X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblSource.java;h=6bbe2e15de923fddfb05a1fa04682aff354ad225;hb=48eba1af1959565659fae9f9e7f4e28d9726c28c;hp=f249fbcbdb3f10fde99134cf86bb3f85d5ef1deb;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index f249fbc..6bbe2e1 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,49 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * 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 java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+import com.stevesoft.pat.Regex;
/**
* @author JimP
*
*/
-public class EmblSource extends EmblXmlSource implements DbSourceProxy
+public class EmblSource extends EmblXmlSource
{
public EmblSource()
{
- addDbSourceProperty(DBRefSource.DNASEQDB);
- addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ super();
}
/*
@@ -51,6 +42,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@ -62,9 +54,10 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
- return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+ return new Regex("^[A-Z]+[0-9]+");
}
/*
@@ -72,6 +65,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.EMBL;
@@ -82,6 +76,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
// TODO Auto-generated method stub
@@ -93,6 +88,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
return getEmblSequenceRecords(DBRefSource.EMBL, queries);
@@ -103,6 +99,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
// most embl refs look like ..
@@ -115,13 +112,21 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
/**
* return LHD_CHICK coding gene
*/
+ @Override
public String getTestQuery()
{
return "X53828";
}
+ @Override
public String getDbName()
{
return "EMBL"; // getDbSource();
}
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
}