From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Aug 2017 18:31:29 +0000 (+0100)
Subject: JAL-2425 raw stockholm download URLs
X-Git-Tag: Release_2_10_2~3^2~12^2~4
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=35c3de415520c5636e12d47d4043e62e5302e24b

JAL-2425 raw stockholm download URLs
---

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 3c5373d..12b193d 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -39,9 +39,15 @@ public class PfamFull extends Pfam
   @Override
   protected String getXFAMURL()
   {
-    return "http://pfam.xfam.org/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";
+    return "http://pfam.xfam.org/family/";
+
   }
 
+  @Override
+  public String getXFAMURLSUFFIX()
+  {
+    return "/alignment/full";
+  }
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index ba9d1e0..9f07e5d 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -41,9 +41,14 @@ public class PfamSeed extends Pfam
   @Override
   protected String getXFAMURL()
   {
-    return "http://pfam.xfam.org/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=";
+    return "http://pfam.xfam.org/family/";
   }
 
+  @Override
+  public String getXFAMURLSUFFIX()
+  {
+    return "/alignment/seed";
+  }
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index e6fc8ff..e263c4b 100644
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -41,10 +41,15 @@ public class RfamFull extends Rfam
   @Override
   protected String getXFAMURL()
   {
-    return "http://rfam.xfam.org/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc=";
+    return "http://rfam.xfam.org/family/";
 
   }
 
+  @Override
+  public String getXFAMURLSUFFIX()
+  {
+    return "/alignment/full";
+  }
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index 580ebe2..b2fe72e 100644
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -42,14 +42,11 @@ public class RfamSeed extends Rfam
   protected String getXFAMURL()
   {
     return "http://rfam.xfam.org/family/";
-    // Janelia Farms url
-    // "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc=";
   }
 
   @Override
   public String getXFAMURLSUFFIX()
   {
-    return "/alignment";
   }
 
   /*