-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws.seqfetcher;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-\r
-import java.util.Hashtable;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-/**\r
- * generic Reference Retrieval interface for a particular database\r
- * source/version as cited in DBRefEntry. TODO: add/define property to describe\r
- * max number of queries that this source can cope with at once. TODO:\r
- * add/define mechanism for retrieval of Trees and distance matrices from a\r
- * database (unify with io)\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public interface DbSourceProxy\r
-{\r
- /**\r
- * \r
- * @return source string constant used for this DB source\r
- */\r
- public String getDbSource();\r
-\r
- /**\r
- * Short meaningful name for this data source for display in menus or\r
- * selection boxes.\r
- * \r
- * @return String\r
- */\r
- public String getDbName();\r
-\r
- /**\r
- * \r
- * @return version string for this database.\r
- */\r
- public String getDbVersion();\r
-\r
- /**\r
- * Separator between individual accession queries for a database that allows\r
- * multiple IDs to be fetched in a single query. Null implies that only a\r
- * single ID can be fetched at a time.\r
- * \r
- * @return string for separating concatenated queries (as individually\r
- * validated by the accession validator)\r
- */\r
- public String getAccessionSeparator();\r
-\r
- /**\r
- * Regular expression for checking form of query string understood by this\r
- * source.\r
- * \r
- * @return null or a validation regex\r
- */\r
- public Regex getAccessionValidator();\r
-\r
- /**\r
- * DbSource properties hash - define the capabilities of this source Property\r
- * hash methods defined in DbSourceProxyImpl. See constants in\r
- * jalview.datamodel.DBRefSource for definition of properties.\r
- * \r
- * @return\r
- */\r
- public Hashtable getDbSourceProperties();\r
-\r
- /**\r
- * \r
- * @return a test/example query that can be used to validate retrieval and\r
- * parsing mechanisms\r
- */\r
- public String getTestQuery();\r
-\r
- /**\r
- * optionally implemented\r
- * \r
- * @param accession\r
- * @return\r
- */\r
- public boolean isValidReference(String accession);\r
-\r
- /**\r
- * make one or more queries to the database and attempt to parse the response\r
- * into an alignment\r
- * \r
- * @param queries\r
- * @return null if queries were successful but result was not parsable\r
- * @throws Exception\r
- * TODO\r
- */\r
- public AlignmentI getSequenceRecords(String queries) throws Exception;\r
-\r
- /**\r
- * \r
- * @return true if a query is currently being made\r
- */\r
- public boolean queryInProgress();\r
-\r
- /**\r
- * get the raw reponse from the last set of queries\r
- * \r
- * @return one or more string buffers for each individual query\r
- */\r
- public StringBuffer getRawRecords();\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.seqfetcher;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * generic Reference Retrieval interface for a particular database
+ * source/version as cited in DBRefEntry.
+ *
+ * TODO: add/define mechanism for retrieval of Trees and distance matrices from
+ * a database (unify with io)
+ *
+ * @author JimP
+ */
+public interface DbSourceProxy
+{
+ /**
+ *
+ * @return source string constant used for this DB source
+ */
+ String getDbSource();
+
+ /**
+ * Short meaningful name for this data source for display in menus or
+ * selection boxes.
+ *
+ * @return String
+ */
+ String getDbName();
+
+ /**
+ *
+ * @return version string for this database.
+ */
+ String getDbVersion();
+
+ /**
+ * Separator between individual accession queries for a database that allows
+ * multiple IDs to be fetched in a single query. Null implies that only a
+ * single ID can be fetched at a time.
+ *
+ * @return string for separating concatenated queries (as individually
+ * validated by the accession validator)
+ */
+ String getAccessionSeparator();
+
+ /**
+ * Regular expression for checking form of query string understood by this
+ * source. If the Regex includes parenthesis, then the first parenthesis
+ * should yield the same accession string as the one used to annotate the
+ * sequence. This is used to match query strings to returned sequences.
+ *
+ * @return null or a validation regex
+ */
+ Regex getAccessionValidator();
+
+ /**
+ *
+ * @return a test/example query that can be used to validate retrieval and
+ * parsing mechanisms
+ */
+ String getTestQuery();
+
+ /**
+ * Required for sources supporting multiple query retrieval for use with the
+ * DBRefFetcher, which attempts to limit its queries with putative accession
+ * strings for a source to only those that are likely to be valid.
+ *
+ * @param accession
+ * @return
+ */
+ boolean isValidReference(String accession);
+
+ /**
+ * make one or more queries to the database and attempt to parse the response
+ * into an alignment
+ *
+ * @param queries
+ * - one or more queries for database in expected form
+ * @return null if queries were successful but result was not parsable.
+ * Otherwise, an AlignmentI object containing properly annotated data
+ * (e.g. sequences with accessions for this datasource)
+ * @throws Exception
+ * - propagated from underlying transport to database (note -
+ * exceptions are not raised if query not found in database)
+ *
+ */
+ AlignmentI getSequenceRecords(String queries) throws Exception;
+
+ /**
+ *
+ * @return true if a query is currently being made
+ */
+ boolean queryInProgress();
+
+ /**
+ * get the raw reponse from the last set of queries
+ *
+ * @return one or more string buffers for each individual query
+ */
+ StringBuffer getRawRecords();
+
+ /**
+ * Tier for this data source
+ *
+ * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
+ */
+ int getTier();
+
+ /**
+ * Extracts valid accession strings from a query string. If there is an
+ * accession id validator, returns the the matched region or the first
+ * subgroup match from the matched region; else just returns the whole query.
+ *
+ * @param query
+ * @return
+ */
+ String getAccessionIdFromQuery(String query);
+
+ /**
+ * Returns the maximum number of accession ids that can be queried in one
+ * request.
+ *
+ * @return
+ */
+ int getMaximumQueryCount();
+
+ /**
+ * Returns true if the source may provide coding DNA i.e. sequences with
+ * implicit peptide products
+ *
+ * @return
+ */
+ boolean isDnaCoding();
+
+ /**
+ * Answers true if the database is a source of alignments (for example, domain
+ * families)
+ *
+ * @return
+ */
+ boolean isAlignmentSource();
+
+ /**
+ * Returns an (optional) description of the source, suitable for display as a
+ * tooltip, or null
+ *
+ * @return
+ */
+ String getDescription();
+
+ /**
+ * Returns the preferred feature colour configuration if there is one, else
+ * null
+ *
+ * @return
+ */
+ FeatureSettingsModelI getFeatureColourScheme();
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff