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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
..
fef82fa
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/
forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@
-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;
@@
-820,7
+825,11
@@
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 );
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 + "\"" );
}