- try
- {
- structureData = new JmolParser("examples/DNMT1_MOUSE.pdb",
- AppletFormatAdapter.FILE);
- assertNotNull(structureData);
- assertNotNull(structureData.getId());
- assertEquals(structureData.getId(), "DNMT1_MOUSE.pdb");
- assertNotNull(structureData.getSeqs());
- assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
- assertEquals(
- structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
- "dnmt1_mouse.pdb");
- } catch (IOException e)
- {
- e.printStackTrace();
- }
+ /*
+ * reads a local structure
+ */
+ structureData = new JmolParser("examples/testdata/localstruct.pdb",
+ AppletFormatAdapter.FILE);
+ assertNotNull(structureData);
+ /*
+ * local structure files should yield a false ID based on the filename
+ */
+ assertNotNull(structureData.getId());
+ assertEquals(structureData.getId(), "localstruct.pdb");
+ assertNotNull(structureData.getSeqs());
+ /*
+ * the ID is also the group for features derived from structure data
+ */
+ assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
+ assertEquals(
+ structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
+ "localstruct.pdb");
+