JAL-2681 source formatting

[jalview.git] / test / jalview / io / CrossRef2xmlTests.java

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index eaf1e79..9e24262 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -65,10 +65,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   public void testRetrieveAndShowCrossref() throws Exception
   {
 
-    List<String> failedDBRetr = new ArrayList<String>();
-    List<String> failedXrefMenuItems = new ArrayList<String>();
-    List<String> failedProjectRecoveries = new ArrayList<String>();
-
+    List<String> failedDBRetr = new ArrayList<>();
+    List<String> failedXrefMenuItems = new ArrayList<>();
+    List<String> failedProjectRecoveries = new ArrayList<>();
     // for every set of db queries
     // retrieve db query
     // verify presence of expected xrefs
@@ -85,9 +84,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
-    List<String> keyseq = new ArrayList<String>();
-    HashMap<String, File> savedProjects = new HashMap<String, File>();
+    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    List<String> keyseq = new ArrayList<>();
+    HashMap<String, File> savedProjects = new HashMap<>();
 
     for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
     { "UNIPROT", "P01731" } })
@@ -140,7 +139,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           Desktop.instance.closeAll_actionPerformed(null);
           // recover stored project
           af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
-                  .get(first).toString(), FormatAdapter.FILE);
+                  .get(first).toString(), DataSourceType.FILE);
           System.out.println("Recovered view for '" + first + "' from '"
                   + savedProjects.get(first).toString() + "'");
           dna = af.getViewport().getAlignment().isNucleotide();
@@ -176,7 +175,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             // build next key so we an retrieve all views
             String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
             // perform crossref action, or retrieve stored project
-            List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+            List<AlignmentViewPanel> cra_views = new ArrayList<>();
             CrossRefAction cra = null;
 
             if (pass2 == 0)
@@ -213,7 +212,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               // recover stored project
               AlignFrame af2 = new FileLoader(false)
                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
-                              .toString(), FormatAdapter.FILE);
+                              .toString(), DataSourceType.FILE);
               System.out.println("Recovered view for '" + nextxref
                       + "' from '" + savedProjects.get(nextxref).toString()
                       + "'");
@@ -237,7 +236,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
               }
             }
-            HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+            HashMap<String, List<String>> xrptypes = new HashMap<>();
             // first save/verify views.
             for (AlignmentViewPanel avp : cra_views)
             {
@@ -274,7 +273,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
                 for (String xrefdb : xrptypes.get(nextxref))
                 {
-                  List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+                  List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
                   int q = 0;
                   String nextnextxref = nextxref + " -> " + xrefdb + "{"
                           + q + "}";
@@ -324,7 +323,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     AlignFrame af2 = new FileLoader(false)
                             .LoadFileWaitTillLoaded(
                                     savedProjects.get(nextnextxref)
-                                            .toString(), FormatAdapter.FILE);
+                                            .toString(),
+                                    DataSourceType.FILE);
                     System.out.println("Recovered view for '"
                             + nextnextxref + "' from '"
                             + savedProjects.get(nextnextxref).toString()
@@ -479,7 +479,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   private void assertType(boolean expectProtein,
           AlignmentViewPanel alignmentViewPanel, String message)
   {
-    List<SequenceI> nonType = new ArrayList<SequenceI>();
+    List<SequenceI> nonType = new ArrayList<>();
     for (SequenceI sq : alignmentViewPanel.getAlignViewport()
             .getAlignment().getSequences())
     {