Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DbSourceProxy	37	0	0	-1.0 -	Show methods

Class DbSourceProxy

Class DbSourceProxy	Line # 37	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
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		}