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

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 6ad78db..ef37f98 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -61,9 +61,17 @@ public final class ParserUtils {
     final public static Pattern  TAXOMONY_CODE_PATTERN_PFR       = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_("
                                                                          + TAX_CODE + ")\\b" );
     final public static Pattern  TAXOMONY_SN_PATTERN             = Pattern
-                                                                         .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)\\b" );
+                                                                         .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]{2,30}_[a-z]{3,30}(?:_[a-z][a-z0-9_]+)?)\\b" );
     final public static Pattern  TAXOMONY_SN_PATTERN_SN          = Pattern
-                                                                         .compile( "\\b([A-Z][a-z]+[_ ][a-z]{2,}(?:[_ ][a-z]+)?)(?:\\b|_)" );
+                                                                         .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}(?:[_ ][a-z]{3,30})?)(?:\\b|_)?" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_STRAIN_1    = Pattern
+                                                                         .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}[_ ](?:str|subsp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_STRAIN_2    = Pattern
+                                                                         .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}[_ ]\\((?:str|subsp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))(?:\\b|_)?" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_SP    = Pattern
+            .compile( "\\b([A-Z][a-z]{2,30}[_ ]sp\\.)(?:\\b|_)?" );
+
+    final public static Pattern  TAXOMONY_SN_PATTERN_GENUS       = Pattern.compile( "([A-Z][a-z]{2,30})" );
     final private static Pattern TAXOMONY_CODE_PATTERN_PFS       = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
                                                                          + TAX_CODE + ")/\\d+-\\d+\\b" );
     final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern
@@ -200,10 +208,25 @@ public final class ParserUtils {
         if ( m.find() ) {
             return m.group( 1 ).replace( '_', ' ' );
         }
+        final Matcher m_str1 = TAXOMONY_SN_PATTERN_STRAIN_1.matcher( name );
+        if ( m_str1.find() ) {
+            return m_str1.group( 1 ).replace( '_', ' ' );
+        }
+        final Matcher m_str2 = TAXOMONY_SN_PATTERN_STRAIN_2.matcher( name );
+        if ( m_str2.find() ) {
+            return m_str2.group( 1 ).replace( '_', ' ' );
+        }
         final Matcher m_sn = TAXOMONY_SN_PATTERN_SN.matcher( name );
+       
         if ( m_sn.find() ) {
             return m_sn.group( 1 ).replace( '_', ' ' );
         }
+        
+        final Matcher m_sp = TAXOMONY_SN_PATTERN_SP.matcher( name );
+        
+        if ( m_sp.find() ) {
+            return m_sp.group( 1 ).replace( '_', ' ' );
+        }
         return null;
     }