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[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.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.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;
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 ) {
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 ) {
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 );
}
}
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 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,
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() ) {
//
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() ) ) {
}
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() ) {
//
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,
}
if ( simple_tab_writer != null ) {
simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,