gene -> domain

[jalview.git] / forester / java / src / org / forester / archaeopteryx / webservices / WebserviceUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
index ea6ff4f..0dad04a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
@@ -45,7 +45,7 @@ public final class WebserviceUtil {
 
     public static final String PFAM_INST                       = "pfam";
     public static final String PFAM_NAME                       = "Pfam";
-    public static final String PFAM_SERVER                     = "http://pfam.janelia.org";
+    public static final String PFAM_SERVER                     = "http://pfam.xfam.org";
     public static final String TOL_NAME                        = "Tree of Life (ToL)";
     public static final String TOL_URL_BASE                    = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=";
     public static final String TOL_WEBSERVER                   = TOL_URL_BASE
@@ -61,21 +61,10 @@ public final class WebserviceUtil {
 
     public static List<PhylogeniesWebserviceClient> createDefaultClients() {
         final List<PhylogeniesWebserviceClient> clients = new ArrayList<PhylogeniesWebserviceClient>();
-        clients.add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
-                                                           "Read Tree from Tree of Life (ToL)...",
-                                                           "Use ToL webservice to obtain a evolutionary tree",
-                                                           "Please enter a Tree of Life node identifier\n(Examples: "
-                                                                   + "14923 for ray-finned fishes, 19386 for Cephalopoda, 2461 for Cnidaria)",
-                                                           WsPhylogenyFormat.TOL_XML_RESPONSE,
-                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
-                                                           WebserviceUtil.TOL_WEBSERVER,
-                                                           true,
-                                                           "http://tolweb.org",
-                                                           null ) );
         clients.add( new BasicPhylogeniesWebserviceClient( TREE_BASE_NAME,
-                                                           "Read Tree(s) from TreeBASE study...",
+                                                           "Read Tree(s) from TreeBASE Study...",
                                                            "Use TreeBASE to obtain evolutionary tree(s) from a study",
-                                                           "Please enter a TreeBASE study (\"S\") identifier (without the \"S\")\n(Examples: 15613, 15632, 14525, 14909)",
+                                                           "Please enter a TreeBASE study (\"S\") identifier (without the \"S\")\n(Examples: 14909, 14525, 15613, 15632)",
                                                            WsPhylogenyFormat.TREEBASE_STUDY,
                                                            null,
                                                            TREEBASE_PHYLOWS_STUDY_URL_BASE
@@ -87,7 +76,7 @@ public final class WebserviceUtil {
         clients.add( new BasicPhylogeniesWebserviceClient( TREE_BASE_NAME,
                                                            "Read Tree from TreeBASE...",
                                                            "Use TreeBASE to obtain a evolutionary tree",
-                                                           "Please enter a TreeBASE tree (\"Tr\") identifier (without the \"Tr\")\n(Examples: 422, 2654, 825, 4931, 2518, 2406, 4934)",
+                                                           "Please enter a TreeBASE tree (\"Tr\") identifier (without the \"Tr\")\n(Examples: 2406, 422, 2654, 825, 4931, 2518, 4934)",
                                                            WsPhylogenyFormat.TREEBASE_TREE,
                                                            null,
                                                            TREEBASE_PHYLOWS_TREE_URL_BASE
@@ -97,7 +86,7 @@ public final class WebserviceUtil {
                                                            "http://www.treebase.org",
                                                            TREE_BASE_INST ) );
         clients.add( new BasicPhylogeniesWebserviceClient( PFAM_NAME,
-                                                           "Read Gene Tree from Pfam...",
+                                                           "Read Domain Tree from Pfam...",
                                                            "Use  Pfam to obtain gene trees for seed alignments",
                                                            "Please enter a Pfam (PF) accession number\n(Examples: 01849 for NAC, 00452 for Bcl-2, 00046 for Homeobox)",
                                                            WsPhylogenyFormat.PFAM,
@@ -120,6 +109,17 @@ public final class WebserviceUtil {
                                                            true,
                                                            "http://www.treefam.org",
                                                            TREE_FAM_INST ) );
+        clients.add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
+                                                           "Read Tree from Tree of Life (ToL)...",
+                                                           "Use ToL webservice to obtain a evolutionary tree",
+                                                           "Please enter a Tree of Life node identifier\n(Examples: "
+                                                                   + "14923 for ray-finned fishes, 19386 for Cephalopoda, 2461 for Cnidaria)",
+                                                           WsPhylogenyFormat.TOL_XML_RESPONSE,
+                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+                                                           WebserviceUtil.TOL_WEBSERVER,
+                                                           true,
+                                                           "http://tolweb.org",
+                                                           null ) );
         return clients;
     }