removed save as NHX

[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 c3691bf..20a25d4 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@ -23,7 +23,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
@@ -556,7 +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;
                     }
@@ -680,8 +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;
                     }