\r
import org.forester.phylogeny.PhylogenyNode;\r
import org.forester.phylogeny.data.Accession;\r
+import org.forester.phylogeny.data.Accession.Source;\r
import org.forester.phylogeny.data.Sequence;\r
\r
public final class SequenceAccessionTools {\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.compile( "\\b([A-Z][0-9][A-Z0-9]{3}[0-9])\\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
public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) {\r
String a = obtainUniProtAccessorFromDataFields( n );\r
if ( !ForesterUtil.isEmpty( a ) ) {\r
- return new Accession( a, Accession.UNIPROT );\r
+ return new Accession( a, Source.UNIPROT );\r
}\r
a = obtainGenbankAccessorFromDataFields( n );\r
if ( !ForesterUtil.isEmpty( a ) ) {\r
- return new Accession( a, Accession.NCBI );\r
+ return new Accession( a, Source.NCBI );\r
}\r
a = obtainRefSeqAccessorFromDataFields( n );\r
if ( !ForesterUtil.isEmpty( a ) ) {\r
- return new Accession( a, Accession.REFSEQ );\r
+ return new Accession( a, Source.REFSEQ );\r
}\r
a = obtainGiNumberFromDataFields( n );\r
if ( !ForesterUtil.isEmpty( a ) ) {\r
- return new Accession( a, Accession.GI );\r
+ return new Accession( a, Source.GI );\r
}\r
return null;\r
}\r
final String value = n.getNodeData().getSequence().getAccession().getValue();\r
if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source\r
.equals( "sp" ) ) ) {\r
- return new Accession( value, Accession.UNIPROT );\r
+ return new Accession( value, Source.UNIPROT );\r
}\r
else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) {\r
- return new Accession( value, Accession.EMBL );\r
+ return new Accession( value, Source.EMBL );\r
}\r
else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) {\r
- return new Accession( value, Accession.NCBI );\r
+ return new Accession( value, Source.NCBI );\r
}\r
else if ( source.equals( "refseq" ) ) {\r
- return new Accession( value, Accession.REFSEQ );\r
+ return new Accession( value, Source.REFSEQ );\r
}\r
else if ( source.equals( "gi" ) ) {\r
- return new Accession( value, Accession.GI );\r
+ return new Accession( value, Source.GI );\r
}\r
}\r
return null;\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
String v = parseUniProtAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.UNIPROT );\r
+ return new Accession( v, Source.UNIPROT );\r
}\r
v = parseGenbankAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.NCBI );\r
+ return new Accession( v, Source.NCBI );\r
}\r
v = parseRefSeqAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.REFSEQ );\r
+ return new Accession( v, Source.REFSEQ );\r
}\r
v = parseGInumberFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.GI );\r
+ return new Accession( v, Source.GI );\r
}\r
}\r
return null;\r
}\r
\r
public final static String parseUniProtAccessorFromString( final String s ) {\r
- Matcher m = UNIPROT_KB_PATTERN_0.matcher( s );\r
- if ( m.find() ) {\r
- return m.group( 1 );\r
- }\r
- m = UNIPROT_KB_PATTERN_1.matcher( s );\r
+ Matcher m = UNIPROT_KB_PATTERN_1.matcher( s );\r
if ( m.find() ) {\r
return m.group( 1 );\r
}\r
if ( m.find() ) {\r
return m.group();\r
}\r
+ m = UNIPROT_KB_PATTERN_0.matcher( s );\r
+ if ( m.find() ) {\r
+ return m.group( 1 );\r
+ }\r
return null;\r
}\r
}\r