X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblCdsSouce.java;h=3a9ebe9e6c43b964be1588d00cae7c534ae03652;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=5b43fc4ba24b6a69854b39bb0d9990e94979e3a7;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 5b43fc4..3a9ebe9 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,88 +1,95 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.dbsources;
-
-import java.util.Hashtable;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
-public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
-{
-
- public EmblCdsSouce()
- {
- super();
- addDbSourceProperty(DBRefSource.CODINGSEQDB);
- }
-
- public String getAccessionSeparator()
- {
- return null;
- }
-
- public Regex getAccessionValidator()
- {
- return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
- }
-
- public String getDbSource()
- {
- return DBRefSource.EMBLCDS;
- }
-
- public String getDbVersion()
- {
- return "0"; // TODO : this is dynamically set for a returned record - not
- // tied to proxy
- }
-
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- if (queries.indexOf(".") > -1)
- {
- queries = queries.substring(0, queries.indexOf("."));
- }
- return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
- }
-
- public boolean isValidReference(String accession)
- {
- // most embl CDS refs look like ..
- // TODO: improve EMBLCDS regex
- return (accession == null || accession.length() < 2) ? false
- : getAccessionValidator().search(accession);
- }
-
- /**
- * cDNA for LDHA_CHICK swissprot sequence
- */
- public String getTestQuery()
- {
- return "CAA37824";
- }
-
- public String getDbName()
- {
- return "EMBL (CDS)";
- }
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
+{
+
+ public EmblCdsSouce()
+ {
+ super();
+ addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ }
+
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ public Regex getAccessionValidator()
+ {
+ return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+ }
+
+ public String getDbSource()
+ {
+ return DBRefSource.EMBLCDS;
+ }
+
+ public String getDbVersion()
+ {
+ return "0"; // TODO : this is dynamically set for a returned record - not
+ // tied to proxy
+ }
+
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ if (queries.indexOf(".") > -1)
+ {
+ queries = queries.substring(0, queries.indexOf("."));
+ }
+ return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
+ }
+
+ public boolean isValidReference(String accession)
+ {
+ // most embl CDS refs look like ..
+ // TODO: improve EMBLCDS regex
+ return (accession == null || accession.length() < 2) ? false
+ : getAccessionValidator().search(accession);
+ }
+
+ /**
+ * cDNA for LDHA_CHICK swissprot sequence
+ */
+ public String getTestQuery()
+ {
+ return "CAA37824";
+ }
+
+ public String getDbName()
+ {
+ return "EMBL (CDS)";
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+}