import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class StockholmFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
@Test(groups = { "Functional" })
public void pfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
+ testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0);
}
@Test(groups = { "Functional" })
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
- AlignmentI al = af.readFile(PfamFile, af.FILE,
- new IdentifyFile().identify(PfamFile, af.FILE));
+ AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE,
+ new IdentifyFile().identify(PfamFile, DataSourceType.FILE));
int numpdb = 0;
for (SequenceI sq : al.getSequences())
{
@Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
+ testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1);
}
/**
* f
*/
- public static void testFileIOwithFormat(File f, String ioformat,
+ public static void testFileIOwithFormat(File f, FileFormatI ioformat,
int naliannot, int nminseqann)
{
System.out.println("Reading file: " + f);
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
+ outputfile + "\n<<EOF\n");
// test for consistency in io
AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
- AppletFormatAdapter.PASTE, ioformat);
+ DataSourceType.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- String identifyoutput = new IdentifyFile().identify(outputfile,
- AppletFormatAdapter.PASTE);
+ FileFormatI identifyoutput = new IdentifyFile().identify(outputfile,
+ DataSourceType.PASTE);
assertNotNull("Identify routine failed for outputformat " + ioformat,
identifyoutput);
assertTrue(