import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
-import jalview.io.FormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MapList;
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
- new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+ new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
/*
* Verify a RESNUM sequence feature in the PDBfile sequence
*/
- SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("GLU: 19 1gaqA", sf.getDescription());
* sequence
*/
StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
- sf = map.sequence.getSequenceFeatures()[0];
+ sf = map.sequence.getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("ALA: 1 1gaqB", sf.getDescription());