// 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 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.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceAccessionTools;
public final class WebserviceUtil {
- public static final String TAX_CODE_TO_SCI_NAME = "tax_code_to_sci_name";
- public static final String TREE_FAM_INST = "tree_fam";
- public static final String PFAM_INST = "pfam";
- 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 TOL_NAME = "Tree of Life";
- public static final String TREE_BASE_NAME = "TreeBASE";
- public static final String TREE_FAM_NAME = "TreeFam";
- public static final String PFAM_NAME = "Pfam";
- public static final String PFAM_SERVER = "http://pfam.janelia.org";
+ 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 = "http://purl.org/phylo/treebase/phylows/study/TB2:S";
+ public static final String TREEBASE_PHYLOWS_TREE_URL_BASE = "http://purl.org/phylo/treebase/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 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,
+ 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://tolweb.org",
- null ) );
+ "http://www.treebase.org",
+ TREE_BASE_INST ) );
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"
+ "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://treebase.nescent.org",
- null ) );
+ "http://www.treebase.org",
+ TREE_BASE_INST ) );
clients.add( new BasicPhylogeniesWebserviceClient( PFAM_NAME,
- "Read Gene Tree from Pfam...",
- "Use Pfam to obtain a (full) gene tree",
+ "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/tree/download?alnType=full&acc=PF"
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER,
+ PFAM_SERVER + "/family/PF"
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ + "/tree/download",
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",
+ "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/cgi-bin/getdata.pl?ac=TF"
+ TREE_FAM_URL_BASE
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
- + "&f=full.nhx",
+ + "/tree/newick",
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",
+ 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://www.treefam.org",
- TREE_FAM_INST ) );
+ "http://tolweb.org",
+ null ) );
return clients;
}
+ public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny )
+ throws PhyloXmlDataFormatException {
+ if ( client.getProcessingInstructions().equals( WebserviceUtil.TREE_FAM_INST ) ) {
+ WebserviceUtil.processTreeFamTrees( phylogeny );
+ }
+ else if ( client.getProcessingInstructions().equals( WebserviceUtil.PFAM_INST ) ) {
+ WebserviceUtil.extractSpTremblAccFromNodeName( phylogeny, "sptrembl" );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny, "bootstrap" );
+ }
+ else if ( client.getProcessingInstructions().equals( WebserviceUtil.TREE_BASE_INST ) ) {
+ if ( PhylogenyMethods.isInternalNamesLookLikeConfidences( phylogeny ) ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny, "" );
+ }
+ WebserviceUtil.processTreeBaseTrees( phylogeny );
+ }
+ }
+
static void extractSpTremblAccFromNodeName( final Phylogeny phy, final String source ) {
final PreorderTreeIterator it = new PreorderTreeIterator( phy );
while ( it.hasNext() ) {
}
}
- 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 );
- }
- else if ( client.getProcessingInstructions().equals( WebserviceUtil.TREE_FAM_INST ) ) {
- WebserviceUtil.transferInternalTaxonomyCodeToScientificName( phylogeny );
- WebserviceUtil.transferExternalScientificNameToTaxonomyCode( phylogeny );
- WebserviceUtil.transferSequenceNameToSequenceAccession( phylogeny, "ensembl" );
- WebserviceUtil.setTaxonomyIdentifierType( phylogeny, "ncbi" );
- }
- else if ( client.getProcessingInstructions().equals( WebserviceUtil.PFAM_INST ) ) {
- WebserviceUtil.extractSpTremblAccFromNodeName( phylogeny, "sptrembl" );
- }
- }
-
- static void setTaxonomyIdentifierType( final Phylogeny phy, final String type ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- 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 ) );
- }
- }
- }
-
- static void transferExternalScientificNameToTaxonomyCode( final Phylogeny phy ) throws PhyloXmlDataFormatException {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ static void processTreeBaseTrees( final Phylogeny phy ) {
+ phy.setDescription( TREE_BASE_DESC );
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
- if ( n.isExternal() && n.getNodeData().isHasTaxonomy() ) {
- final String name = n.getNodeData().getTaxonomy().getScientificName();
- if ( !ForesterUtil.isEmpty( name ) && PhyloXmlUtil.TAXOMONY_CODE_PATTERN_STRICT.matcher( name ).matches() ) {
- n.getNodeData().getTaxonomy().setScientificName( "" );
- n.getNodeData().getTaxonomy().setTaxonomyCode( name );
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ final Accession acc = SequenceAccessionTools.parseAccessorFromString( n.getName() );
+ if ( acc != null ) {
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new Sequence() );
+ }
+ final Sequence s = n.getNodeData().getSequence();
+ if ( s.getAccession() == null ) {
+ s.setAccession( acc );
+ }
}
}
}
}
- static void transferInternalTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
+ static void processTreeFamTrees( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
- if ( !n.isExternal() && n.getNodeData().isHasTaxonomy() ) {
- final String name = n.getNodeData().getTaxonomy().getTaxonomyCode();
- if ( !ForesterUtil.isEmpty( name ) ) {
- n.getNodeData().getTaxonomy().setScientificName( name );
- n.getNodeData().getTaxonomy().setTaxonomyCode( "" );
+ if ( n.isExternal() ) {
+ n.getNodeData().setEvent( null );
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ final Accession acc = SequenceAccessionTools.parseAccessorFromString( n.getName() );
+ if ( acc != null ) {
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new Sequence() );
+ }
+ final Sequence s = n.getNodeData().getSequence();
+ if ( s.getAccession() == null ) {
+ s.setAccession( acc );
+ }
+ }
}
}
- }
- }
-
- static void transferSequenceNameToSequenceAccession( final Phylogeny phy, final String source ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasSequence() ) {
- final String name = n.getNodeData().getSequence().getName();
- if ( !ForesterUtil.isEmpty( name ) ) {
- n.getNodeData().getSequence().setName( "" );
- n.getNodeData().getSequence().setAccession( new Accession( name, source ) );
+ else {
+ if ( ( n.getBranchData() != null ) && n.getBranchData().isHasConfidences()
+ && ( n.getBranchData().getConfidence( 0 ) != null ) ) {
+ n.getBranchData().getConfidence( 0 ).setType( "bootstrap" );
}
- }
- }
- }
-
- static void transferTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- final String name = n.getNodeData().getTaxonomy().getTaxonomyCode();
- if ( !ForesterUtil.isEmpty( name ) ) {
- n.getNodeData().getTaxonomy().setScientificName( name );
- n.getNodeData().getTaxonomy().setTaxonomyCode( "" );
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().addTaxonomy( new Taxonomy() );
+ }
+ final Taxonomy t = n.getNodeData().getTaxonomy();
+ if ( ForesterUtil.isEmpty( t.getScientificName() ) ) {
+ t.setScientificName( n.getName() );
+ n.setName( "" );
+ }
}
}
+ if ( n.getNodeData().isHasTaxonomy() && ( n.getNodeData().getTaxonomy().getIdentifier() != null ) ) {
+ n.getNodeData()
+ .getTaxonomy()
+ .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(),
+ "ncbi" ) );
+ }
}
}
}
git://source.jalview.org / jalview.git / blobdiff