X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=0977669cf62501104800e02c93c2c61f77486362;hb=55ebdfcc6bd979605c9bb2b4092a422b035bc27e;hp=a094fb0c686d2acd3f98cee6586c8411695b2fec;hpb=59d2feb135a7da8e92b68491f177159913c60244;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index a094fb0..0977669 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -62,9 +62,9 @@ public class JmolParserTest
    * 1GAQ has been reduced to alpha carbons only
    * 1QCF is the full PDB file including headers, HETATM etc
    */
-  String[] testFile = new String[] { "./examples/1GAQ.txt",
+  String[] testFile = new String[] { "./examples/1gaq.txt",
       "./test/jalview/ext/jmol/1xyz.pdb",
-      "./test/jalview/ext/jmol/1qcf.pdb" };
+      "./test/jalview/ext/jmol/1QCF.pdb" };
 
   //@formatter:off
   // a modified and very cut-down extract of 4UJ4
@@ -98,11 +98,11 @@ public class JmolParserTest
   public void setUp()
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+    Cache.setPropertyNoSave("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+    Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
             Boolean.FALSE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+    Cache.setPropertyNoSave("ADD_SS_ANN",
             Boolean.TRUE.toString());
     StructureImportSettings.setDefaultStructureFileFormat("PDB");
     StructureImportSettings
@@ -130,17 +130,17 @@ public class JmolParserTest
       JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
-      assertTrue(
-              "No sequences extracted from testfile\n"
-                      + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
-                              : "(No warnings raised)"), seqs != null
-                      && seqs.size() > 0);
+      assertTrue("No sequences extracted from testfile\n"
+              + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+                      : "(No warnings raised)"),
+              seqs != null && seqs.size() > 0);
       for (SequenceI sq : seqs)
       {
-        assertEquals("JMol didn't process " + pdbStr
-                + " to the same sequence as MCView",
-                sq.getSequenceAsString(), mcseqs.remove(0)
-                        .getSequenceAsString());
+        assertEquals(
+                "JMol didn't process " + pdbStr
+                        + " to the same sequence as MCView",
+                sq.getSequenceAsString(),
+                mcseqs.remove(0).getSequenceAsString());
         AlignmentI al = new Alignment(new SequenceI[] { sq });
         validateSecStrRows(al);
       }
@@ -175,13 +175,15 @@ public class JmolParserTest
 
   private void checkFirstAAIsAssoc(SequenceI sq)
   {
-    assertTrue("No secondary structure assigned for protein sequence for "
-            + sq.getName(),
+    assertTrue(
+            "No secondary structure assigned for protein sequence for "
+                    + sq.getName(),
             sq.getAnnotation() != null && sq.getAnnotation().length >= 1
                     && sq.getAnnotation()[0].hasIcons);
     assertTrue(
             "Secondary structure not associated for sequence "
-                    + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+                    + sq.getName(),
+            sq.getAnnotation()[0].sequenceRef == sq);
   }
 
   /**
@@ -194,7 +196,8 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false,
             pastePDBDataWithChainBreak, DataSourceType.PASTE);
-    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
+            DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -216,8 +219,7 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             DataSourceType.PASTE);
-    JmolParser jtest = new JmolParser(pdbWithAltLoc,
-            DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();