*/
package jalview.ws.dbsources;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
-import MCview.PDBfile;
-
import com.stevesoft.pat.Regex;
-import jalview.datamodel.AlignmentI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* @author JimP
*
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- AlignmentI pdbfile = null;
+ AlignmentI pdbAlignment = null;
Vector result = new Vector();
String chain = null;
String id = null;
try
{
- pdbfile = new FormatAdapter().readFile(file,
+ pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE, "PDB");
- if (pdbfile != null)
+ 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;
- for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
{
if (pid.getFile() == file)
{
- chid = (String) pid.getProperty().get("CHAIN");
+ chid = pid.getChainCode();
}
;
// now remove marked sequences
for (SequenceI pdbcs : toremove)
{
- pdbfile.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation()!=null)
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
{
- for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ 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, ((chain == null) ? "' '" : chain)}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.no_pdb_records_for_chain", new String[] { id,
+ ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file
stopQuery();
throw (ex);
}
- return pdbfile;
+ return pdbAlignment;
}
/*