X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPairwiseGenomeComparator.java;h=4c3e442a73f43ad67bf2b18b6e2d654d9e1ad38c;hb=f4f236fff9a5f19dc9cf5dfb960f4a6d13ddb2fb;hp=ae94f8174570d9840abe7d9a46b31e7c577fe5af;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index ae94f81..4c3e442 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,7 +16,7 @@
 // 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
@@ -43,6 +43,8 @@ import org.forester.evoinference.matrix.distance.DistanceMatrix;
 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;
@@ -99,7 +101,6 @@ public class PairwiseGenomeComparator {
                                             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();
@@ -164,7 +165,6 @@ public class PairwiseGenomeComparator {
                                                                                                                                                               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
@@ -216,6 +216,7 @@ public class PairwiseGenomeComparator {
                                                                                 new StringBuilder( species_i + "-"
                                                                                         + species_j ),
                                                                                 writer,
+                                                                                null,
                                                                                 similarities,
                                                                                 true,
                                                                                 null,
@@ -229,23 +230,13 @@ public class PairwiseGenomeComparator {
                                 + 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" );
                     }
                 }
             }