inprogress

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

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 73cee01..55bfb6f 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -85,9 +85,9 @@ import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.Domain;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
+import org.forester.surfacing.DomainSimilarity.PRINT_OPTION;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
-import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
 import org.forester.util.AsciiHistogram;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.BasicTable;
@@ -158,7 +158,7 @@ public final class SurfacingUtil {
         }
     }
 
-    public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+    public static void checkWriteabilityForPairwiseComparisons( final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                                                 final String[][] input_file_properties,
                                                                 final String automated_pairwise_comparison_suffix,
                                                                 final File outdir ) {
@@ -378,8 +378,8 @@ public final class SurfacingUtil {
     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
                                                             final Detailedness detailedness ) {
         for( final DomainSimilarity domain_similarity : domain_similarities ) {
-            if ( domain_similarity instanceof PrintableDomainSimilarity ) {
-                final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
+            if ( domain_similarity instanceof DomainSimilarity ) {
+                final DomainSimilarity printable_domain_similarity = domain_similarity;
                 printable_domain_similarity.setDetailedness( detailedness );
             }
         }
@@ -2221,7 +2221,7 @@ public final class SurfacingUtil {
                                                       final SortedSet<DomainSimilarity> similarities,
                                                       final boolean treat_as_binary,
                                                       final List<Species> species_order,
-                                                      final PrintableDomainSimilarity.PRINT_OPTION print_option,
+                                                      final DomainSimilarity.PRINT_OPTION print_option,
                                                       final DomainSimilarity.DomainSimilarityScoring scoring,
                                                       final boolean verbose,
                                                       final Map<String, Integer> tax_code_to_id_map,
@@ -2264,7 +2264,7 @@ public final class SurfacingUtil {
         //
         for( final DomainSimilarity similarity : similarities ) {
             if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+                ( similarity ).setSpeciesOrder( species_order );
             }
             if ( single_writer != null ) {
                 if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
@@ -2349,7 +2349,7 @@ public final class SurfacingUtil {
         //
         for( final DomainSimilarity similarity : similarities ) {
             if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+                ( similarity ).setSpeciesOrder( species_order );
             }
             if ( simple_tab_writer != null ) {
                 simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,