X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fgo%2Fetc%2FMetaOntologizer.java;h=11afb543f7a3e370370bb886d634d4e1a9085b19;hb=656be28debec520e0e35a8b311114398a40ea366;hp=970f939b845a9978fe95ef2512383dd7ad79530f;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git diff --git a/forester/java/src/org/forester/go/etc/MetaOntologizer.java b/forester/java/src/org/forester/go/etc/MetaOntologizer.java index 970f939..11afb54 100644 --- a/forester/java/src/org/forester/go/etc/MetaOntologizer.java +++ b/forester/java/src/org/forester/go/etc/MetaOntologizer.java @@ -5,7 +5,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // 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 @@ -15,13 +15,13 @@ // 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 +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go.etc; @@ -51,9 +51,9 @@ import org.forester.go.GoTerm; import org.forester.go.GoUtils; import org.forester.go.OBOparser; import org.forester.go.PfamToGoMapping; -import org.forester.surfacing.BasicSpecies; -import org.forester.surfacing.DomainId; -import org.forester.surfacing.Species; +import org.forester.protein.DomainId; +import org.forester.species.BasicSpecies; +import org.forester.species.Species; import org.forester.surfacing.SurfacingConstants; import org.forester.surfacing.SurfacingUtil; import org.forester.util.ForesterUtil; @@ -66,7 +66,10 @@ public class MetaOntologizer { final static private String PRG_NAME = "meta_ontologizer"; private static final boolean VERBOSE = true; //table-a_41_dollo_all_gains_d-Topology-Elim-Bonferroni.txt: - private final static Pattern PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)_dollo_.*", + //TODO change back + // private final static Pattern PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)_dollo_.*", + // Pattern.CASE_INSENSITIVE ); //TODO this might need some work... + private final static Pattern PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)\\.txt", Pattern.CASE_INSENSITIVE ); //TODO this might need some work... private static boolean hasResultsForSpecies( final Map go_id_to_terms, @@ -146,6 +149,9 @@ public class MetaOntologizer { else if ( line.startsWith( "#" ) ) { current_species = new BasicSpecies( line.substring( 1 ) ); speciesto_to_domain_id.put( current_species, new TreeSet() ); + if ( VERBOSE ) { + ForesterUtil.programMessage( PRG_NAME, "saw " + current_species ); + } } else { if ( current_species == null ) { @@ -438,22 +444,18 @@ public class MetaOntologizer { w.write( ForesterUtil.LINE_SEPARATOR ); w.write( "a.new_type:link { font-size: 7pt; color : #505050; text-decoration : none; }" ); w.write( ForesterUtil.LINE_SEPARATOR ); - w - .write( "a.new_type:hover { font-size: 7pt; color : #000000; background-color : #FFFF00; text-decoration : none; }" ); + w.write( "a.new_type:hover { font-size: 7pt; color : #000000; background-color : #FFFF00; text-decoration : none; }" ); w.write( ForesterUtil.LINE_SEPARATOR ); - w - .write( "a.new_type:hover { font-size: 7pt; color : #000000; background-color : #FFFF00; text-decoration : none; }" ); + w.write( "a.new_type:hover { font-size: 7pt; color : #000000; background-color : #FFFF00; text-decoration : none; }" ); w.write( ForesterUtil.LINE_SEPARATOR ); w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" ); w.write( ForesterUtil.LINE_SEPARATOR ); - w - .write( "th { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 10pt; font-weight: bold }" ); + w.write( "th { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 10pt; font-weight: bold }" ); w.write( ForesterUtil.LINE_SEPARATOR ); w.write( "h1 { color : #000000; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" ); w.write( ForesterUtil.LINE_SEPARATOR ); w.write( "h2 { color : #000000; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" ); - w - .write( "h3 { margin-top: 12px; margin-bottom: 0px; color : #000000; font-family: Verdana, Arial, Helvetica; font-size: 12pt; font-weight: bold }" ); + w.write( "h3 { margin-top: 12px; margin-bottom: 0px; color : #000000; font-family: Verdana, Arial, Helvetica; font-size: 12pt; font-weight: bold }" ); w.write( ForesterUtil.LINE_SEPARATOR ); w.write( "" ); w.write( ForesterUtil.LINE_SEPARATOR ); @@ -592,8 +594,11 @@ public class MetaOntologizer { writer.write( String.valueOf( ontologizer_result.getStudyTerm() ) ); writer.write( "" ); if ( domains_per_species != null ) { - final StringBuilder sb = obtainDomainsForGoId( pfam_to_go, domains_per_species, go_id_to_terms, go_term - .getGoId(), domain_ids_with_go_annot ); + final StringBuilder sb = obtainDomainsForGoId( pfam_to_go, + domains_per_species, + go_id_to_terms, + go_term.getGoId(), + domain_ids_with_go_annot ); writer.write( sb.toString() ); } else {