import java.util.regex.Pattern;\r
\r
import org.forester.phylogeny.data.Identifier;\r
-import org.forester.ws.uniprot.DatabaseTools;\r
\r
public final class SequenceIdParser {\r
\r
.compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6})(?:[^a-zA-Z0-9]|\\Z)" );\r
private final static Pattern GENBANK_PROTEIN_AC_PATTERN = Pattern\r
.compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );\r
- private final static boolean DEBUG = false;\r
+ \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
\r
+ \r
\r
- \r
+ /**\r
+ * Returns null if no match.\r
+ * \r
+ */\r
public final static Identifier parse( final String s ) {\r
- String v = DatabaseTools.parseGenbankAccessor( s );\r
+ String v = parseGenbankAccessor( s );\r
+ if ( !ForesterUtil.isEmpty( v ) ) {\r
+\r
+ return new Identifier( v, Identifier.NCBI );\r
+ }\r
+ v = parseRefSeqAccessor( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Identifier( v, "genbank" );\r
+ return new Identifier( v, Identifier.REFSEQ );\r
}\r
- \r
return null;\r
}\r
\r
+ /**\r
+ * Returns null if no match.\r
+ * \r
+ */\r
+ public static String parseGenbankAccessor( final String query ) {\r
+ Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );\r
+ if ( m.lookingAt() ) {\r
+ return m.group( 1 );\r
+ }\r
+ else {\r
+ m = GENBANK_NUCLEOTIDE_AC_PATTERN_2.matcher( query );\r
+ if ( m.lookingAt() ) {\r
+ return m.group( 1 );\r
+ }\r
+ else {\r
+ m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );\r
+ if ( m.lookingAt() ) {\r
+ return m.group( 1 );\r
+ }\r
+ else {\r
+ return null;\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
+ /**\r
+ * Returns null if no match.\r
+ * \r
+ */\r
+ private final static String parseRefSeqAccessor( final String query ) {\r
+ Matcher m = REFSEQ_PATTERN.matcher( query );\r
+ if ( m.lookingAt() ) {\r
+ return m.group( 1 );\r
+ }\r
+ return null;\r
+ }\r
\r
\r
\r