From 4cdad3c78a8ce85b18a977a916ed7ed91a350f3a Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 1 Dec 2012 01:32:03 +0000 Subject: [PATCH] in progress --- .../src/org/forester/analysis/TaxonomyDataManager.java | 2 +- forester/java/src/org/forester/util/ForesterConstants.java | 2 +- .../java/src/org/forester/ws/seqdb/SequenceDbWsTools.java | 12 ++++-------- .../java/src/org/forester/ws/seqdb/UniProtTaxonomy.java | 7 +++---- 4 files changed, 9 insertions(+), 14 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index 50cd1cc..2bc654f 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -335,7 +335,6 @@ public final class TaxonomyDataManager extends RunnableProcess { .get( lineage.size() - 1 ) ); if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) { for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) { - System.out.println( "up_taxonomy=" + up_taxonomy.getScientificName() ); boolean match = true; I: for( int i = 0; i < lineage.size(); ++i ) { if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) { @@ -345,6 +344,7 @@ public final class TaxonomyDataManager extends RunnableProcess { } if ( match ) { if ( up_tax != null ) { + //TODO this is dead code?! throw new AncestralTaxonomyInferenceException( "lineage \"" + ForesterUtil.stringListToString( lineage, " > " ) + "\" is not unique" ); } diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index 6ff9c10..71246dd 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,7 +27,7 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.007"; + public final static String FORESTER_VERSION = "1.007+"; public final static String FORESTER_DATE = "121130"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index 5c1cc73..b56a633 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -121,20 +121,16 @@ public final class SequenceDbWsTools { final int max_taxonomies_return ) throws IOException { // Hack! Craniata? .. - // if ( sn.equals( "Drosophila" ) ) { - // return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS ); - // } - /* else*/if ( sn.equals( "Xenopus" ) ) { + if ( sn.equals( "Drosophila" ) ) { + return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS ); + } + else if ( sn.equals( "Xenopus" ) ) { return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS ); } // else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) { // return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA ); // } final List result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return ); - System.out.println( "SN=" + sn ); - for( final String string : result ) { - System.out.println( "|" + string ); - } if ( result.size() > 0 ) { return parseUniProtTaxonomy( result ); } diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java index 145569d..0884a6f 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java @@ -45,8 +45,9 @@ public final class UniProtTaxonomy { public final static String CELLULAR_ORGANISMS = "cellular organisms"; public final static String VIRUSES = "Viruses"; public final static UniProtTaxonomy DROSOPHILA_GENUS = new UniProtTaxonomy( new String[] { - CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera", - "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" }, + CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Ecdysozoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", + "Neoptera", "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", + "Drosophila" }, "", "fruit flies", "Drosophila", @@ -72,8 +73,6 @@ public final class UniProtTaxonomy { "species", "283909" ); - // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] { - // CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" ); public UniProtTaxonomy( final String line ) { final String[] items = line.split( "\t" ); if ( items.length < 5 ) { -- 1.7.10.2