From 1a94ef601e050dcda8d2b5492918f49ea7c430d9 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Mon, 4 Jun 2012 17:54:49 +0000 Subject: [PATCH] in progress --- .../org/forester/analysis/TaxonomyDataManager.java | 25 +++++++++++++------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index c2c625b..15d58a2 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -126,8 +126,8 @@ public final class TaxonomyDataManager extends RunnableProcess { } private final static UniProtTaxonomy obtainTaxonomy( final HashMap cache, - final Object query, - final QUERY_TYPE qt ) throws IOException, + final Object query, + final QUERY_TYPE qt ) throws IOException, AncestralTaxonomyInferenceException { if ( cache.containsKey( query ) ) { return cache.get( query ).copy(); @@ -236,13 +236,22 @@ public final class TaxonomyDataManager extends RunnableProcess { uniprot_tax = obtainUniProtTaxonomy( tax, null, qt ); } else { - uniprot_tax = obtainUniProtTaxonomy( node.getName(), null, qt ); + uniprot_tax = obtainUniProtTaxonomy( node.getName(), qt ); } if ( uniprot_tax != null ) { + if ( tax == null ) { + tax = new Taxonomy(); + node.getNodeData().addTaxonomy( tax ); + } updateTaxonomy( qt, node, tax, uniprot_tax ); } else { - not_found.add( tax.toString() ); + if ( tax != null ) { + not_found.add( tax.toString() ); + } + else { + not_found.add(node.getName() ); + } if ( delete && node.isExternal() ) { not_found_external_nodes.add( node ); } @@ -294,20 +303,20 @@ public final class TaxonomyDataManager extends RunnableProcess { } } - public final static UniProtTaxonomy obtainUniProtTaxonomy( final String simple_name, Object query, QUERY_TYPE qt ) + public final static UniProtTaxonomy obtainUniProtTaxonomy( final String simple_name, QUERY_TYPE qt ) throws IOException, AncestralTaxonomyInferenceException { if ( ForesterUtil.isEmpty( simple_name ) ) { throw new IllegalArgumentException( "illegal attempt to use empty simple name" ); } qt = QUERY_TYPE.SN; - UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), query, qt ); + UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), simple_name, qt ); if ( ut == null ) { qt = QUERY_TYPE.CODE; - ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), query, qt ); + ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), simple_name, qt ); } if ( ut == null ) { qt = QUERY_TYPE.CN; - ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), query, qt ); + ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), simple_name, qt ); } return ut; } -- 1.7.10.2