X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=c45a46597a156607f325ace2191e050261f445f3;hb=aec85d6dfc1dd5970a50a53dc9d161635d1e9960;hp=67097efe11ec68c0ba933ffd01629898cb42f988;hpb=56d8f0b05df600ea54388d58cf505d911beb630a;p=jalview.git
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 67097ef..c45a465 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,131 +1,147 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-package jalview.ws.seqfetcher;
-
-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)
- *
- * @author JimP
- *
- */
-public interface DbSourceProxy
-{
- /**
- *
- * @return source string constant used for this DB source
- */
- public String getDbSource();
-
- /**
- * Short meaningful name for this data source for display in menus or
- * selection boxes.
- *
- * @return String
- */
- public String getDbName();
-
- /**
- *
- * @return version string for this database.
- */
- public 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)
- */
- public String getAccessionSeparator();
-
- /**
- * Regular expression for checking form of query string understood by this
- * source.
- *
- * @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();
-
- /**
- *
- * @return a test/example query that can be used to validate retrieval and
- * parsing mechanisms
- */
- public String getTestQuery();
-
- /**
- * optionally implemented
- *
- * @param accession
- * @return
- */
- public boolean isValidReference(String accession);
-
- /**
- * make one or more queries to the database and attempt to parse the response
- * into an alignment
- *
- * @param queries
- * @return null if queries were successful but result was not parsable
- * @throws Exception
- * TODO
- */
- public AlignmentI getSequenceRecords(String queries) throws Exception;
-
- /**
- *
- * @return true if a query is currently being made
- */
- public 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();
-
-
- /**
- * Find out more info about the source.
- * @param dbsourceproperty - one of the database reference source properties in jalview.datamodel.DBRefSource
- * @return true if the source has this property
- */
- public boolean isA(Object dbsourceproperty);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.seqfetcher;
+
+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)
+ *
+ * @author JimP TODO: promote to API
+ */
+public interface DbSourceProxy
+{
+ /**
+ *
+ * @return source string constant used for this DB source
+ */
+ public String getDbSource();
+
+ /**
+ * Short meaningful name for this data source for display in menus or
+ * selection boxes.
+ *
+ * @return String
+ */
+ public String getDbName();
+
+ /**
+ *
+ * @return version string for this database.
+ */
+ public 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)
+ */
+ public 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
+ */
+ 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();
+
+ /**
+ *
+ * @return a test/example query that can be used to validate retrieval and
+ * parsing mechanisms
+ */
+ public String getTestQuery();
+
+ /**
+ * optionally implemented
+ *
+ * @param accession
+ * @return
+ */
+ public 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
+ * @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;
+
+ /**
+ *
+ * @return true if a query is currently being made
+ */
+ public 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();
+
+ /**
+ * Find out more info about the source.
+ *
+ * @param dbsourceproperty
+ * - one of the database reference source properties in
+ * jalview.datamodel.DBRefSource
+ * @return true if the source has this property
+ */
+ public boolean isA(Object dbsourceproperty);
+
+ /**
+ * Tier for this data source
+ *
+ * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
+ */
+ public int getTier();
+}