +162,8 @@ 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(
@@ -182,13 +182,8 @@ public class JmolParserTest
     PDBfile mctest = new PDBfile(false, false, false,
             pastePDBDataWithChainBreak,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct,
-            pastePDBDataWithChainBreak,
-            jalview.io.AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
+            AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -210,12 +205,8 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
-            jalview.io.AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc,
+            AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();