in progress

[jalview.git] / forester / java / src / org / forester / io / parsers / HmmscanPerDomainTableParser.java

diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index dfde916..f595349 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -45,7 +45,6 @@ import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
 import org.forester.protein.Protein;
-import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
 
 public final class HmmscanPerDomainTableParser {
@@ -165,9 +164,9 @@ public final class HmmscanPerDomainTableParser {
         if ( ( getMaxAllowedOverlap() != HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT )
                 || isIgnoreEngulfedDomains() ) {
             final int domains_count = current_protein.getNumberOfProteinDomains();
-            current_protein = SurfacingUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
-                                                                      isIgnoreEngulfedDomains(),
-                                                                      current_protein );
+            current_protein = ForesterUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
+                                                                     isIgnoreEngulfedDomains(),
+                                                                     current_protein );
             final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
             _domains_stored -= domains_removed;
             _domains_ignored_due_to_overlap += domains_removed;