*/
package jalview.ws.dbsources;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
super();
}
+ public static final String FEATURE_INSERTION = "INSERTION";
+
+ public static final String FEATURE_RES_NUM = "RESNUM";
+
+ private static String currentDefaultFomart = DBRefSource.PDB;
+
/*
* (non-Javadoc)
*
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- AlignmentI pdbfile = null;
+ AlignmentI pdbAlignment = null;
Vector result = new Vector();
String chain = null;
String id = null;
stopQuery();
return null;
}
+ String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+ : ".xml";
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ file = ebi.fetchDataAsFile("pdb:" + id,
+ getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+ .getAbsolutePath();
stopQuery();
if (file == null)
{
try
{
- pdbfile = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE, "PDB");
- if (pdbfile != null)
+ pdbAlignment = new FormatAdapter().readFile(file,
+ jalview.io.AppletFormatAdapter.FILE,
+ getCurrentDefaultFomart());
+ if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbfile.getSequences())
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
{
String chid = null;
// Mapping map=null;
// now remove marked sequences
for (SequenceI pdbcs : toremove)
{
- pdbfile.deleteSequence(pdbcs);
+ pdbAlignment.deleteSequence(pdbcs);
if (pdbcs.getAnnotation() != null)
{
for (AlignmentAnnotation aa : pdbcs.getAnnotation())
{
- pdbfile.deleteAnnotation(aa);
+ pdbAlignment.deleteAnnotation(aa);
}
}
}
}
- if (pdbfile == null || pdbfile.getHeight() < 1)
+ if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
"exception.no_pdb_records_for_chain", new String[] { id,
stopQuery();
throw (ex);
}
- return pdbfile;
+ return pdbAlignment;
}
/*
{
return 0;
}
+
+ public static String getCurrentDefaultFomart()
+ {
+ return currentDefaultFomart;
+ }
+
+ public static void setCurrentDefaultFomart(String currentDefaultFomart)
+ {
+ Pdb.currentDefaultFomart = currentDefaultFomart;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}