*/
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;
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));
/*
@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);
* 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);
}
* 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)