"rio" work

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

diff --git a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
index 9414d39..1a742fd 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@ -47,6 +47,10 @@ import java.util.TreeSet;
 import org.forester.application.surfacing;
 import org.forester.go.GoId;
 import org.forester.go.GoTerm;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.DomainId;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterUtil;
@@ -552,7 +556,7 @@ public final class DomainCountsDifferenceUtil {
         for( final BinaryDomainCombination bdc : all_bdcs ) {
             if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
                     && ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
-                if ( high_copy_target_values.get( bdc ) >= min_diff + ( factor * low_copy_values.get( bdc ) ) ) {
+                if ( high_copy_target_values.get( bdc ) >= ( min_diff + ( factor * low_copy_values.get( bdc ) ) ) ) {
                     if ( low_copy_values.get( bdc ) <= 0.0 ) {
                         ++total_absense_counter;
                     }
@@ -676,8 +680,8 @@ public final class DomainCountsDifferenceUtil {
         for( final DomainId domain_id : all_domains ) {
             if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
                     && ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
-                if ( high_copy_target_values.get( domain_id ) >= min_diff
-                        + ( factor * low_copy_values.get( domain_id ) ) ) {
+                if ( high_copy_target_values.get( domain_id ) >= ( min_diff + ( factor * low_copy_values
+                        .get( domain_id ) ) ) ) {
                     if ( low_copy_values.get( domain_id ) <= 0.0 ) {
                         ++total_absense_counter;
                     }
@@ -825,7 +829,8 @@ public final class DomainCountsDifferenceUtil {
                                            domain_id,
                                            proteins_file_writer,
                                            "\t",
-                                           surfacing.LIMIT_SPEC_FOR_PROT_EX );
+                                           surfacing.LIMIT_SPEC_FOR_PROT_EX,
+                                           -1 );
         proteins_file_writer.close();
         System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
     }