Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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 fb71f01..131ef41 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -29,15 +29,16 @@ 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;
 
-import java.io.IOException;
 import java.util.Vector;
 
 import org.jmol.c.STR;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -49,6 +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
@@ -106,8 +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());
     }
   }
@@ -118,8 +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(
@@ -185,9 +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();
 
@@ -208,9 +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();
 
@@ -252,24 +259,28 @@ public class JmolParserTest
   }
 
   @Test(groups = "Functional")
-  public void testLocalPDBId()
+  public void testLocalPDBId() throws Exception
   {
     JmolParser structureData;
-    try
-    {
-      structureData = new JmolParser("examples/DNMT1_MOUSE.pdb",
-              AppletFormatAdapter.FILE);
-      assertNotNull(structureData);
-      assertNotNull(structureData.getId());
-      assertEquals(structureData.getId(), "DNMT1_MOUSE.pdb");
-      assertNotNull(structureData.getSeqs());
-      assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
-      assertEquals(
-              structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
-              "dnmt1_mouse.pdb");
-    } catch (IOException e)
-    {
-      e.printStackTrace();
-    }
+    /*
+     * 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");
+
   }
 }