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 com.stevesoft.pat.Regex;
28 * generic Reference Retrieval interface for a particular database
29 * source/version as cited in DBRefEntry. TODO: add/define property to describe
30 * max number of queries that this source can cope with at once. TODO:
31 * add/define mechanism for retrieval of Trees and distance matrices from a
32 * database (unify with io)
34 * @author JimP TODO: promote to API
36 public interface DbSourceProxy
40 * @return source string constant used for this DB source
42 public String getDbSource();
45 * Short meaningful name for this data source for display in menus or
50 public String getDbName();
54 * @return version string for this database.
56 public String getDbVersion();
59 * Separator between individual accession queries for a database that allows
60 * multiple IDs to be fetched in a single query. Null implies that only a
61 * single ID can be fetched at a time.
63 * @return string for separating concatenated queries (as individually
64 * validated by the accession validator)
66 public String getAccessionSeparator();
69 * Regular expression for checking form of query string understood by this
70 * source. If the Regex includes parenthesis, then the first parenthesis
71 * should yield the same accession string as the one used to annotate the
72 * sequence. This is used to match query strings to returned sequences.
74 * @return null or a validation regex
76 public Regex getAccessionValidator();
80 * @return a test/example query that can be used to validate retrieval and
83 public String getTestQuery();
86 * Required for sources supporting multiple query retrieval for use with the
87 * DBRefFetcher, which attempts to limit its queries with putative accession
88 * strings for a source to only those that are likely to be valid.
93 public boolean isValidReference(String accession);
96 * make one or more queries to the database and attempt to parse the response
100 * - one or more queries for database in expected form
101 * @return null if queries were successful but result was not parsable.
102 * Otherwise, an AlignmentI object containing properly annotated data
103 * (e.g. sequences with accessions for this datasource)
105 * - propagated from underlying transport to database (note -
106 * exceptions are not raised if query not found in database)
109 public AlignmentI getSequenceRecords(String queries) throws Exception;
113 * @return true if a query is currently being made
115 public boolean queryInProgress();
118 * get the raw reponse from the last set of queries
120 * @return one or more string buffers for each individual query
122 public StringBuffer getRawRecords();
125 * Tier for this data source
127 * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
129 public int getTier();
132 * Extracts valid accession strings from a query string. If there is an
133 * accession id validator, returns the the matched region or the first
134 * subgroup match from the matched region; else just returns the whole query.
139 String getAccessionIdFromQuery(String query);
142 * Returns the maximum number of accession ids that can be queried in one
147 public int getMaximumQueryCount();
150 * Returns true if the source may provide coding DNA i.e. sequences with
151 * implicit peptide products
155 public boolean isDnaCoding();
158 * Answers true if the database is a source of alignments (for example, domain
163 public boolean isAlignmentSource();