From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 26 Apr 2016 15:57:05 +0000 (+0100)
Subject: JAL-2079 update URL for RFAM and PFAM sources
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5bd021923d7743ab6041606723afdc9ddda01921;p=jalview.git

JAL-2079 update URL for RFAM and PFAM sources
---

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;