// 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;
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;
}
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;
}
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 + "\"" );
}