X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=2ea0b8001fc9d892e839789e923234eb88febcba;hb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;hp=a68f7c85f31bf8231c545fc5272a9ef958d9e67e;hpb=8a693367d8a0f6113d21248993ca4e0355b32659;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index a68f7c8..2ea0b80 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -30,6 +30,8 @@ import jalview.datamodel.SequenceI;
 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;
 
@@ -50,11 +52,12 @@ public class JmolParserTest
    * 1QCF is the full PDB file including headers, HETATM etc
    */
   String[] testFile = new String[] { "./examples/1GAQ.txt",
-      "./test/jalview/ext/jmol/1xyz.pdb" };
+      "./test/jalview/ext/jmol/1xyz.pdb",
+      "./test/jalview/ext/jmol/1qcf.pdb" };
 
   //@formatter:off
   // a modified and very cut-down extract of 4UJ4
-  String pdbWithChainBreak =
+  String pastePDBDataWithChainBreak =
      "HEADER    TRANSPORT PROTEIN                       08-APR-15   4UJ4\n" +
      // chain B has missing residues; these should all go in the same sequence:
      "ATOM   1909  CA  VAL B 358      21.329 -19.739 -67.740  1.00201.05           C\n" +
@@ -87,6 +90,9 @@ public class JmolParserTest
             Boolean.TRUE.toString());
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -104,6 +110,31 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testFileParser() throws Exception
   {
+    StructureImportSettings.setProcessHETATMs(false);
+    for (String pdbStr : testFile)
+    {
+      PDBfile mctest = new PDBfile(false, false, false, pdbStr,
+              AppletFormatAdapter.FILE);
+      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
+              jalview.io.AppletFormatAdapter.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);
+      for (SequenceI sq : seqs)
+      {
+        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);
+      }
+    }
+    StructureImportSettings.setProcessHETATMs(true);
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
@@ -172,14 +203,15 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testParse_missingResidues() throws Exception
   {
-    PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
+    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,
-            pdbWithChainBreak,
+            pastePDBDataWithChainBreak,
             jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();