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.api.FeatureSettingsModelI;
24 import jalview.datamodel.AlignmentI;
26 import com.stevesoft.pat.Regex;
29 * generic Reference Retrieval interface for a particular database
30 * source/version as cited in DBRefEntry.
32 * TODO: add/define mechanism for retrieval of Trees and distance matrices from
33 * a database (unify with io)
37 public interface DbSourceProxy extends DbSourceProxyRoot
40 * Short meaningful name for this data source for display in menus or
49 * @return version string for this database.
51 String getDbVersion();
54 * Separator between individual accession queries for a database that allows
55 * multiple IDs to be fetched in a single query. Null implies that only a
56 * single ID can be fetched at a time.
58 * @return string for separating concatenated queries (as individually
59 * validated by the accession validator)
61 String getAccessionSeparator();
64 * Regular expression for checking form of query string understood by this
65 * source. If the Regex includes parenthesis, then the first parenthesis
66 * should yield the same accession string as the one used to annotate the
67 * sequence. This is used to match query strings to returned sequences.
69 * @return null or a validation regex
71 Regex getAccessionValidator();
75 * @return a test/example query that can be used to validate retrieval and
78 String getTestQuery();
81 * Required for sources supporting multiple query retrieval for use with the
82 * DBRefFetcher, which attempts to limit its queries with putative accession
83 * strings for a source to only those that are likely to be valid.
88 boolean isValidReference(String accession);
91 * make one or more queries to the database and attempt to parse the response
95 * - one or more queries for database in expected form
96 * @return null if queries were successful but result was not parsable.
97 * Otherwise, an AlignmentI object containing properly annotated data
98 * (e.g. sequences with accessions for this datasource)
100 * - propagated from underlying transport to database (note -
101 * exceptions are not raised if query not found in database)
104 AlignmentI getSequenceRecords(String queries) throws Exception;
108 * @return true if a query is currently being made
110 boolean queryInProgress();
113 * get the raw reponse from the last set of queries
115 * @return one or more string buffers for each individual query
117 StringBuffer getRawRecords();
120 * Tier for this data source
122 * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
127 * Extracts valid accession strings from a query string. If there is an
128 * accession id validator, returns the the matched region or the first
129 * subgroup match from the matched region; else just returns the whole query.
134 String getAccessionIdFromQuery(String query);
137 * Returns the maximum number of accession ids that can be queried in one
142 int getMaximumQueryCount();
145 * Returns true if the source may provide coding DNA i.e. sequences with
146 * implicit peptide products
150 boolean isDnaCoding();
153 * Answers true if the database is a source of alignments (for example, domain
158 boolean isAlignmentSource();
161 * Returns an (optional) description of the source, suitable for display as a
166 String getDescription();
169 * Returns the preferred feature colour configuration if there is one, else
174 FeatureSettingsModelI getFeatureColourScheme();