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
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;
}