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 27cfa5e..b589e94 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -20,8 +20,6 @@
  */
 package jalview.io;
 
-import java.util.Locale;
-
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotEquals;
@@ -53,15 +51,14 @@ public class FileFormatsTest
   public void testIsIdentifiable()
   {
     FileFormats formats = FileFormats.getInstance();
-    assertTrue(formats
-            .isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
-    assertTrue(formats
-            .isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
-    assertTrue(formats
-            .isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
-    assertTrue(formats
-            .isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
-    // GenBank/ENA
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
+            .getName())));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
+            .getName())));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
+            .getName())));
+    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
+            .getName())));
     assertFalse(formats.isIdentifiable(null));
 
     /*
@@ -86,25 +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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    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);
 
@@ -112,8 +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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, 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);
   }
@@ -169,7 +167,8 @@ public class FileFormatsTest
      * verify the list of file formats registered matches the enum values
      */
     FileFormats instance = FileFormats.getInstance();
-    Iterator<FileFormatI> formats = instance.getFormats().iterator();
+    Iterator<FileFormatI> formats = instance.getFormats()
+            .iterator();
     FileFormatI[] builtIn = FileFormat.values();
 
     for (FileFormatI ff : builtIn)