\r
public final class SequenceAccessionTools {\r
\r
- // gb_ADF31344_1_segmented_worms_\r
- // gb_AAA96518_1\r
- // gb_EHB07727_1_rodents_\r
- // dbj_BAF37827_1_turtles_\r
- // emb_CAA73223_1_primates_\r
- // lcl_91970_unknown_\r
- // mites|ref_XP_002434188_1\r
- // ref_XP_002434188_1_mites___ticks_\r
- // ref_NP_001121530_1_frogs___toads_\r
//The format for GenBank Accession numbers are:\r
//Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals\r
//Protein: 3 letters + 5 numerals\r
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html\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.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
// by their distinct prefix format of 2 characters followed by an\r
- // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. \r
- private final static Pattern REFSEQ_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ // underscore character ('_'). For example, a RefSeq protein accession is NP_015325.\r
+ private final static Pattern REFSEQ_PATTERN = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
\r
private SequenceAccessionTools() {\r
// Hiding the constructor.\r