Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / ws / SequenceFetcherTest.java

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 32afd5f..8e18cc0 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -49,36 +49,35 @@ public class SequenceFetcherTest
    * simple run method to test dbsources.
    * 
    * @param argv
+   * @j2sIgnore
    */
   public static void main(String[] argv)
   {
-    // TODO: extracted from SequenceFetcher - convert to proper unit test with
+    // TODO: extracted from SequenceFetcher - convert to network dependent
+    // functional integration test with
     // assertions
 
     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
             + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
-            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
-            + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
-    boolean withDas = true;
-    if (argv != null && argv.length > 0
-            && argv[0].toLowerCase().startsWith("-nodas"))
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
+
+    if (argv != null && argv.length > 0)
     {
-      withDas = false;
       String targs[] = new String[argv.length - 1];
       System.arraycopy(argv, 1, targs, 0, targs.length);
       argv = targs;
     }
     if (argv != null && argv.length > 0)
     {
-      List<DbSourceProxy> sps = new SequenceFetcher(withDas)
+      List<DbSourceProxy> sps = SequenceFetcher.getInstance()
               .getSourceProxy(argv[0]);
 
       if (sps != null)
       {
         for (DbSourceProxy sp : sps)
         {
-          AlignmentI al = null;
+          // AlignmentI al = null;
           try
           {
             testRetrieval(argv[0], sp,
@@ -97,12 +96,12 @@ public class SequenceFetcherTest
       {
         System.err.println("Can't resolve " + argv[0]
                 + " as a database name. Allowed values are :\n"
-                + new SequenceFetcher().getSupportedDb());
+                + SequenceFetcher.getInstance().getSupportedDb());
       }
       System.out.println(usage);
       return;
     }
-    ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
+    ASequenceFetcher sfetcher = SequenceFetcher.getInstance();
     String[] dbSources = sfetcher.getSupportedDb();
     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
@@ -124,7 +123,7 @@ public class SequenceFetcherTest
           String testQuery)
   {
     AlignmentI ds = null;
-    Vector<Object[]> noProds = new Vector<Object[]>();
+    Vector<Object[]> noProds = new Vector<>();
     System.out.println("Source: " + sp.getDbName() + " (" + db
             + "): retrieving test:" + sp.getTestQuery());
     {