public final class ParserUtils {
- final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA";
- final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")\\b" );
- final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" );
- final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_("
- + TAX_CODE + ")\\b" );
- final public static Pattern TAXOMONY_SN_PATTERN = Pattern
- .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]{2,30}_[a-z]{3,30}(?:_[a-z][a-z0-9_]+)?)\\b" );
- final public static Pattern TAXOMONY_SN_PATTERN_SN = Pattern
- .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}(?:[_ ][a-z]{3,30})?)(?:\\b|_)?" );
- final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_1 = Pattern
- .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}[_ ](?:str|subsp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
- final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_2 = Pattern
- .compile( "\\b([A-Z][a-z]{2,30}[_ ][a-z]{3,30}[_ ]\\((?:str|subsp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))(?:\\b|_)?" );
- final public static Pattern TAXOMONY_SN_PATTERN_SP = Pattern
- .compile( "\\b([A-Z][a-z]{2,30}[_ ]sp\\.?)(?:\\b|_)?" );
-
- final public static Pattern TAXOMONY_SN_PATTERN_GENUS = Pattern.compile( "([A-Z][a-z]{2,30})" );
- final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
- + TAX_CODE + ")/\\d+-\\d+\\b" );
- final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern
- .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" );
- final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFS = Pattern
- .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" );
+ final private static String SN_BN = "[A-Z][a-z]{2,30}[_ ][a-z]{3,30}";
+ final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA";
+ final public static String TAX_CODE_LO = "(?:[A-Z]{5})|RAT|PIG|PEA";
+ final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE
+ + ")(?:\\b|_)" );
+ final public static Pattern TAXOMONY_CODE_PATTERN_A_LO = Pattern.compile( "_(" + TAX_CODE_LO
+ + ")(?:\\b|_)" );
+ final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" );
+ final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_("
+ + TAX_CODE + ")\\b" );
+ final public static Pattern TAXOMONY_SN_PATTERN_GENUS = Pattern.compile( "([A-Z][a-z]{2,30})" );
+ final public static Pattern TAXOMONY_SN_PATTERN_SN = Pattern.compile( "(?:\\b|_)(" + SN_BN
+ + ")(?:(\\s*$)|([_ ][a-z]*[A-Z0-9]))" );
+ final public static Pattern TAXOMONY_SN_PATTERN_SNS = Pattern.compile( "(?:\\b|_)(" + SN_BN
+ + "[_ ][a-z]{3,30}"
+ + ")[_ ][a-z]*[A-Z0-9]" );
+ final public static Pattern TAXOMONY_SN_PATTERN_SNS2 = Pattern.compile( "[A-Z0-9][a-z]*[_ ](" + SN_BN
+ + "[_ ][a-z]{3,30}" + ")\\s*$" );
+ final public static Pattern TAXOMONY_SN_PATTERN_SP = Pattern
+ .compile( "(?:\\b|_)([A-Z][a-z]{2,30}[_ ]sp\\.?)(?:\\b|_)?" );
+ final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_1 = Pattern
+ .compile( "(?:\\b|_)("
+ + SN_BN
+ + "[_ ](?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
+ final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_2 = Pattern
+ .compile( "(?:\\b|_)("
+ + SN_BN
+ + "[_ ]\\((?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))" );
+ final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN = Pattern
+ .compile( "(?:\\b|_)("
+ + SN_BN
+ + "[_ ]str[a-z]{0,3}\\.?[_ ]\\S{1,60}[_ ]substr[a-z]{0,3}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
+ final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
+ + TAX_CODE + ")/\\d+-\\d+\\b" );
+ final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern
+ .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" );
+ final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFS = Pattern
+ .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" );
final public static PhylogenyParser createParserDependingFileContents( final File file,
final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
+ throws FileNotFoundException, IOException {
PhylogenyParser parser = null;
final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
if ( first_line.startsWith( "<" ) ) {
final public static PhylogenyParser createParserDependingOnFileType( final File file,
final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
+ throws FileNotFoundException, IOException {
PhylogenyParser parser = null;
parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
if ( parser == null ) {
final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
+ throws FileNotFoundException, IOException {
final String lc_filename = url.getFile().toString().toLowerCase();
PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
if ( parser == null ) {
}
else {
throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
- + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
+ + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
}
return reader;
}
public final static String extractScientificNameFromNodeName( final String name ) {
- final Matcher m = TAXOMONY_SN_PATTERN.matcher( name );
- if ( m.find() ) {
- return m.group( 1 ).replace( '_', ' ' );
+ final Matcher m_ss = TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN.matcher( name );
+ if ( m_ss.find() ) {
+ String s = m_ss.group( 1 ).replace( '_', ' ' );
+ if ( s.indexOf( " str " ) > 4 ) {
+ s = s.replaceFirst( " str ", " str. " );
+ }
+ if ( s.indexOf( " substr " ) > 4 ) {
+ s = s.replaceFirst( " substr ", " substr. " );
+ }
+ return s;
}
final Matcher m_str1 = TAXOMONY_SN_PATTERN_STRAIN_1.matcher( name );
if ( m_str1.find() ) {
- return m_str1.group( 1 ).replace( '_', ' ' );
+ String s = m_str1.group( 1 ).replace( '_', ' ' );
+ if ( s.indexOf( " str " ) > 4 ) {
+ s = s.replaceFirst( " str ", " str. " );
+ }
+ else if ( s.indexOf( " subsp " ) > 4 ) {
+ s = s.replaceFirst( " subsp ", " subsp. " );
+ }
+ else if ( s.indexOf( " ssp " ) > 4 ) {
+ s = s.replaceFirst( " ssp ", " subsp. " );
+ }
+ else if ( s.indexOf( " ssp. " ) > 4 ) {
+ s = s.replaceFirst( " ssp. ", " subsp. " );
+ }
+ else if ( s.indexOf( " var " ) > 4 ) {
+ s = s.replaceFirst( " var ", " var. " );
+ }
+ return s;
}
final Matcher m_str2 = TAXOMONY_SN_PATTERN_STRAIN_2.matcher( name );
if ( m_str2.find() ) {
- return m_str2.group( 1 ).replace( '_', ' ' );
+ String s = m_str2.group( 1 ).replace( '_', ' ' );
+ if ( s.indexOf( " (str " ) > 4 ) {
+ s = s.replaceFirst( " \\(str ", " (str. " );
+ }
+ else if ( s.indexOf( " (subsp " ) > 4 ) {
+ s = s.replaceFirst( " \\(subsp ", " (subsp. " );
+ }
+ else if ( s.indexOf( " (ssp " ) > 4 ) {
+ s = s.replaceFirst( " \\(ssp ", " (subsp. " );
+ }
+ else if ( s.indexOf( " (ssp. " ) > 4 ) {
+ s = s.replaceFirst( " \\(ssp. ", " (subsp. " );
+ }
+ else if ( s.indexOf( " (var " ) > 4 ) {
+ s = s.replaceFirst( " \\(var ", " (var. " );
+ }
+ return s;
+ }
+ final Matcher m_sns = TAXOMONY_SN_PATTERN_SNS.matcher( name );
+ if ( m_sns.find() ) {
+ return m_sns.group( 1 ).replace( '_', ' ' );
+ }
+ final Matcher m_sns2 = TAXOMONY_SN_PATTERN_SNS2.matcher( name );
+ if ( m_sns2.find() ) {
+ return m_sns2.group( 1 ).replace( '_', ' ' );
}
final Matcher m_sn = TAXOMONY_SN_PATTERN_SN.matcher( name );
-
if ( m_sn.find() ) {
return m_sn.group( 1 ).replace( '_', ' ' );
}
-
final Matcher m_sp = TAXOMONY_SN_PATTERN_SP.matcher( name );
-
if ( m_sp.find() ) {
- return m_sp.group( 1 ).replace( '_', ' ' );
+ String s = m_sp.group( 1 ).replace( '_', ' ' );
+ if ( s.endsWith( " sp" ) ) {
+ s = s + ".";
+ }
+ return s;
}
return null;
}
public final static String extractTaxonomyDataFromNodeName( final PhylogenyNode node,
final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction )
- throws PhyloXmlDataFormatException {
+ throws PhyloXmlDataFormatException {
if ( taxonomy_extraction == TAXONOMY_EXTRACTION.NO ) {
throw new IllegalArgumentException();
}
return id;
}
else {
- final String code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction );
+ String code = null;
+ if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
+ code = extractTaxonomyCodeFromNodeNameLettersOnly( node.getName() );
+ if ( ForesterUtil.isEmpty( code ) ) {
+ final String sn = extractScientificNameFromNodeName( node.getName() );
+ if ( !ForesterUtil.isEmpty( sn ) ) {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ node.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ node.getNodeData().getTaxonomy().setScientificName( sn );
+ return sn;
+ }
+ }
+ }
+ if ( ForesterUtil.isEmpty( code ) ) {
+ code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction );
+ }
if ( !ForesterUtil.isEmpty( code ) ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
node.getNodeData().getTaxonomy().setTaxonomyCode( code );
return code;
}
- else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
- final String sn = extractScientificNameFromNodeName( node.getName() );
- if ( !ForesterUtil.isEmpty( sn ) ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node.getNodeData().getTaxonomy().setScientificName( sn );
- return sn;
- }
- }
}
return null;
}
if ( m.find() ) {
return m.group( 1 );
}
- //else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
- // m = TAXOMONY_UNIPROT_ID_PATTERN_A.matcher( name );
- // if ( m.find() ) {
- // return m.group( 1 );
- // }
- //}
}
return null;
}
/**
* Return null if it can not guess the parser to use based on name suffix.
- *
+ *
* @param filename
* @return
*/
}
return parser;
}
+
+ private final static String extractTaxonomyCodeFromNodeNameLettersOnly( final String name ) {
+ final Matcher m = TAXOMONY_CODE_PATTERN_A_LO.matcher( name );
+ if ( m.find() ) {
+ return m.group( 1 );
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff