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[jalview.git] / forester / java / src / org / forester / tools / PhylogenyDecorator.java

diff --git a/forester/java/src/org/forester/tools/PhylogenyDecorator.java b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
index 086e51a..6f62d8b 100644 (file)
--- a/forester/java/src/org/forester/tools/PhylogenyDecorator.java
+++ b/forester/java/src/org/forester/tools/PhylogenyDecorator.java
@@ -5,7 +5,7 @@
 // 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
@@ -15,7 +15,7 @@
 // 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
@@ -32,6 +32,7 @@ import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.forester.archaeopteryx.AptxUtil;
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -90,59 +91,63 @@ public final class PhylogenyDecorator {
                     }
                     if ( new_values != null ) {
                         if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
                             node.getNodeData().getTaxonomy().setTaxonomyCode( new_values.get( TP_TAXONOMY_CODE ) );
                         }
                         if ( new_values.containsKey( TP_TAXONOMY_ID )
                                 && new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
-                            node.getNodeData().getTaxonomy().setIdentifier( new Identifier( new_values
-                                    .get( TP_TAXONOMY_ID ), new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
+                            node.getNodeData()
+                                    .getTaxonomy()
+                                    .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ),
+                                                                    new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
                         }
                         else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
-                            node.getNodeData().getTaxonomy().setIdentifier( new Identifier( new_values
-                                    .get( TP_TAXONOMY_ID ) ) );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
+                            node.getNodeData().getTaxonomy()
+                                    .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
                         }
                         if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
                             node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
                         }
                         if ( new_values.containsKey( TP_TAXONOMY_CN ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
                             node.getNodeData().getTaxonomy().setCommonName( new_values.get( TP_TAXONOMY_CN ) );
                         }
                         if ( new_values.containsKey( TP_TAXONOMY_SYN ) ) {
-                            ForesterUtil.ensurePresenceOfTaxonomy( node );
+                            AptxUtil.ensurePresenceOfTaxonomy( node );
                             node.getNodeData().getTaxonomy().getSynonyms().add( new_values.get( TP_TAXONOMY_SYN ) );
                         }
                         if ( new_values.containsKey( TP_SEQ_ACCESSION )
                                 && new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
-                            node.getNodeData().getSequence().setAccession( new Accession( new_values
-                                    .get( TP_SEQ_ACCESSION ), new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
+                            AptxUtil.ensurePresenceOfSequence( node );
+                            node.getNodeData()
+                                    .getSequence()
+                                    .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ),
+                                                                  new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
                         }
                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
+                            AptxUtil.ensurePresenceOfSequence( node );
                             final Annotation ann = new Annotation( "?" );
                             ann.setDesc( new_values.get( TP_SEQ_ANNOTATION_DESC ) );
                             node.getNodeData().getSequence().addAnnotation( ann );
                         }
                         if ( new_values.containsKey( TP_SEQ_ANNOTATION_REF ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
+                            AptxUtil.ensurePresenceOfSequence( node );
                             final Annotation ann = new Annotation( new_values.get( TP_SEQ_ANNOTATION_REF ) );
                             node.getNodeData().getSequence().addAnnotation( ann );
                         }
                         if ( new_values.containsKey( TP_SEQ_SYMBOL ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
+                            AptxUtil.ensurePresenceOfSequence( node );
                             node.getNodeData().getSequence().setSymbol( new_values.get( TP_SEQ_SYMBOL ) );
                         }
                         if ( new_values.containsKey( TP_SEQ_NAME ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
+                            AptxUtil.ensurePresenceOfSequence( node );
                             node.getNodeData().getSequence().setName( new_values.get( TP_SEQ_NAME ) );
                         }
                         if ( new_values.containsKey( TP_SEQ_MOL_SEQ ) ) {
-                            ForesterUtil.ensurePresenceOfSequence( node );
+                            AptxUtil.ensurePresenceOfSequence( node );
                             node.getNodeData().getSequence().setMolecularSequence( new_values.get( TP_SEQ_MOL_SEQ ) );
                         }
                         if ( new_values.containsKey( TP_NODE_NAME ) ) {
@@ -270,14 +275,14 @@ public final class PhylogenyDecorator {
                                 if ( PhylogenyDecorator.VERBOSE ) {
                                     System.out.println( name + ": " + new_value );
                                 }
-                                ForesterUtil.ensurePresenceOfTaxonomy( node );
+                                AptxUtil.ensurePresenceOfTaxonomy( node );
                                 node.getNodeData().getTaxonomy().setTaxonomyCode( new_value );
                                 break;
                             case TAXONOMY_SCIENTIFIC_NAME:
                                 if ( PhylogenyDecorator.VERBOSE ) {
                                     System.out.println( name + ": " + new_value );
                                 }
-                                ForesterUtil.ensurePresenceOfTaxonomy( node );
+                                AptxUtil.ensurePresenceOfTaxonomy( node );
                                 node.getNodeData().getTaxonomy().setScientificName( new_value );
                                 break;
                             case SEQUENCE_NAME:
@@ -410,7 +415,7 @@ public final class PhylogenyDecorator {
     private static void extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) {
         final int i = new_value.lastIndexOf( "[" );
         final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 );
-        ForesterUtil.ensurePresenceOfTaxonomy( node );
+        AptxUtil.ensurePresenceOfTaxonomy( node );
         node.getNodeData().getTaxonomy().setScientificName( scientific_name );
     }