import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import java.io.IOException;
import java.util.ArrayList;
public void setUp() throws IOException
{
alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
+ DataSourceType.PASTE, FileFormat.Fasta);
AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
for (int i = 0; i < anns.length; i++)
anns[4].graphGroup = -1;
anns[4].visible = true;
- BitSet result = AlignmentAnnotationUtils
- .getVisibleLineGraphGroups(AlignmentAnnotationUtils
- .asList(anns));
+ BitSet result = AlignmentAnnotationUtils.getVisibleLineGraphGroups(
+ AlignmentAnnotationUtils.asList(anns));
assertTrue(result.get(5));
assertFalse(result.get(0));
assertFalse(result.get(1));