X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=f5e637c7355143927726cec759e7f1f3b239232f;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=f2b32c60cecd8b669adf04494e11f419f1e9a5fc;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index f2b32c6..f5e637c 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;
@@ -28,6 +29,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.structure.StructureImportSettings;
@@ -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");
@@ -113,8 +127,7 @@ public class JmolParserTest
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
               DataSourceType.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              DataSourceType.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -162,7 +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(
@@ -180,12 +194,7 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false,
             pastePDBDataWithChainBreak, DataSourceType.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct,
-            pastePDBDataWithChainBreak, DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -207,15 +216,11 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             DataSourceType.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
+    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());
@@ -252,4 +257,29 @@ 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");
+    assertNotNull(structureData.getSeqs());
+    /*
+     * the ID is also the group for features derived from structure data 
+     */
+    String featureGroup = structureData.getSeqs().get(0)
+            .getSequenceFeatures().get(0).featureGroup;
+    assertNotNull(featureGroup);
+    assertEquals(featureGroup, "localstruct");
+  }
 }