+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.util;
-import java.util.Vector;
-import java.util.Hashtable;
+import java.util.*;
+
+import jalview.datamodel.*;
public class DBRefUtils
{
- /**
- * Utilities for handling DBRef objects and their collections.
- */
- public static Vector selectRefs(java.util.Vector dbrefs, String[] sources) {
- if (dbrefs==null)
- return null;
- if (sources==null)
- return dbrefs;
- Hashtable srcs = new Hashtable();
- Vector res=new Vector();
- for (int i=0; i<sources.length; i++)
- srcs.put(new String(sources[i]), new Integer(i));
- for (int i=0, j=dbrefs.size(); i<j; i++)
- if (dbrefs.get(i) instanceof jalview.datamodel.DBRefEntry) {
- jalview.datamodel.DBRefEntry entry = (jalview.datamodel.DBRefEntry) dbrefs.get(i);
- if (srcs.containsKey(entry.getSource()))
- res.add(entry);
- }
- if (res.size()>0)
- return res;
- res = null;
- // there are probable memory leaks in the hashtable!
+ /**
+ * Utilities for handling DBRef objects and their collections.
+ */
+ /**
+ *
+ * @param dbrefs Vector of DBRef objects to search
+ * @param sources String[] array of source DBRef IDs to retrieve
+ * @return Vector
+ */
+ public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
+ {
+ if (dbrefs == null)
+ {
return null;
}
+ if (sources == null)
+ {
+ return dbrefs;
+ }
+ Hashtable srcs = new Hashtable();
+ Vector res = new Vector();
+
+ for (int i = 0; i < sources.length; i++)
+ {
+ srcs.put(new String(sources[i]), new Integer(i));
+ }
+ for (int i = 0, j = dbrefs.length; i < j; i++)
+ {
+ if (srcs.containsKey(dbrefs[i].getSource()))
+ {
+ res.addElement(dbrefs[i]);
+ }
+ }
+
+ if (res.size() > 0)
+ {
+ DBRefEntry[] reply = new DBRefEntry[res.size()];
+ for (int i = 0; i < res.size(); i++)
+ {
+ reply[i] = (DBRefEntry) res.elementAt(i);
+ }
+ return reply;
+ }
+ res = null;
+ // there are probable memory leaks in the hashtable!
+ return null;
+ }
+
+ /**
+ * isDasCoordinateSystem
+ *
+ * @param string String
+ * @param dBRefEntry DBRefEntry
+ * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
+ */
+ public static Hashtable DasCoordinateSystemsLookup = null;
+ public static boolean isDasCoordinateSystem(String string,
+ DBRefEntry dBRefEntry)
+ {
+ if (DasCoordinateSystemsLookup == null)
+ { // Initialise
+ DasCoordinateSystemsLookup = new Hashtable();
+ DasCoordinateSystemsLookup.put("pdbresnum",
+ jalview.datamodel.DBRefSource.PDB);
+ DasCoordinateSystemsLookup.put("uniprot",
+ jalview.datamodel.DBRefSource.UNIPROT);
+ DasCoordinateSystemsLookup.put("EMBL",
+ jalview.datamodel.DBRefSource.EMBL);
+ //DasCoordinateSystemsLookup.put("EMBL",
+ // jalview.datamodel.DBRefSource.EMBLCDS);
+ }
+
+ String coordsys = (String) DasCoordinateSystemsLookup.get(string.
+ toLowerCase());
+ if (coordsys != null)
+ {
+ return coordsys.equals(dBRefEntry.getSource());
+ }
+ return false;
+ }
+ public static Hashtable CanonicalSourceNameLookup=null;
+ /**
+ * look up source in an internal list of database reference sources
+ * and return the canonical jalview name for the source, or the original
+ * string if it has no canonical form.
+ * @param source
+ * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
+ */
+ public static String getCanonicalName(String source)
+ {
+ if (CanonicalSourceNameLookup==null) {
+ CanonicalSourceNameLookup = new Hashtable();
+ CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
+ CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
+ CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
+ }
+ String canonical = (String) CanonicalSourceNameLookup.get(source.
+ toLowerCase());
+ if (canonical==null)
+ {
+ return source;
+ }
+ return canonical;
+ }
+ /**
+ * find RefEntry corresponding to a particular pattern
+ * the equals method of each entry is used, from String attributes right down to Mapping attributes.
+ * @param ref Set of references to search
+ * @param entry pattern to collect - null any entry for wildcard match
+ * @return
+ */
+ public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
+ {
+ if (ref==null || entry==null)
+ return null;
+ Vector rfs = new Vector();
+ for (int i=0; i<ref.length;i++)
+ {
+ if (entry.getSource()==null || ref[i].getSource().equals(entry.getSource()))
+ {
+ if (entry.getVersion()==null || ref[i].getVersion().equals(entry.getVersion()))
+ {
+ if (entry.getAccessionId()==null || ref[i].getAccessionId().equals(entry.getAccessionId()))
+ {
+ if (entry.getMap()==null || (ref[i].getMap()!=null && ref[i].getMap().equals(entry.getMap())))
+ {
+ rfs.addElement(ref[i]);
+ }
+ }
+ }
+ }
+ }
+ // TODO Auto-generated method stub
+ if (rfs.size()>0)
+ {
+ DBRefEntry[] rf = new DBRefEntry[rfs.size()];
+ rfs.copyInto(rf);
+ return rf;
+ }
+ return null;
}
+}
git://source.jalview.org / jalview.git / blobdiff