- clients
- .add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
- "Read Tree from Tree of Life...",
- "Use ToL webservice to obtain a phylogeny",
- "Please enter a Tree of Life node identifier\n(Examples: "
- + "19386 for Cephalopoda, 2461 for Cnidaria, 2466 for Deuterostomia)",
- WsPhylogenyFormat.TOL_XML_RESPONSE,
- PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- WebserviceUtil.TOL_WEBSERVER,
- true,
- "http://tolweb.org",
- null ) );
- clients
- .add( new BasicPhylogeniesWebserviceClient( TREE_BASE_NAME,
- "Read Tree from TreeBASE...",
- "Use TreeBASE to obtain a phylogeny",
- "Please enter a TreeBASE tree identifier\n(Examples: 2654, 825, 4931, 2518, 2406, 4934)",
- WsPhylogenyFormat.NEXUS,
- PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
- "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "?format=nexus",
- true,
- "http://treebase.nescent.org",
- null ) );
- clients
- .add( new BasicPhylogeniesWebserviceClient( PFAM_NAME,
- "Read Gene Tree from Pfam...",
- "Use Pfam to obtain a (full) gene tree",
- "Please enter a Pfam (PF) accession number\n(Examples: 01849 for NAC, 00452 for Bcl-2, 00046 for Homeobox)",
- WsPhylogenyFormat.PFAM,
- null,
- PFAM_SERVER + "/family/tree/download?alnType=full&acc=PF"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER,
- false,
- PFAM_SERVER,
- PFAM_INST ) );
- clients
- .add( new BasicPhylogeniesWebserviceClient( TREE_FAM_NAME,
- "Read Full Gene Tree from TreeFam...",
- "Use TreeFam to obtain a (full) 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/cgi-bin/getdata.pl?ac=TF"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "&f=full.nhx",
- true,
- "http://www.treefam.org",
- TREE_FAM_INST ) );
- clients
- .add( new BasicPhylogeniesWebserviceClient( TREE_FAM_NAME,
- "Read Clean Gene Tree from TreeFam...",
- "Use TreeFam to obtain a (\"clean\") 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/cgi-bin/getdata.pl?ac=TF"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "&f=clean.nhx",
- true,
- "http://www.treefam.org",
- TREE_FAM_INST ) );
+ 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: 14909, 14525, 15613, 15632)",
+ WsPhylogenyFormat.TREEBASE_STUDY,
+ null,
+ TREEBASE_PHYLOWS_STUDY_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "?format=nexus",
+ true,
+ "http://www.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: 2406, 422, 2654, 825, 4931, 2518, 4934)",
+ WsPhylogenyFormat.TREEBASE_TREE,
+ null,
+ TREEBASE_PHYLOWS_TREE_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "?format=nexus",
+ true,
+ "http://www.treebase.org",
+ TREE_BASE_INST ) );
+ clients.add( new BasicPhylogeniesWebserviceClient( PFAM_NAME,
+ "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,
+ null,
+ PFAM_SERVER + "/family/PF"
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "/tree/download",
+ 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,
+ 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 ) );