1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.ws.seqfetcher

File DbSourceProxy.java

 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ws.seqfetcher;
22   
23    import jalview.api.FeatureSettingsModelI;
24    import jalview.datamodel.AlignmentI;
25   
26    import com.stevesoft.pat.Regex;
27   
28    /**
29    * generic Reference Retrieval interface for a particular database
30    * source/version as cited in DBRefEntry.
31    *
32    * TODO: add/define mechanism for retrieval of Trees and distance matrices from
33    * a database (unify with io)
34    *
35    * @author JimP
36    */
 
37    public interface DbSourceProxy
38    {
39    /**
40    *
41    * @return source string constant used for this DB source
42    */
43    String getDbSource();
44   
45    /**
46    * Short meaningful name for this data source for display in menus or
47    * selection boxes.
48    *
49    * @return String
50    */
51    String getDbName();
52   
53    /**
54    *
55    * @return version string for this database.
56    */
57    String getDbVersion();
58   
59    /**
60    * Separator between individual accession queries for a database that allows
61    * multiple IDs to be fetched in a single query. Null implies that only a
62    * single ID can be fetched at a time.
63    *
64    * @return string for separating concatenated queries (as individually
65    * validated by the accession validator)
66    */
67    String getAccessionSeparator();
68   
69    /**
70    * Regular expression for checking form of query string understood by this
71    * source. If the Regex includes parenthesis, then the first parenthesis
72    * should yield the same accession string as the one used to annotate the
73    * sequence. This is used to match query strings to returned sequences.
74    *
75    * @return null or a validation regex
76    */
77    Regex getAccessionValidator();
78   
79    /**
80    *
81    * @return a test/example query that can be used to validate retrieval and
82    * parsing mechanisms
83    */
84    String getTestQuery();
85   
86    /**
87    * Required for sources supporting multiple query retrieval for use with the
88    * DBRefFetcher, which attempts to limit its queries with putative accession
89    * strings for a source to only those that are likely to be valid.
90    *
91    * @param accession
92    * @return
93    */
94    boolean isValidReference(String accession);
95   
96    /**
97    * make one or more queries to the database and attempt to parse the response
98    * into an alignment
99    *
100    * @param queries
101    * - one or more queries for database in expected form
102    * @return null if queries were successful but result was not parsable.
103    * Otherwise, an AlignmentI object containing properly annotated data
104    * (e.g. sequences with accessions for this datasource)
105    * @throws Exception
106    * - propagated from underlying transport to database (note -
107    * exceptions are not raised if query not found in database)
108    *
109    */
110    AlignmentI getSequenceRecords(String queries) throws Exception;
111   
112    /**
113    *
114    * @return true if a query is currently being made
115    */
116    boolean queryInProgress();
117   
118    /**
119    * get the raw reponse from the last set of queries
120    *
121    * @return one or more string buffers for each individual query
122    */
123    StringBuffer getRawRecords();
124   
125    /**
126    * Tier for this data source
127    *
128    * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
129    */
130    int getTier();
131   
132    /**
133    * Extracts valid accession strings from a query string. If there is an
134    * accession id validator, returns the the matched region or the first
135    * subgroup match from the matched region; else just returns the whole query.
136    *
137    * @param query
138    * @return
139    */
140    String getAccessionIdFromQuery(String query);
141   
142    /**
143    * Returns the maximum number of accession ids that can be queried in one
144    * request.
145    *
146    * @return
147    */
148    int getMaximumQueryCount();
149   
150    /**
151    * Returns true if the source may provide coding DNA i.e. sequences with
152    * implicit peptide products
153    *
154    * @return
155    */
156    boolean isDnaCoding();
157   
158    /**
159    * Answers true if the database is a source of alignments (for example, domain
160    * families)
161    *
162    * @return
163    */
164    boolean isAlignmentSource();
165   
166    /**
167    * Returns an (optional) description of the source, suitable for display as a
168    * tooltip, or null
169    *
170    * @return
171    */
172    String getDescription();
173   
174    /**
175    * Returns the preferred feature colour configuration if there is one, else
176    * null
177    *
178    * @return
179    */
180    FeatureSettingsModelI getFeatureColourScheme();
181    }