private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
- PhylipFile.FILE_DESC);
+ AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+ FileFormat.Phylip);
assertNotNull("Couldn't read supplied alignment data.", al);
Map<String, String> data = PhylipFileTests.getTestData();
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
- PhylipFile.FILE_DESC);
+ AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+ FileFormat.Phylip);
assertNotNull("Couldn't read supplied alignment data.", al);
- String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
+ String outputfile = rf.formatSequences(FileFormat.Phylip, al, true);
AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
- AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
+ DataSourceType.PASTE, FileFormat.Phylip);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
+ false);
}
}