2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.seqfetcher;
23 import jalview.datamodel.AlignmentI;
25 import java.util.Hashtable;
27 import com.stevesoft.pat.Regex;
30 * generic Reference Retrieval interface for a particular database
31 * source/version as cited in DBRefEntry. TODO: add/define property to describe
32 * max number of queries that this source can cope with at once. TODO:
33 * add/define mechanism for retrieval of Trees and distance matrices from a
34 * database (unify with io)
36 * @author JimP TODO: promote to API
38 public interface DbSourceProxy
42 * @return source string constant used for this DB source
44 public String getDbSource();
47 * Short meaningful name for this data source for display in menus or
52 public String getDbName();
56 * @return version string for this database.
58 public String getDbVersion();
61 * Separator between individual accession queries for a database that allows
62 * multiple IDs to be fetched in a single query. Null implies that only a
63 * single ID can be fetched at a time.
65 * @return string for separating concatenated queries (as individually
66 * validated by the accession validator)
68 public String getAccessionSeparator();
71 * Regular expression for checking form of query string understood by this
72 * source. If the Regex includes parenthesis, then the first parenthesis
73 * should yield the same accession string as the one used to annotate the
74 * sequence. This is used to match query strings to returned sequences.
76 * @return null or a validation regex
78 public Regex getAccessionValidator();
81 * DbSource properties hash - define the capabilities of this source Property
82 * hash methods defined in DbSourceProxyImpl. See constants in
83 * jalview.datamodel.DBRefSource for definition of properties.
87 public Hashtable getDbSourceProperties();
91 * @return a test/example query that can be used to validate retrieval and
94 public String getTestQuery();
97 * optionally implemented
102 public boolean isValidReference(String accession);
105 * make one or more queries to the database and attempt to parse the response
109 * - one or more queries for database in expected form
110 * @return null if queries were successful but result was not parsable
112 * - propagated from underlying transport to database (note -
113 * exceptions are not raised if query not found in database)
116 public AlignmentI getSequenceRecords(String queries) throws Exception;
120 * @return true if a query is currently being made
122 public boolean queryInProgress();
125 * get the raw reponse from the last set of queries
127 * @return one or more string buffers for each individual query
129 public StringBuffer getRawRecords();
132 * Find out more info about the source.
134 * @param dbsourceproperty
135 * - one of the database reference source properties in
136 * jalview.datamodel.DBRefSource
137 * @return true if the source has this property
139 public boolean isA(Object dbsourceproperty);
142 * Tier for this data source
144 * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
146 public int getTier();