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 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_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 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
public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) {\r
String a = obtainUniProtAccessorFromDataFields( n );\r
if ( !ForesterUtil.isEmpty( a ) ) {\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
final String value = n.getNodeData().getSequence().getAccession().getValue();\r
if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source\r
.equals( "sp" ) ) ) {\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
String v = parseUniProtAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
String v = parseUniProtAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r