in progress

[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 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;
@@ -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 ) );
-        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 + "\"" );
     }