Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 542336f..faf05d3 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -10,41 +10,52 @@ import static org.testng.Assert.assertTrue;
 import java.util.Iterator;
 
 import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class FileFormatsTest
 {
-  @AfterMethod()
+  @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
     FileFormats.getInstance().reset();
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    FileFormats.getInstance().reset();
+  }
+
   @Test(groups = "Functional")
-  public void testIsDynamic()
+  public void testIsIdentifiable()
   {
     FileFormats formats = FileFormats.getInstance();
-    for (FileFormatI ff : FileFormat.values())
-    {
-      assertFalse(formats.isDynamic(ff));
-    }
-    assertTrue(formats.isDynamic(null));
+    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));
 
     /*
-     * remove and re-add a format: it is now considered 'dynamically added'
+     * remove and re-add a format: it is still 'identifiable'
      */
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
     assertNull(formats.forName(FileFormat.Fasta.getName()));
     formats.registerFileFormat(FileFormat.Fasta);
     assertSame(FileFormat.Fasta,
             formats.forName(FileFormat.Fasta.getName()));
-    assertTrue(formats.isDynamic(FileFormat.Fasta));
+    assertTrue(formats.isIdentifiable(FileFormat.Fasta));
   }
 
   @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]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -52,25 +63,26 @@ 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]";
+    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, 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]";
+    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, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -78,8 +90,8 @@ 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, 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, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }
@@ -104,7 +116,7 @@ public class FileFormatsTest
     FileFormats formats = FileFormats.getInstance();
     assertSame(FileFormat.MMCif,
             formats.forName(FileFormat.MMCif.getName()));
-    assertFalse(formats.isDynamic(FileFormat.MMCif));
+    assertTrue(formats.isIdentifiable(FileFormat.MMCif));
 
     /*
      * deregister mmCIF format
@@ -114,12 +126,12 @@ public class FileFormatsTest
 
     /*
      * re-register mmCIF format
-     * it is reinstated (but now classed as 'dynamic')
+     * it is reinstated (still 'identifiable')
      */
     formats.registerFileFormat(FileFormat.MMCif);
     assertSame(FileFormat.MMCif,
             formats.forName(FileFormat.MMCif.getName()));
-    assertTrue(formats.isDynamic(FileFormat.MMCif));
+    assertTrue(formats.isIdentifiable(FileFormat.MMCif));
     // repeating does nothing
     formats.registerFileFormat(FileFormat.MMCif);
     assertSame(FileFormat.MMCif,