JAL-2164 changed to be Java 1.7 compliant

[jalview.git] / test / jalview / io / Jalview2xmlTests.java

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index d941242..e01e785 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -30,6 +30,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
@@ -42,7 +43,6 @@ import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureImportSettings;
-import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.io.File;
@@ -67,8 +67,20 @@ public class Jalview2xmlTests
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/io/testProps.jvprops" });
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+    /*
+     * set news feed last read to a future time to ensure no
+     * 'unread' news item is displayed
+     */
+    String oneHourFromNow = Cache.date_format
+            .format(System.currentTimeMillis() + 3600 * 1000);
+    Cache.setProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+    Jalview.main(new String[] {});
   }
 
   /**
@@ -272,13 +284,11 @@ public class Jalview2xmlTests
   @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
-            Boolean.TRUE.toString());
-     StructureImportSettings.setDefaultStructureFileFormat("PDB");
-    StructureImportSettings
-            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+    // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
@@ -369,40 +379,29 @@ public class Jalview2xmlTests
   }
 
   /**
-   * test store and recovery of expanded views - currently this is disabled
-   * since the Desktop.explodeViews method doesn't seem to result in the views
-   * being expanded to distinct align frames when executed programmatically.
+   * test store and recovery of expanded views
    * 
    * @throws Exception
    */
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    StructureImportSettings
-            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
-    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    Desktop.instance.closeAll_actionPerformed(null);
+
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
+    Assert.assertEquals(Desktop.getAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
-    {
-      final AlignFrame xaf = af;
-      af = null;
-      new Thread(new Runnable()
-      {
-        @Override
-        public void run()
-        {
-          Desktop.instance.explodeViews(xaf);
-        }
-      }).start();
-      Thread.sleep(1000);
-    }
-    // int times = 0;
-    // while (++times < 5 && Desktop.getAlignFrames().length < )
-    // {
-    // Thread.sleep(300);
-    // }
+
+    // check FileLoader returned a reference to the one alignFrame that is
+    // actually on the Desktop
+    assertTrue(
+            "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+            af == Desktop.getAlignFrameFor(af.getViewport()));
+
+    Desktop.explodeViews(af);
+
     int oldviews = Desktop.getAlignFrames().length;
     Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(afid).length);
@@ -443,7 +442,6 @@ public class Jalview2xmlTests
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);
-    StructureImportSettings.setDefaultStructureFileFormat("PDB");
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);