*/
package jalview.io;
-import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.gui.JvOptionPane;
}
@Test(groups = { "Functional" }, dataProvider = "identifyFiles")
- public void testIdentify(String data, String expectedFileType)
+ public void testIdentify(String data, FileFormatI expectedFileType)
+ throws FileFormatException
{
- String protocol = AppletFormatAdapter.FILE;
+ DataSourceType protocol = DataSourceType.FILE;
IdentifyFile ider = new IdentifyFile();
- String actualFiletype = ider.identify(data, protocol);
- Assert.assertEquals(actualFiletype, expectedFileType,
+ FileFormatI actualFiletype = ider.identify(data, protocol);
+ Assert.assertSame(actualFiletype, expectedFileType,
"File identification Failed!");
}
/**
* Additional tests for Jalview features file
+ *
+ * @throws FileFormatException
*/
@Test(groups = "Functional")
- public void testIdentify_featureFile()
+ public void testIdentify_featureFile() throws FileFormatException
{
IdentifyFile ider = new IdentifyFile();
*/
String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
- assertEquals(IdentifyFile.FeaturesFile,
- ider.identify(data, AppletFormatAdapter.PASTE));
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
/*
* Jalview feature colour followed by GFF format feature data
*/
data = "METAL\tcc9900\n" + "GFF\n"
+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
- assertEquals(IdentifyFile.FeaturesFile,
- ider.identify(data, AppletFormatAdapter.PASTE));
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
/*
* Feature with '<' in the name (JAL-2098)
*/
data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
- assertEquals(IdentifyFile.FeaturesFile,
- ider.identify(data, AppletFormatAdapter.PASTE));
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
}
@DataProvider(name = "identifyFiles")
public Object[][] IdentifyFileDP()
{
return new Object[][] {
- { "examples/example.json", "JSON" },
- { "examples/plantfdx.fa", "FASTA" },
- { "examples/dna_interleaved.phy", "PHYLIP" },
- { "examples/2GIS.pdb", "PDB" },
- { "examples/rf00031_folded.stk", "STH" },
- { "examples/testdata/test.rnaml", "RNAML" },
- { "examples/testdata/test.aln", "CLUSTAL" },
- { "examples/testdata/test.pfam", "PFAM" },
- { "examples/testdata/test.msf", "MSF" },
- { "examples/testdata/test.pir", "PIR" },
- { "examples/testdata/test.html", "HTML" },
- { "examples/testdata/test.pileup", "PileUp" },
- { "examples/testdata/test.blc", "BLC" },
- { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
- { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
- { "examples/testdata/test.jvp", "Jalview" },
- { "examples/testdata/test.cif", "mmCIF" },
+ { "examples/example.json", FileFormat.Json },
+ { "examples/plantfdx.fa", FileFormat.Fasta },
+ { "examples/dna_interleaved.phy", FileFormat.Phylip },
+ { "examples/2GIS.pdb", FileFormat.PDB },
+ { "examples/RF00031_folded.stk", FileFormat.Stockholm },
+ { "examples/testdata/test.rnaml", FileFormat.Rnaml },
+ { "examples/testdata/test.aln", FileFormat.Clustal },
+ { "examples/testdata/test.pfam", FileFormat.Pfam },
+ { "examples/testdata/test.msf", FileFormat.MSF },
+ { "examples/testdata/test.pir", FileFormat.PIR },
+ { "examples/testdata/test.html", FileFormat.Html },
+ { "examples/testdata/test.pileup", FileFormat.Pileup },
+ { "examples/testdata/test.blc", FileFormat.BLC },
+ { "examples/exampleFeatures.txt", FileFormat.Features },
+ { "examples/testdata/simpleGff3.gff", FileFormat.Features },
+ { "examples/testdata/test.jvp", FileFormat.Jalview },
+ { "examples/testdata/test.cif", FileFormat.MMCif },
{
"examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
- "FASTA" },
-
+ FileFormat.Fasta },
+ { "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix },
+ { "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix }
// { "examples/testdata/test.amsa", "AMSA" },
// { "examples/test.jnet", "JnetFile" },
};