inprogress

[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 a36aa12..20a25d4 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@ -7,7 +7,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -17,13 +17,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
 
@@ -44,8 +44,13 @@ import java.util.SortedSet;
 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.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;
@@ -72,8 +77,8 @@ public final class DomainCountsDifferenceUtil {
         }
         if ( bdc.contains( dc )
                 && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
-            final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc
-                    .getId1() );
+            final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
+                    .get( dc.getId1() );
             copy_counts.get( dc ).add( count );
         }
         else {
@@ -220,16 +225,22 @@ public final class DomainCountsDifferenceUtil {
             for( final GenomeWideCombinableDomains genome : genomes ) {
                 final String species = genome.getSpecies().getSpeciesId();
                 if ( high_copy_base_species.contains( species ) ) {
-                    DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc, dc, genome, bdcs_per_genome
-                            .get( species ) );
+                    DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc,
+                                                          dc,
+                                                          genome,
+                                                          bdcs_per_genome.get( species ) );
                 }
                 if ( high_copy_target_species.contains( species ) ) {
-                    DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc, dc, genome, bdcs_per_genome
-                            .get( species ) );
+                    DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc,
+                                                          dc,
+                                                          genome,
+                                                          bdcs_per_genome.get( species ) );
                 }
                 if ( low_copy_species.contains( species ) ) {
-                    DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc, dc, genome, bdcs_per_genome
-                            .get( species ) );
+                    DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc,
+                                                          dc,
+                                                          genome,
+                                                          bdcs_per_genome.get( species ) );
                 }
             }
         }
@@ -485,8 +496,8 @@ public final class DomainCountsDifferenceUtil {
         }
         html_writer.write( "</td><td>" );
         if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
-            final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains().get( bdc
-                    .getId1() );
+            final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains()
+                    .get( bdc.getId1() );
             html_writer.write( count + "" );
         }
         else {
@@ -545,7 +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;
                     }
@@ -669,8 +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;
                     }
@@ -814,7 +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 ) );
-        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 + "\"" );
     }