merge

[jalview.git] / test / jalview / io / AnnotatedPDBFileInputTest.java

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index b4a8bf6..91e816a 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -11,9 +11,6 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
 
 import java.io.File;
 
@@ -28,10 +25,14 @@ public class AnnotatedPDBFileInputTest
 
   AlignmentI al;
 
-  String pdbStr = "examples/1gaq.txt";
-
   String pdbId;
 
+  /**
+   * Ensure 'process secondary structure from PDB and add annotations' are set
+   * in preferences, and load PDB example file 1gaq
+   * 
+   * @throws Exception
+   */
  @BeforeMethod(alwaysRun = true)
   public void setup() throws Exception
   {
@@ -40,7 +41,7 @@ public class AnnotatedPDBFileInputTest
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
-    AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
+    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
@@ -88,11 +89,6 @@ public class AnnotatedPDBFileInputTest
   @Test(groups ={ "Functional" })
   public void checkPDBSequenceFeatures()
   {
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    StructureMapping[] mappings = ssm.getMapping("1gaq");
-    // suspect we really want to make assertions on sequence features
-    // in these mappings' sequencess
     /*
      * 1GAQ/A
      */
@@ -159,8 +155,7 @@ public class AnnotatedPDBFileInputTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
- { "-props",
+    jalview.bin.Jalview.main(new String[] { "-props",
         "test/jalview/io/testProps.jvprops" });
   }