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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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";
   }
 
   /*