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JAL-2079 update URL for RFAM and PFAM sources
author
Jim Procter
<jprocter@issues.jalview.org>
Tue, 26 Apr 2016 15:57:05 +0000
(16:57 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Tue, 26 Apr 2016 15:57:05 +0000
(16:57 +0100)
src/jalview/ws/dbsources/PfamFull.java
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src/jalview/ws/dbsources/PfamSeed.java
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src/jalview/ws/dbsources/RfamFull.java
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src/jalview/ws/dbsources/RfamSeed.java
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diff --git
a/src/jalview/ws/dbsources/PfamFull.java
b/src/jalview/ws/dbsources/PfamFull.java
index
a07c90e
..
c876756
100644
(file)
--- a/
src/jalview/ws/dbsources/PfamFull.java
+++ b/
src/jalview/ws/dbsources/PfamFull.java
@@
-38,9
+38,10
@@
public class PfamFull extends Pfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
protected String getXFAMURL()
{
- return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";
+ return "http://pfam.xfam.org/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";
}
/*
}
/*
@@
-48,21
+49,25
@@
public class PfamFull extends Pfam implements DbSourceProxy
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
+ @Override
public String getDbName()
{
return "PFAM (Full)";
}
public String getDbName()
{
return "PFAM (Full)";
}
+ @Override
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
+ @Override
public String getTestQuery()
{
return "PF03760";
}
public String getTestQuery()
{
return "PF03760";
}
+ @Override
public String getDbVersion()
{
return null;
public String getDbVersion()
{
return null;
diff --git
a/src/jalview/ws/dbsources/PfamSeed.java
b/src/jalview/ws/dbsources/PfamSeed.java
index
e39fe31
..
289ea03
100644
(file)
--- a/
src/jalview/ws/dbsources/PfamSeed.java
+++ b/
src/jalview/ws/dbsources/PfamSeed.java
@@
-40,9
+40,10
@@
public class PfamSeed extends Pfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
protected String getXFAMURL()
{
- return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=";
+ return "http://pfam.xfam.org/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=";
}
/*
}
/*
@@
-50,16
+51,19
@@
public class PfamSeed extends Pfam implements DbSourceProxy
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
+ @Override
public String getDbName()
{
return "PFAM (Seed)";
}
public String getDbName()
{
return "PFAM (Seed)";
}
+ @Override
public String getDbSource()
{
return jalview.datamodel.DBRefSource.PFAM; // archetype source
}
public String getDbSource()
{
return jalview.datamodel.DBRefSource.PFAM; // archetype source
}
+ @Override
public String getTestQuery()
{
return "PF03760";
public String getTestQuery()
{
return "PF03760";
diff --git
a/src/jalview/ws/dbsources/RfamFull.java
b/src/jalview/ws/dbsources/RfamFull.java
index
a214d51
..
e937b20
100644
(file)
--- a/
src/jalview/ws/dbsources/RfamFull.java
+++ b/
src/jalview/ws/dbsources/RfamFull.java
@@
-40,9
+40,11
@@
public class RfamFull extends Rfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Rfam#getXFAMURL()
*/
*
* @see jalview.ws.dbsources.Rfam#getXFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
protected String getXFAMURL()
{
- return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc=";
+ return "http://rfam.xfam.org/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc=";
+
}
/*
}
/*
@@
-50,16
+52,19
@@
public class RfamFull extends Rfam implements DbSourceProxy
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
+ @Override
public String getDbName()
{
return "RFAM (Full)";
}
public String getDbName()
{
return "RFAM (Full)";
}
+ @Override
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
+ @Override
public String getTestQuery()
{
// Can be retrieved from http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
public String getTestQuery()
{
// Can be retrieved from http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
@@
-68,6
+73,7
@@
public class RfamFull extends Rfam implements DbSourceProxy
return "RF00014";
}
return "RF00014";
}
+ @Override
public String getDbVersion()
{
return null;
public String getDbVersion()
{
return null;
diff --git
a/src/jalview/ws/dbsources/RfamSeed.java
b/src/jalview/ws/dbsources/RfamSeed.java
index
e1993dd
..
8a6c25f
100644
(file)
--- a/
src/jalview/ws/dbsources/RfamSeed.java
+++ b/
src/jalview/ws/dbsources/RfamSeed.java
@@
-40,9
+40,10
@@
public class RfamSeed extends Rfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Rfam#getRFAMURL()
*/
*
* @see jalview.ws.dbsources.Rfam#getRFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
protected String getXFAMURL()
{
- return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&nseLabels=0&format=stockholm&acc=";
+ return "http://rfam.xfam.org/family/alignment/download/format?alnType=seed&nseLabels=0&format=stockholm&acc=";
// Janelia Farms url
// "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc=";
}
// Janelia Farms url
// "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc=";
}
@@
-52,21
+53,25
@@
public class RfamSeed extends Rfam implements DbSourceProxy
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
+ @Override
public String getDbName()
{
return "RFAM (Seed)";
}
public String getDbName()
{
return "RFAM (Seed)";
}
+ @Override
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
+ @Override
public String getTestQuery()
{
return "RF00014";
} // http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
public String getTestQuery()
{
return "RF00014";
} // http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
+ @Override
public String getDbVersion()
{
return null;
public String getDbVersion()
{
return null;