git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'releases/Release_2_10_0_Branch'
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
GeneDbSource.java
diff --git
a/src/jalview/ws/dbsources/GeneDbSource.java
b/src/jalview/ws/dbsources/GeneDbSource.java
index
6fbc081
..
992a128
100644
(file)
--- a/
src/jalview/ws/dbsources/GeneDbSource.java
+++ b/
src/jalview/ws/dbsources/GeneDbSource.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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,11
+20,10
@@
*/
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 com.stevesoft.pat.Regex;
/**
* Test class for accessing GeneDB - not yet finished.
/**
* Test class for accessing GeneDB - not yet finished.
@@
-32,13
+31,12
@@
import jalview.ws.seqfetcher.DbSourceProxy;
* @author JimP
*
*/
* @author JimP
*
*/
-public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
+public class GeneDbSource extends EmblXmlSource
{
public GeneDbSource()
{
{
public GeneDbSource()
{
- addDbSourceProperty(DBRefSource.DNASEQDB);
- addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ super();
}
/*
}
/*
@@
-46,6
+44,7
@@
public class GeneDbSource 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
@@
-57,6
+56,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@
-68,6
+68,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.GENEDB;
public String getDbSource()
{
return DBRefSource.GENEDB;
@@
-78,6
+79,7
@@
public class GeneDbSource 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
@@
-89,6
+91,7
@@
public class GeneDbSource 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
{
// query of form
public AlignmentI getSequenceRecords(String queries) throws Exception
{
// query of form
@@
-102,6
+105,7
@@
public class GeneDbSource 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)
{
// TODO Auto-generated method stub
public boolean isValidReference(String accession)
{
// TODO Auto-generated method stub
@@
-111,11
+115,13
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
/**
* return T.Brucei Mannosyl-Transferase TbPIG-M
*/
/**
* return T.Brucei Mannosyl-Transferase TbPIG-M
*/
+ @Override
public String getTestQuery()
{
return "Tb927.6.3300";
}
public String getTestQuery()
{
return "Tb927.6.3300";
}
+ @Override
public String getDbName()
{
return "GeneDB"; // getDbSource();
public String getDbName()
{
return "GeneDB"; // getDbSource();