//
// Copyright (C) 2008-2010 Christian M. Zmasek
// Copyright (C) 2008-2010 Burnham Institute for Medical Research
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx.webservices;
import java.util.List;
import org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
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...",
- "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( 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,
+ PhylogenyMethods.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,
+ PhylogenyMethods.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 ) );
return clients;
}
}
}
- public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny ) {
+ public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny )
+ throws PhyloXmlDataFormatException {
if ( client.getProcessingInstructions().equals( WebserviceUtil.TAX_CODE_TO_SCI_NAME ) ) {
WebserviceUtil.transferTaxonomyCodeToScientificName( phylogeny );
}
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
if ( n.getNodeData().isHasTaxonomy() && ( n.getNodeData().getTaxonomy().getIdentifier() != null ) ) {
- n.getNodeData().getTaxonomy().setIdentifier( new Identifier( n.getNodeData().getTaxonomy()
- .getIdentifier().getValue(), type ) );
+ n.getNodeData()
+ .getTaxonomy()
+ .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(), type ) );
}
}
}
- static void transferExternalScientificNameToTaxonomyCode( final Phylogeny phy ) {
+ static void transferExternalScientificNameToTaxonomyCode( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
}
}
- static void transferInternalTaxonomyCodeToScientificName( final Phylogeny phy ) {
+ static void transferInternalTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
}
}
- static void transferTaxonomyCodeToScientificName( final Phylogeny phy ) {
+ static void transferTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
git://source.jalview.org / jalview.git / blobdiff