\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
\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.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
- // 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
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
+ v = parseEnsemlAccessorFromString( s );\r
+ if ( !ForesterUtil.isEmpty( v ) ) {\r
+ return new Accession( v, Source.ENSEMBL );\r
}\r
}\r
return null;\r
return null;\r
}\r
\r
+ public final static String parseEnsemlAccessorFromString( final String s ) {\r
+ final Matcher m = ENSEMBL_PATTERN.matcher( s );\r
+ if ( m.find() ) {\r
+ return m.group( 1 );\r
+ }\r
+ return null;\r
+ }\r
+\r
public final static String parseRefSeqAccessorFromString( final String s ) {\r
final Matcher m = REFSEQ_PATTERN.matcher( s );\r
if ( m.lookingAt() ) {\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
git://source.jalview.org / jalview.git / blobdiff