Merge branch 'develop' into efficiency/JAL-2034_JAL-1421

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

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 915625f..e1bc3ae 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -41,10 +41,13 @@ import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureImportSettings;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.io.File;
+import java.time.Instant;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -67,6 +70,9 @@ public class Jalview2xmlTests
   {
     jalview.bin.Jalview.main(new String[] { "-props",
         "test/jalview/io/testProps.jvprops" });
+    jalview.bin.Cache.setProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
+            Cache.date_format.format(Date.from(Instant.now().plusSeconds(
+                    3600))));
   }
 
   /**
@@ -270,10 +276,11 @@ 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());
+    // 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);
@@ -371,10 +378,12 @@ public class Jalview2xmlTests
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
+    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();
 
     // check FileLoader returned a reference to the one alignFrame that is