From 5bd021923d7743ab6041606723afdc9ddda01921 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 26 Apr 2016 16:57:05 +0100 Subject: [PATCH] JAL-2079 update URL for RFAM and PFAM sources --- src/jalview/ws/dbsources/PfamFull.java | 7 ++++++- src/jalview/ws/dbsources/PfamSeed.java | 6 +++++- src/jalview/ws/dbsources/RfamFull.java | 8 +++++++- src/jalview/ws/dbsources/RfamSeed.java | 7 ++++++- 4 files changed, 24 insertions(+), 4 deletions(-) diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java index a07c90e..c876756 100644 --- 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() */ + @Override 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() */ + @Override public String getDbName() { return "PFAM (Full)"; } + @Override public String getDbSource() { return getDbName(); // so we have unique DbSource string. } + @Override public String getTestQuery() { return "PF03760"; } + @Override 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 --- 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() */ + @Override 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() */ + @Override public String getDbName() { return "PFAM (Seed)"; } + @Override public String getDbSource() { return jalview.datamodel.DBRefSource.PFAM; // archetype source } + @Override 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 --- 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() */ + @Override 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() */ + @Override public String getDbName() { return "RFAM (Full)"; } + @Override 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 @@ -68,6 +73,7 @@ public class RfamFull extends Rfam implements DbSourceProxy return "RF00014"; } + @Override 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 --- 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() */ + @Override 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="; } @@ -52,21 +53,25 @@ public class RfamSeed extends Rfam implements DbSourceProxy * * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName() */ + @Override public String getDbName() { return "RFAM (Seed)"; } + @Override 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 + @Override public String getDbVersion() { return null; -- 1.7.10.2