/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.seqfetcher;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
-import java.util.Hashtable;
-
import com.stevesoft.pat.Regex;
/**
* generic Reference Retrieval interface for a particular database
- * source/version as cited in DBRefEntry. TODO: add/define property to describe
- * max number of queries that this source can cope with at once. TODO:
- * add/define mechanism for retrieval of Trees and distance matrices from a
- * database (unify with io)
+ * 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 TODO: promote to API
+ * @author JimP
*/
public interface DbSourceProxy
{
*
* @return source string constant used for this DB source
*/
- public String getDbSource();
+ String getDbSource();
/**
* Short meaningful name for this data source for display in menus or
*
* @return String
*/
- public String getDbName();
+ String getDbName();
/**
*
* @return version string for this database.
*/
- public String getDbVersion();
+ String getDbVersion();
/**
* Separator between individual accession queries for a database that allows
* @return string for separating concatenated queries (as individually
* validated by the accession validator)
*/
- public String getAccessionSeparator();
+ String getAccessionSeparator();
/**
* Regular expression for checking form of query string understood by this
*
* @return null or a validation regex
*/
- public Regex getAccessionValidator();
-
- /**
- * DbSource properties hash - define the capabilities of this source Property
- * hash methods defined in DbSourceProxyImpl. See constants in
- * jalview.datamodel.DBRefSource for definition of properties.
- *
- * @return
- */
- public Hashtable getDbSourceProperties();
+ Regex getAccessionValidator();
/**
*
* @return a test/example query that can be used to validate retrieval and
* parsing mechanisms
*/
- public String getTestQuery();
+ String getTestQuery();
/**
- * optionally implemented
+ * 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
*/
- public boolean isValidReference(String accession);
+ boolean isValidReference(String accession);
/**
* make one or more queries to the database and attempt to parse the response
*
* @param queries
* - one or more queries for database in expected form
- * @return null if queries were successful but result was not parsable
+ * @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)
*
*/
- public AlignmentI getSequenceRecords(String queries) throws Exception;
+ AlignmentI getSequenceRecords(String queries) throws Exception;
/**
*
* @return true if a query is currently being made
*/
- public boolean queryInProgress();
+ boolean queryInProgress();
/**
* get the raw reponse from the last set of queries
*
* @return one or more string buffers for each individual query
*/
- public StringBuffer getRawRecords();
+ StringBuffer getRawRecords();
/**
- * Find out more info about the source.
+ * Tier for this data source
*
- * @param dbsourceproperty
- * - one of the database reference source properties in
- * jalview.datamodel.DBRefSource
- * @return true if the source has this property
+ * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
*/
- public boolean isA(Object dbsourceproperty);
+ int getTier();
/**
- * Tier for this data source
+ * 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.
*
- * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
+ * @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
*/
- public int getTier();
-}
+ FeatureSettingsModelI getFeatureColourScheme();
+}
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git://source.jalview.org / jalview.git / blobdiff