JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[jalview.git] / test / jalview / ws / jabaws / RNAStructExportImport.java

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 4e9741e..e66f016 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -20,19 +20,22 @@
  */
 package jalview.ws.jabaws;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
+import jalview.project.Jalview2XML;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
@@ -86,7 +89,7 @@ public class RNAStructExportImport
   public static void setUpBeforeClass() throws Exception
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.initLogger();
+    Console.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
     while (disc.isRunning())
@@ -98,7 +101,7 @@ public class RNAStructExportImport
     for (Jws2Instance svc : disc.getServices())
     {
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+      if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
       }
@@ -118,7 +121,7 @@ public class RNAStructExportImport
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
     // remove any existing annotation
-    List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aal = new ArrayList<>();
     for (AlignmentAnnotation rna : af.getViewport().getAlignment()
             .getAlignmentAnnotation())
     {
@@ -202,7 +205,9 @@ public class RNAStructExportImport
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
-
+    // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+    // annotation is mistakenly recognised as an RNA annotation row when read in
+    // as an annotation file.
     verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
@@ -242,7 +247,8 @@ public class RNAStructExportImport
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
@@ -256,7 +262,7 @@ public class RNAStructExportImport
   @Test(groups = { "Network" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<Argument> opts = new ArrayList<Argument>();
+    List<Argument> opts = new ArrayList<>();
     for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
             .getArguments())
     {