// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 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
// 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
// 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.
// 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
// 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
* @param categories the set of super terms to be counted
* @param experiment_set the list of GO terms to be analyzed
* @param all_go_terms all terms in the ontology
* @param categories the set of super terms to be counted
* @param experiment_set the list of GO terms to be analyzed
* @param all_go_terms all terms in the ontology
penultimate = my_go_term;
if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )
penultimate = my_go_term;
if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )
while ( ( my_go_term.getSuperGoIds() != null ) && ( my_go_term.getSuperGoIds().size() > 0 ) ) {
if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )
while ( ( my_go_term.getSuperGoIds() != null ) && ( my_go_term.getSuperGoIds().size() > 0 ) ) {
if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )