forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2010 Christian M. Zmasek
   6 // Copyright (C) 2008-2010 Burnham Institute for Medical Research
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // Contact: phylosoft @ gmail . com
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  24
  25 package org.forester.archaeopteryx.webservices;
  26
  27 import java.util.ArrayList;
  28 import java.util.List;
  29
  30 import org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat;
  31 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  32 import org.forester.phylogeny.Phylogeny;
  33 import org.forester.phylogeny.PhylogenyMethods;
  34 import org.forester.phylogeny.PhylogenyNode;
  35 import org.forester.phylogeny.data.Accession;
  36 import org.forester.phylogeny.data.Identifier;
  37 import org.forester.phylogeny.data.Sequence;
  38 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  39 import org.forester.phylogeny.iterators.PreorderTreeIterator;
  40 import org.forester.util.ForesterUtil;
  41
  42 public final class WebserviceUtil {
  43
  44     public static final String TREE_FAM_INST  = "tree_fam";
  45     public static final String PFAM_INST      = "pfam";
  46     public static final String TOL_WEBSERVER  = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="
  47                                                       + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER;
  48     public static final String TOL_NAME       = "Tree of Life";
  49     public static final String TREE_BASE_NAME = "TreeBASE";
  50     public static final String TREE_FAM_NAME  = "TreeFam";
  51     public static final String PFAM_NAME      = "Pfam";
  52     public static final String PFAM_SERVER    = "http://pfam.janelia.org";
  53
  54     public static List<PhylogeniesWebserviceClient> createDefaultClients() {
  55         final List<PhylogeniesWebserviceClient> clients = new ArrayList<PhylogeniesWebserviceClient>();
  56         clients.add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
  57                                                            "Read Tree from Tree of Life...",
  58                                                            "Use ToL webservice to obtain a evolutionary tree",
  59                                                            "Please enter a Tree of Life node identifier\n(Examples: "
  60                                                                    + "19386 for Cephalopoda, 2461 for Cnidaria, 2466 for Deuterostomia)",
  61                                                            WsPhylogenyFormat.TOL_XML_RESPONSE,
  62                                                            PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
  63                                                            WebserviceUtil.TOL_WEBSERVER,
  64                                                            true,
  65                                                            "http://tolweb.org",
  66                                                            null ) );
  67         clients.add( new BasicPhylogeniesWebserviceClient( TREE_BASE_NAME,
  68                                                            "Read Tree from TreeBASE...",
  69                                                            "Use TreeBASE to obtain a evolutionary tree",
  70                                                            "Please enter a TreeBASE tree identifier\n(Examples: 2654, 825, 4931, 2518, 2406, 4934)",
  71                                                            WsPhylogenyFormat.TREEBASE,
  72                                                            null,
  73                                                            "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
  74                                                                    + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
  75                                                                    + "?format=nexus",
  76                                                            true,
  77                                                            "http://www.treebase.org",
  78                                                            null ) );
  79         clients.add( new BasicPhylogeniesWebserviceClient( PFAM_NAME,
  80                                                            "Read Gene Tree from Pfam...",
  81                                                            "Use  Pfam to obtain gene trees for seed alignments",
  82                                                            "Please enter a Pfam (PF) accession number\n(Examples: 01849 for NAC, 00452 for Bcl-2, 00046 for Homeobox)",
  83                                                            WsPhylogenyFormat.PFAM,
  84                                                            null,
  85                                                            PFAM_SERVER + "/family/PF"
  86                                                                    + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
  87                                                                    + "/tree/download",
  88                                                            false,
  89                                                            PFAM_SERVER,
  90                                                            PFAM_INST ) );
  91         clients.add( new BasicPhylogeniesWebserviceClient( TREE_FAM_NAME,
  92                                                            "Read Gene Tree from TreeFam...",
  93                                                            "Use TreeFam to obtain a gene tree",
  94                                                            "Please enter a TreeFam (TF) accession number\n(Examples: 101004 for Cyclin D, 315938 for Hox, 105310 for Wnt)",
  95                                                            WsPhylogenyFormat.NHX,
  96                                                            null,
  97                                                            "http://www.treefam.org/family/TF"
  98                                                                    + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
  99                                                                    + "/tree/newick",
 100                                                            true,
 101                                                            "http://www.treefam.org",
 102                                                            TREE_FAM_INST ) );
 103         return clients;
 104     }
 105
 106     static void extractSpTremblAccFromNodeName( final Phylogeny phy, final String source ) {
 107         final PreorderTreeIterator it = new PreorderTreeIterator( phy );
 108         while ( it.hasNext() ) {
 109             final PhylogenyNode n = it.next();
 110             if ( !ForesterUtil.isEmpty( n.getName() ) ) {
 111                 final String name = n.getName();
 112                 final int i = name.lastIndexOf( "/" );
 113                 if ( i > 0 ) {
 114                     final String acc_str = name.substring( 0, i );
 115                     if ( !ForesterUtil.isEmpty( acc_str ) ) {
 116                         final Sequence seq = new Sequence();
 117                         final Accession acc = new Accession( acc_str, source );
 118                         seq.setAccession( acc );
 119                         n.getNodeData().setSequence( seq );
 120                     }
 121                 }
 122             }
 123         }
 124     }
 125
 126     public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny )
 127             throws PhyloXmlDataFormatException {
 128         if ( client.getProcessingInstructions().equals( WebserviceUtil.TREE_FAM_INST ) ) {
 129
 130             WebserviceUtil.processTreeFamTrees( phylogeny );
 131         }
 132         else if ( client.getProcessingInstructions().equals( WebserviceUtil.PFAM_INST ) ) {
 133             WebserviceUtil.extractSpTremblAccFromNodeName( phylogeny, "sptrembl" );
 134             PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny, "bootstrap" );        }
 135     }
 136
 137     static void processTreeFamTrees( final Phylogeny phy ) {
 138         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 139         while ( it.hasNext() ) {
 140             final PhylogenyNode n = it.next();
 141             if ( n.isExternal() ) {
 142                 n.getNodeData().setEvent( null );
 143             }
 144
 145             if ( n.getNodeData().isHasTaxonomy() && ( n.getNodeData().getTaxonomy().getIdentifier() != null ) ) {
 146                 n.getNodeData()
 147                         .getTaxonomy()
 148                         .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(), "ncbi" ) );
 149             }
 150         }
 151     }
 152
 153
 154 }