gsdi work

[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 7d31a11..0bb224c 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -41,11 +41,11 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
-import org.forester.surfacing.BasicDomain;
-import org.forester.surfacing.BasicProtein;
-import org.forester.surfacing.Domain;
-import org.forester.surfacing.DomainId;
-import org.forester.surfacing.Protein;
+import org.forester.protein.BasicDomain;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.Domain;
+import org.forester.protein.DomainId;
+import org.forester.protein.Protein;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
 
@@ -407,7 +407,7 @@ public final class HmmscanPerDomainTableParser {
                     addProtein( proteins, current_protein );
                 }
                 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
-                    current_protein = new BasicProtein( query, getSpecies() );
+                    current_protein = new BasicProtein( query, getSpecies(), qlen );
                 }
                 else {
                     throw new IllegalArgumentException( "unknown return type" );