*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
@Test(groups = { "Functional" }, dataProvider = "identifyFiles")
public void testIdentify(String data, String expectedFileType)
+ throws FileFormatException
{
- String protocol = AppletFormatAdapter.FILE;
+ DataSourceType protocol = DataSourceType.FILE;
IdentifyFile ider = new IdentifyFile();
- String actualFiletype = ider.identify(data, protocol);
+ String actualFiletype = ider.identify(data, protocol).toString();
Assert.assertEquals(actualFiletype, expectedFileType,
"File identification Failed!");
}
/**
- * Additional tests for (a) Jalview features file with no colour
- * specifications (old style 'groups' file) and (b) Jalview features file with
- * embedded GFF
+ * 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();
- // Jalview format with features only, no feature colours
+ /*
+ * Jalview format with features only, no feature colours
+ */
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";
- Assert.assertEquals(IdentifyFile.FeaturesFile, ider.identify(data, AppletFormatAdapter.PASTE));
+ assertEquals(IdentifyFile.FeaturesFile,
+ ider.identify(data, DataSourceType.PASTE));
- // Jalview feature colour followed by GFF format feature data
+ /*
+ * 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";
- Assert.assertEquals(IdentifyFile.FeaturesFile,
- ider.identify(data, AppletFormatAdapter.PASTE));
+ assertEquals(IdentifyFile.FeaturesFile,
+ 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, DataSourceType.PASTE));
}
@DataProvider(name = "identifyFiles")
{ "examples/testdata/test.pileup", "PileUp" },
{ "examples/testdata/test.blc", "BLC" },
{ "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
- { "examples/testdata/simplegff3.gff", IdentifyFile.FeaturesFile },
+ { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
{ "examples/testdata/test.jvp", "Jalview" },
+ { "examples/testdata/test.cif", "mmCIF" },
{
"examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
"FASTA" },