// 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
// 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/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.surfacing;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
+import org.forester.protein.DomainId;
+import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
final boolean verbose,
final String automated_pairwise_comparison_prefix,
final String command_line_prg_name,
- final boolean display_histograms,
final File out_dir,
final boolean write_pairwise_comparisons ) {
init();
list_of_genome_wide_combinable_domains
.get( j ) );
genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
- // TODO make histos for these 5 values
double dissimilarity_score_mean;
if ( stats.getN() < 1 ) {
// No domains in common
new StringBuilder( species_i + "-"
+ species_j ),
writer,
+ null,
similarities,
true,
null,
+ pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
}
}
- // pairwise_matrix.setValue( i, j, cdc_list.get( cdc_list.size()
- // - 1 ) );
if ( pw_stats != null ) {
if ( pw_stats.getMin() >= pw_stats.getMax() ) {
- ForesterUtil.printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
- + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
- + pw_stats.getMax() + "], possibly indicating that a genome is compared to itself" );
- }
- if ( display_histograms && ( pw_stats.getMin() < pw_stats.getMax() ) ) {
- //final double[] values = pw_stats.getDataAsDoubleArray();
- // List<HistogramDataItem> data_items = new
- // ArrayList<HistogramDataItem>( values.length );
- // for( int n = 0; n < values.length; i++ ) {
- // data_items.add( new BasicHistogramDataItem( "", values[ n ] )
- // );
- // }
- //~ _histogram_datas.add( new HistogramData( species_i + "-" + species_j, values, null, 20 ) );
+ ForesterUtil
+ .printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
+ + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
+ + pw_stats.getMax()
+ + "], possibly indicating that a genome is compared to itself" );
}
}
}