Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 677a6e9..b589e94 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.testng.Assert.assertEquals;
@@ -55,7 +75,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -63,26 +83,26 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetWritableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), expected);
-    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
     assertEquals(formats.getWritableFormats(false).toString(), expected);
   }
 
   @Test(groups = "Functional")
   public void testDeregisterFileFormat()
   {
-    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
+    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
     FileFormats formats = FileFormats.getInstance();
     System.out.println(formats.getReadableFormats().toString());
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -90,8 +110,8 @@ public class FileFormatsTest
      * re-register the format: it gets added to the end of the list
      */
     formats.registerFileFormat(FileFormat.Fasta);
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML, Fasta]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }
@@ -103,8 +123,10 @@ public class FileFormatsTest
     for (FileFormatI ff : FileFormat.values())
     {
       assertSame(ff, formats.forName(ff.getName()));
-      assertSame(ff, formats.forName(ff.getName().toUpperCase()));
-      assertSame(ff, formats.forName(ff.getName().toLowerCase()));
+      assertSame(ff,
+              formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
+      assertSame(ff,
+              formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
     }
     assertNull(formats.forName(null));
     assertNull(formats.forName("rubbish"));