taxonomy extraction changed

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

diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
index 42f94ee..090a052 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,13 +16,13 @@
 // 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.io.parsers;
 
@@ -40,11 +40,11 @@ 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;
 
@@ -355,7 +355,7 @@ public final class HmmPfamOutputParser {
                             + getInputFile().getCanonicalPath() + "]" );
                 }
                 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
-                    current_protein = new BasicProtein( query, getSpecies() );
+                    current_protein = new BasicProtein( query, getSpecies(), 0 );
                 }
                 else {
                     throw new IllegalArgumentException( "unknown return type" );
@@ -376,7 +376,7 @@ public final class HmmPfamOutputParser {
                 if ( was_not_unique ) {
                     if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
                         current_protein = new BasicProtein( current_protein.getProteinId() + " "
-                                + line.substring( 13 ).trim(), getSpecies() );
+                                + line.substring( 13 ).trim(), getSpecies(), 0 );
                     }
                 }
                 else {