- public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- public final static Pattern GENBANK_PROT_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- public final static Pattern GI_PATTERN = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
- public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern\r
- .compile( "(?:\\b|_)([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );\r
- public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern\r
- .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );\r
- public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern\r
- .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
- public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );\r
- // RefSeq accession numbers can be distinguished from GenBank accessions \r
+ public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GENBANK_PROT_PATTERN = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GI_PATTERN = Pattern\r
+ .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
+ public final static String UNIPROT_KB_BASE_PATTERN_STR = "((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))";\r
+ public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "(?:\\b|_)"\r
+ + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+ public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]"\r
+ + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+ public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern\r
+ .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"\r
+ + UNIPROT_KB_BASE_PATTERN_STR\r
+ + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
+ public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );\r
+ // RefSeq accession numbers can be distinguished from GenBank accessions\r