Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / test / jalview / ext / jmol / JmolParserTest.java

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index b2d3253..f5e637c 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -29,7 +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;
@@ -37,6 +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;
 
@@ -48,6 +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
@@ -105,8 +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());
     }
   }
@@ -117,8 +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(
@@ -184,9 +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();
 
@@ -207,9 +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();
 
@@ -258,21 +266,20 @@ public class JmolParserTest
      * reads a local structure
      */
     structureData = new JmolParser("examples/testdata/localstruct.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
     assertNotNull(structureData);
     /*
      * local structure files should yield a false ID based on the filename
      */
     assertNotNull(structureData.getId());
-    assertEquals(structureData.getId(), "localstruct.pdb");
+    assertEquals(structureData.getId(), "localstruct");
     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");
-
+    String featureGroup = structureData.getSeqs().get(0)
+            .getSequenceFeatures().get(0).featureGroup;
+    assertNotNull(featureGroup);
+    assertEquals(featureGroup, "localstruct");
   }
 }