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 TOL_NAME = "Tree of Life";
- public static final String TOL_WEBSERVER = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER;
- public static final String TREE_BASE_DESC = "This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment.";
- public static final String TREE_BASE_INST = "treebase";
- public static final String TREE_BASE_NAME = "TreeBASE";
- public static final String TREE_FAM_INST = "tree_fam";
- public static final String TREE_FAM_NAME = "TreeFam";
-
+ public static final String PFAM_INST = "pfam";
+ public static final String PFAM_NAME = "Pfam";
+ 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
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER;
+ public static final String TREE_BASE_DESC = "This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment.";
+ public static final String TREE_BASE_INST = "treebase";
+ public static final String TREE_BASE_NAME = "TreeBASE";
+ public static final String TREE_FAM_INST = "tree_fam";
+ public static final String TREE_FAM_NAME = "TreeFam";
+ public static final String TREE_FAM_URL_BASE = "http://www.treefam.org/family/TF";
+ public static final String TREEBASE_PHYLOWS_STUDY_URL_BASE = "https://treebase.org/treebase-web/phylows/study/TB2:S";
+ public static final String TREEBASE_PHYLOWS_TREE_URL_BASE = "https://treebase.org/treebase-web/phylows/tree/TB2:Tr";
+
+
+
public static List<PhylogeniesWebserviceClient> createDefaultClients() {
final List<PhylogeniesWebserviceClient> clients = new ArrayList<PhylogeniesWebserviceClient>();
- clients.add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
- "Read Tree from Tree of Life...",
- "Use ToL webservice to obtain a evolutionary tree",
- "Please enter a Tree of Life node identifier\n(Examples: "
- + "19386 for Cephalopoda, 2461 for Cnidaria, 2466 for Deuterostomia)",
- 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...",
"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: 13246, 11662, 562, 16424, 17878, 10190, 14909, 14525, 15613, 15632)",
WsPhylogenyFormat.TREEBASE_STUDY,
null,
- "http://purl.org/phylo/treebase/phylows/study/TB2:S"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "?format=nexus",
+ TREEBASE_PHYLOWS_STUDY_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "?format=nexus",
true,
- "http://www.treebase.org",
+ "https://treebase.org",
TREE_BASE_INST ) );
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,
- "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "?format=nexus",
+ TREEBASE_PHYLOWS_TREE_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "?format=nexus",
true,
- "http://www.treebase.org",
+ "https://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,
PFAM_SERVER + "/family/PF"
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ "/tree/download",
- false,
- PFAM_SERVER,
- PFAM_INST ) );
+ false,
+ PFAM_SERVER,
+ PFAM_INST ) );
clients.add( new BasicPhylogeniesWebserviceClient( TREE_FAM_NAME,
"Read Gene Tree from TreeFam...",
"Use TreeFam to obtain a gene tree",
"Please enter a TreeFam (TF) accession number\n(Examples: 101004 for Cyclin D, 315938 for Hox, 105310 for Wnt)",
WsPhylogenyFormat.NHX,
null,
- "http://www.treefam.org/family/TF"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "/tree/newick",
+ TREE_FAM_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "/tree/newick",
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;
}
}
if ( n.getNodeData().isHasTaxonomy() && ( n.getNodeData().getTaxonomy().getIdentifier() != null ) ) {
n.getNodeData()
- .getTaxonomy()
- .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(),
- "ncbi" ) );
+ .getTaxonomy()
+ .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(),
+ "ncbi" ) );
}
}
}
git://source.jalview.org / jalview.git / blobdiff