X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=131ef41af1cc88b1d35c811d4ecde9456f4cff6c;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=2ea0b8001fc9d892e839789e923234eb88febcba;hpb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 2ea0b80..131ef41 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -21,6 +21,7 @@
 package jalview.ext.jmol;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
@@ -28,7 +29,8 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
@@ -36,6 +38,7 @@ import jalview.structure.StructureImportSettings.StructureParser;
 import java.util.Vector;
 
 import org.jmol.c.STR;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -47,6 +50,14 @@ import MCview.PDBfile;
  */
 public class JmolParserTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /*
    * 1GAQ has been reduced to alpha carbons only
    * 1QCF is the full PDB file including headers, HETATM etc
@@ -86,8 +97,11 @@ 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");
@@ -101,8 +115,7 @@ public class JmolParserTest
     for (String f : testFile)
     {
       FileLoader fl = new jalview.io.FileLoader(false);
-      AlignFrame af = fl
-              .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+      AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE);
       validateSecStrRows(af.getViewport().getAlignment());
     }
   }
@@ -110,13 +123,11 @@ 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);
+              DataSourceType.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -134,30 +145,7 @@ public class JmolParserTest
         validateSecStrRows(al);
       }
     }
-    StructureImportSettings.setProcessHETATMs(true);
-    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);
-      }
-    }
   }
 
   private void validateSecStrRows(AlignmentI al)
@@ -187,7 +175,8 @@ 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(
@@ -204,15 +193,8 @@ public class JmolParserTest
   public void testParse_missingResidues() throws Exception
   {
     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);
+            pastePDBDataWithChainBreak, DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -233,16 +215,12 @@ public class JmolParserTest
   public void testParse_alternativeResidues() throws Exception
   {
     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);
+            DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc,
+            DataSourceType.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());
@@ -279,4 +257,30 @@ public class JmolParserTest
     assertEquals('H', structCode[4]);
     assertEquals('E', structCode[5]);
   }
+
+  @Test(groups = "Functional")
+  public void testLocalPDBId() throws Exception
+  {
+    JmolParser structureData;
+    /*
+     * reads a local structure
+     */
+    structureData = new JmolParser("examples/testdata/localstruct.pdb",
+            DataSourceType.FILE);
+    assertNotNull(structureData);
+    /*
+     * local structure files should yield a false ID based on the filename
+     */
+    assertNotNull(structureData.getId());
+    assertEquals(structureData.getId(), "localstruct.pdb");
+    assertNotNull(structureData.getSeqs());
+    /*
+     * the ID is also the group for features derived from structure data 
+     */
+    assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
+    assertEquals(
+            structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
+            "localstruct.pdb");
+
+  }
 }