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3253-omnibus save
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
EmblSource.java
diff --git
a/src/jalview/ws/dbsources/EmblSource.java
b/src/jalview/ws/dbsources/EmblSource.java
index
e5f0c62
..
ec75b04
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblSource.java
+++ b/
src/jalview/ws/dbsources/EmblSource.java
@@
-1,6
+1,6
@@
/*
/*
- * 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.
*
*
* This file is part of Jalview.
*
@@
-20,23
+20,24
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.util.Platform;
+
+import com.stevesoft.pat.Regex;
/**
* @author JimP
*
*/
/**
* @author JimP
*
*/
-public class EmblSource extends EmblXmlSource implements DbSourceProxy
+public class EmblSource extends EmblXmlSource
{
{
+ private static Regex ACCESSION_REGEX;
+
public EmblSource()
{
public EmblSource()
{
- addDbSourceProperty(DBRefSource.DNASEQDB);
- addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ super();
}
/*
}
/*
@@
-44,6
+45,7
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@
-55,9
+57,14
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
public Regex getAccessionValidator()
{
- return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+", null);
+ }
+ return ACCESSION_REGEX;
}
/*
}
/*
@@
-65,6
+72,7
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.EMBL;
public String getDbSource()
{
return DBRefSource.EMBL;
@@
-75,6
+83,7
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
// TODO Auto-generated method stub
public String getDbVersion()
{
// TODO Auto-generated method stub
@@
-86,6
+95,7
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
return getEmblSequenceRecords(DBRefSource.EMBL, queries);
public AlignmentI getSequenceRecords(String queries) throws Exception
{
return getEmblSequenceRecords(DBRefSource.EMBL, queries);
@@
-96,6
+106,7
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
// most embl refs look like ..
public boolean isValidReference(String accession)
{
// most embl refs look like ..
@@
-108,11
+119,13
@@
public class EmblSource extends EmblXmlSource implements DbSourceProxy
/**
* return LHD_CHICK coding gene
*/
/**
* return LHD_CHICK coding gene
*/
+ @Override
public String getTestQuery()
{
return "X53828";
}
public String getTestQuery()
{
return "X53828";
}
+ @Override
public String getDbName()
{
return "EMBL"; // getDbSource();
public String getDbName()
{
return "EMBL"; // getDbSource();