From: cmzmasek <chris.zma@outlook.com>
Date: Thu, 2 Mar 2017 02:07:41 +0000 (-0800)
Subject: need to allow virus taxonomy codes (e.g. HHV3)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d963c6703bcbb8a75b13d6d69b96a9cba9bc0479;p=jalview.git

need to allow virus taxonomy codes (e.g. HHV3)
---

diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
index b278cb9..674713d 100644
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -56,8 +56,8 @@ import org.forester.util.ForesterUtil;
 public final class ParserUtils {
 
     final private static String  SN_BN                                = "[A-Z][a-z]{2,30}[_ ][a-z]{3,30}";
-    final public static String   TAX_CODE                             = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|(?:[A-Z1-9]{4})";
-    final public static String   TAX_CODE_LO                          = "(?:[A-Z]{5})|RAT|PIG|PEA|(?:[A-Z1-9]{4})";
+    final public static String   TAX_CODE                             = "(?:[A-Z0-9]{3,5})";
+    final public static String   TAX_CODE_LO                          = "(?:[A-Z]{5})|RAT|PIG|PEA";
     final public static Pattern  TAXOMONY_CODE_PATTERN_A              = Pattern.compile( "(?:\\b|_)(" + TAX_CODE
                                                                                          + ")(?:\\b|_)" );
     final public static Pattern  TAXOMONY_CODE_PATTERN_A_LO           = Pattern.compile( "_(" + TAX_CODE_LO
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index fe52a87..d6df5a9 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -5085,7 +5085,7 @@ public final class Test {
                     .equals( "ECOLI" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blagg_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
                     .equals( "9YX45" ) ) {
                 return false;
             }
@@ -13192,7 +13192,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n3 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAGG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n3.toString() );
                 return false;
@@ -13210,62 +13210,62 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n6 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAGG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n6.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n6.toString() );
                 return false;
             }
             final PhylogenyNode n7 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BL-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n7.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n7.toString() );
                 return false;
             }
             final PhylogenyNode n8 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAGG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n8.toString() );
                 return false;
             }
             final PhylogenyNode n9 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAGG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n9.toString() );
                 return false;
             }
             final PhylogenyNode n10x = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAG!_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n10x.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n10x.toString() );
                 return false;
             }
             final PhylogenyNode n10xx = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAG!_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n10xx.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n10xx.toString() );
                 return false;
             }
             final PhylogenyNode n10 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    .createInstanceFromNhxString( "BLAGG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
                 System.out.println( n10.toString() );
                 return false;
             }
             final PhylogenyNode n11 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+                    .createInstanceFromNhxString( "BLAG@_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
             if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
                 System.out.println( n11.toString() );
                 return false;
             }
             final PhylogenyNode n12 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
+                    .createInstanceFromNhxString( "BLA_G_Mus_musculus_musculus",
                                                   NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
             if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
                 System.out.println( n12.toString() );
                 return false;
             }
             final PhylogenyNode n13 = PhylogenyNode
-                    .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+                    .createInstanceFromNhxString( "BLAaG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
             if ( n13.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n13.toString() );
                 return false;