in progress

[jalview.git] / forester / java / src / org / forester / application / surfacing.java

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 20e5b1f..a085c9d 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -46,7 +46,7 @@ import java.util.TreeSet;
 
 import org.forester.evoinference.distance.NeighborJoining;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
@@ -286,6 +286,7 @@ public class surfacing {
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists_MAPPED.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
+    private static final boolean                              PERFORM_DC_REGAIN_PROTEINS_STATS                                              = true;
 
     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                                                  final String[][] input_file_properties,
@@ -545,7 +546,8 @@ public class surfacing {
         return intrees;
     }
 
-    private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
+    private static List<Phylogeny> inferSpeciesTrees( final File outfile,
+                                                      final List<BasicSymmetricalDistanceMatrix> distances_list ) {
         final NeighborJoining nj = NeighborJoining.createInstance();
         final List<Phylogeny> phylogenies = nj.execute( distances_list );
         final PhylogenyWriter w = new PhylogenyWriter();
@@ -1760,9 +1762,13 @@ public class surfacing {
         catch ( final IOException e3 ) {
             e3.printStackTrace();
         }
-        final Map<String, DescriptiveStatistics> protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
-        final Map<String, DescriptiveStatistics> domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
+        Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
+        Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
         final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
+        if ( PERFORM_DC_REGAIN_PROTEINS_STATS ) {
+            protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
+            domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
+        }
         // Main loop:
         for( int i = 0; i < number_of_genomes; ++i ) {
             System.out.println();