X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=a094fb0c686d2acd3f98cee6586c8411695b2fec;hb=a11ce31b3e8ff7571b0e95e11758bbcfa2821596;hp=fb092f6f9d2fa3772471448047a8c4967a3e26bb;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index fb092f6..a094fb0 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;
@@ -36,10 +38,11 @@ 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;
 
-import MCview.PDBfile;
+import mc_view.PDBfile;
 
 /**
  * @author jimp
@@ -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
@@ -104,8 +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());
     }
   }
@@ -116,8 +126,8 @@ public class JmolParserTest
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
-              AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
+              DataSourceType.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -183,9 +193,8 @@ public class JmolParserTest
   public void testParse_missingResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false,
-            pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
-    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
-            AppletFormatAdapter.PASTE);
+            pastePDBDataWithChainBreak, DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -206,9 +215,9 @@ public class JmolParserTest
   public void testParse_alternativeResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
     JmolParser jtest = new JmolParser(pdbWithAltLoc,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -248,4 +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");
+  }
 }