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Merge branch 'develop' into features/JAL-1793VCF
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Rfam.java
diff --git
a/src/jalview/ws/dbsources/Rfam.java
b/src/jalview/ws/dbsources/Rfam.java
index
62f2b28
..
97f73d0
100644
(file)
--- a/
src/jalview/ws/dbsources/Rfam.java
+++ b/
src/jalview/ws/dbsources/Rfam.java
@@
-20,24
+20,21
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
+import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
/**
* Contains methods for fetching sequences from Rfam database
*
* @author Lauren Michelle Lui
*/
/**
* Contains methods for fetching sequences from Rfam database
*
* @author Lauren Michelle Lui
*/
-abstract public class Rfam extends Xfam implements DbSourceProxy
+abstract public class Rfam extends Xfam
{
public Rfam()
{
super();
{
public Rfam()
{
super();
- // all extensions of this RFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
}
/*
}
/*
@@
-46,6
+43,7
@@
abstract public class Rfam extends Xfam implements DbSourceProxy
* @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
* consistency with Pfam class
*/
* @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
* consistency with Pfam class
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@
-57,6
+55,7
@@
abstract public class Rfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@
-100,6
+99,7
@@
abstract public class Rfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("RF") == 0;
public boolean isValidReference(String accession)
{
return accession.indexOf("RF") == 0;
@@
-110,9
+110,10
@@
abstract public class Rfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Xfam#getXfamSource()
*/
*
* @see jalview.ws.dbsources.Xfam#getXfamSource()
*/
+ @Override
public String getXfamSource()
{
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.RFAM;
+ return DBRefSource.RFAM;
}
}
}
}