2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 import jalview.datamodel.*;
25 public class DBRefUtils
28 * Utilities for handling DBRef objects and their collections.
32 * @param dbrefs Vector of DBRef objects to search
33 * @param sources String[] array of source DBRef IDs to retrieve
36 public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
46 Hashtable srcs = new Hashtable();
47 Vector res = new Vector();
49 for (int i = 0; i < sources.length; i++)
51 srcs.put(new String(sources[i]), new Integer(i));
53 for (int i = 0, j = dbrefs.length; i < j; i++)
55 if (srcs.containsKey(dbrefs[i].getSource()))
57 res.addElement(dbrefs[i]);
63 DBRefEntry[] reply = new DBRefEntry[res.size()];
64 for (int i = 0; i < res.size(); i++)
66 reply[i] = (DBRefEntry) res.elementAt(i);
71 // there are probable memory leaks in the hashtable!
76 * isDasCoordinateSystem
78 * @param string String
79 * @param dBRefEntry DBRefEntry
80 * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
82 public static Hashtable DasCoordinateSystemsLookup = null;
83 public static boolean isDasCoordinateSystem(String string,
84 DBRefEntry dBRefEntry)
86 if (DasCoordinateSystemsLookup == null)
88 DasCoordinateSystemsLookup = new Hashtable();
89 DasCoordinateSystemsLookup.put("pdbresnum",
90 jalview.datamodel.DBRefSource.PDB);
91 DasCoordinateSystemsLookup.put("uniprot",
92 jalview.datamodel.DBRefSource.UNIPROT);
93 DasCoordinateSystemsLookup.put("EMBL",
94 jalview.datamodel.DBRefSource.EMBL);
95 //DasCoordinateSystemsLookup.put("EMBL",
96 // jalview.datamodel.DBRefSource.EMBLCDS);
99 String coordsys = (String) DasCoordinateSystemsLookup.get(string.
101 if (coordsys != null)
103 return coordsys.equals(dBRefEntry.getSource());
107 public static Hashtable CanonicalSourceNameLookup=null;
109 * look up source in an internal list of database reference sources
110 * and return the canonical jalview name for the source, or the original
111 * string if it has no canonical form.
113 * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
115 public static String getCanonicalName(String source)
117 if (CanonicalSourceNameLookup==null) {
118 CanonicalSourceNameLookup = new Hashtable();
119 CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
120 CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
121 CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
123 String canonical = (String) CanonicalSourceNameLookup.get(source.
132 * find RefEntry corresponding to a particular pattern
133 * the equals method of each entry is used, from String attributes right down to Mapping attributes.
134 * @param ref Set of references to search
135 * @param entry pattern to collect - null any entry for wildcard match
138 public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
140 if (ref==null || entry==null)
142 Vector rfs = new Vector();
143 for (int i=0; i<ref.length;i++)
145 if (entry.getSource()==null || ref[i].getSource().equals(entry.getSource()))
147 if (entry.getVersion()==null || ref[i].getVersion().equals(entry.getVersion()))
149 if (entry.getAccessionId()==null || ref[i].getAccessionId().equals(entry.getAccessionId()))
151 if (entry.getMap()==null || (ref[i].getMap()!=null && ref[i].getMap().equals(entry.getMap())))
153 rfs.addElement(ref[i]);
159 // TODO Auto-generated method stub
162 DBRefEntry[] rf = new DBRefEntry[rfs.size()];