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[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
6996ef3
..
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
// 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;
package org.forester.surfacing;
@@
-44,8
+44,13
@@
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.TreeMap;
import java.util.TreeSet;
+import org.forester.application.surfacing;
import org.forester.go.GoId;
import org.forester.go.GoTerm;
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;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
@@
-551,7
+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 ) ) ) {
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;
}
if ( low_copy_values.get( bdc ) <= 0.0 ) {
++total_absense_counter;
}
@@
-675,8
+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 ) ) ) {
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;
}
if ( low_copy_values.get( domain_id ) <= 0.0 ) {
++total_absense_counter;
}
@@
-820,7
+825,12
@@
public final class DomainCountsDifferenceUtil {
+ domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
+ domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
- SurfacingUtil.extractProteinNames( protein_lists_per_species, domain_id, proteins_file_writer, "\t" );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species,
+ domain_id,
+ proteins_file_writer,
+ "\t",
+ surfacing.LIMIT_SPEC_FOR_PROT_EX,
+ -1 );
proteins_file_writer.close();
System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
}
proteins_file_writer.close();
System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
}