package org.forester.ws.seqdb;
import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import org.forester.go.GoTerm;
import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.ForesterUtil;
public final class EbiDbEntry implements SequenceDatabaseEntry {
-
- //http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
- private String _pa;
- private String _de;
- private String _os;
- private String _tax_id;
- private String _symbol;
- private String _provider;
-
+
+ private final static boolean DEBUG = false;
+
+ private final static Pattern LETTERS_PATTERN = Pattern.compile( "^[A-Z]+" );
+ private final static Pattern chromosome_PATTERN = Pattern.compile( "\\s+/chromosome=\"(\\w+)\"" );
+ private final static Pattern map_PATTERN = Pattern.compile( "\\s+/map=\"([\\w\\.]+)\"" );
+ private final static Pattern gene_PATTERN = Pattern.compile( "\\s+/gene=\"(.+)\"" );
+ private final static Pattern mim_PATTERN = Pattern.compile( "\\s+/db_xref=\"MIM:(\\d+)\"" );
+ private final static Pattern taxon_PATTERN = Pattern.compile( "\\s+/db_xref=\"taxon:(\\d+)\"" );
+ private final static Pattern interpro_PATTERN = Pattern.compile( "\\s+/db_xref=\"InterPro:([A-Z0-9]+)\"" );
+ private final static Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/[A-Za-z-]*:(\\w+)\"" );
+ private final static Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
+ private final static Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
+ private final static Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
+ private final static Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
+ private final static Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
+
+ private SortedSet<Annotation> _annotations;
+ private String _chromosome;
+ private SortedSet<Accession> _cross_references;
+ private String _de;
+ private String _gene_name;
+ private String _map;
+ private String _os;
+ private String _pa;
+ private String _provider;
+ private String _symbol;
+ private String _tax_id;
+
private EbiDbEntry() {
}
throw new CloneNotSupportedException();
}
- public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
- final EbiDbEntry e = new EbiDbEntry();
- for( final String line : lines ) {
- // System.out.println( "-" + line );
- if ( line.startsWith( "ACCESSION" ) ) {
- e.setPA( DatabaseTools.extract( line, "ACCESSION" ) );
- }
- else if ( line.startsWith( "DEFINITION" ) ) {
- if ( line.indexOf( "[" ) > 0 ) {
- e.setDe( DatabaseTools.extract( line, "DEFINITION", "[" ) );
- }
- else {
- e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
- }
- }
- else if ( line.startsWith( "SOURCE" ) ) {
- if ( line.indexOf( "(" ) > 0 ) {
- e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
- }
- else {
- e.setOs( DatabaseTools.extract( line, "SOURCE" ) );
- }
- }
- }
- return e;
- }
-
- public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
- final EbiDbEntry e = new EbiDbEntry();
- for( final String line : lines ) {
- if ( line.startsWith( "PA" ) ) {
- e.setPA( DatabaseTools.extract( line, "PA" ) );
- }
- else if ( line.startsWith( "DE" ) ) {
- e.setDe( DatabaseTools.extract( line, "DE" ) );
- }
- else if ( line.startsWith( "OS" ) ) {
- if ( line.indexOf( "(" ) > 0 ) {
- e.setOs( DatabaseTools.extract( line, "OS", "(" ) );
- }
- else {
- e.setOs( DatabaseTools.extract( line, "OS" ) );
- }
- }
- else if ( line.startsWith( "OX" ) ) {
- if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
- e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
- }
- }
- }
- return e;
- }
-
@Override
public String getAccession() {
return _pa;
}
- private void setPA( final String pa ) {
- if ( _pa == null ) {
- _pa = pa;
- }
+ @Override
+ public SortedSet<Annotation> getAnnotations() {
+ return _annotations;
}
@Override
- public String getSequenceName() {
- return _de;
+ public String getChromosome() {
+ return _chromosome;
}
- private void setDe( final String rec_name ) {
- if ( _de == null ) {
- _de = rec_name;
- }
+ @Override
+ public SortedSet<Accession> getCrossReferences() {
+ return _cross_references;
}
@Override
- public String getTaxonomyScientificName() {
- return _os;
+ public String getGeneName() {
+ return _gene_name;
}
- private void setOs( final String os ) {
- if ( _os == null ) {
- _os = os;
- }
+ @Override
+ public SortedSet<GoTerm> getGoTerms() {
+ return null;
}
@Override
- public String getTaxonomyIdentifier() {
- return _tax_id;
+ public String getMap() {
+ return _map;
}
- private void setTaxId( final String tax_id ) {
- if ( _tax_id == null ) {
- _tax_id = tax_id;
- }
+ @Override
+ public String getProvider() {
+ return _provider;
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _de;
}
@Override
}
@Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os;
+ }
+
+ @Override
public boolean isEmpty() {
return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
&& ForesterUtil.isEmpty( getTaxonomyScientificName() )
&& ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
}
+
@Override
- public String getProvider() {
- return _provider;
+ public MolecularSequence getMolecularSequence() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ private void addAnnotation( final Annotation annotation ) {
+ if ( _annotations == null ) {
+ _annotations = new TreeSet<Annotation>();
+ }
+ _annotations.add( annotation );
}
- public void setProvider( final String provider ) {
- _provider = provider;
+ private void addCrossReference( final Accession accession ) {
+ if ( _cross_references == null ) {
+ _cross_references = new TreeSet<Accession>();
+ }
+ if ( DEBUG ) {
+ System.out.println( "XREF ADDED: " + accession );
+ }
+ _cross_references.add( accession );
}
- @Override
- public String getGeneName() {
- return null;
+ private void setAccession( final String pa ) {
+ if ( _pa == null ) {
+ _pa = pa;
+ }
}
- @Override
- public List<GoTerm> getGoTerms() {
- return null;
+ private void setChromosome( final String chromosome ) {
+ _chromosome = chromosome;
}
- @Override
- public List<Accession> getCrossReferences() {
- return null;
+ private void setGeneName( final String gene_name ) {
+ if ( _gene_name == null ) {
+ _gene_name = gene_name;
+ }
+ }
+
+ private void setMap( final String map ) {
+ _map = map;
+ }
+
+ private void setSequenceName( final String rec_name ) {
+ if ( _de == null ) {
+ _de = rec_name;
+ }
+ }
+
+ private void setSequenceSymbol( final String symbol ) {
+ _symbol = symbol;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
+ private void setTaxonomyScientificName( final String os ) {
+ if ( _os == null ) {
+ _os = os;
+ }
+ }
+
+ private static void append( final StringBuilder sb, final String s ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( s.trim() );
+ }
+
+ public final static SequenceDatabaseEntry createInstance( final List<String> lines ) {
+
+ final EbiDbEntry e = new EbiDbEntry();
+ final StringBuilder def = new StringBuilder();
+ boolean in_definition = false;
+ boolean in_features = false;
+ boolean in_source = false;
+ boolean in_gene = false;
+ boolean in_cds = false;
+ boolean in_mrna = false;
+ boolean in_protein = false;
+ for( final String line : lines ) {
+ if ( line.startsWith( "ACCESSION " ) ) {
+ e.setAccession( SequenceDbWsTools.extractFrom( line, "ACCESSION" ) );
+ in_definition = false;
+ }
+ else if ( line.startsWith( "ID " ) ) {
+ e.setAccession( SequenceDbWsTools.extractFromTo( line, "ID", ";" ) );
+ in_definition = false;
+ }
+ else if ( line.startsWith( "DEFINITION " ) || ( line.startsWith( "DE " ) ) ) {
+ boolean definiton = false;
+ if ( line.startsWith( "DEFINITION " ) ) {
+ definiton = true;
+ }
+ if ( line.indexOf( "[" ) > 0 ) {
+ if ( definiton ) {
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) ) );
+ }
+ else {
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "[" ) ) );
+ }
+ }
+ else if ( line.indexOf( "." ) > 0 ) {
+ if ( definiton ) {
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) ) );
+ }
+ else {
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "." ) ) );
+ }
+ }
+ else {
+ if ( definiton ) {
+ append( def, ( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) ) );
+ }
+ else {
+ append( def, ( SequenceDbWsTools.extractFrom( line, "DE" ) ) );
+ }
+ }
+ if ( definiton ) {
+ in_definition = true;
+ }
+ }
+ else if ( line.startsWith( " ORGANISM " ) ) {
+ if ( line.indexOf( "(" ) > 0 ) {
+ e.setTaxonomyScientificName( SequenceDbWsTools.extractFromTo( line, " ORGANISM", "(" ) );
+ }
+ else {
+ e.setTaxonomyScientificName( SequenceDbWsTools.extractFrom( line, " ORGANISM" ) );
+ }
+ }
+ else if ( line.startsWith( "OS " ) ) {
+ if ( line.indexOf( "(" ) > 0 ) {
+ e.setTaxonomyScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
+ }
+ else {
+ e.setTaxonomyScientificName( SequenceDbWsTools.extractFrom( line, "OS" ) );
+ }
+ }
+ else if ( line.startsWith( " " ) && in_definition ) {
+ def.append( " " );
+ if ( line.indexOf( "[" ) > 0 ) {
+ def.append( SequenceDbWsTools.extractTo( line, "[" ) );
+ }
+ else if ( line.indexOf( "." ) > 0 ) {
+ def.append( SequenceDbWsTools.extractTo( line, "." ) );
+ }
+ else {
+ def.append( line.trim() );
+ }
+ }
+ else {
+ in_definition = false;
+ }
+ if ( !line.startsWith( "FT " ) && LETTERS_PATTERN.matcher( line ).find() ) {
+ in_features = false;
+ in_source = false;
+ in_gene = false;
+ in_cds = false;
+ in_mrna = false;
+ in_protein = false;
+ }
+ if ( line.startsWith( "FEATURES " ) || line.startsWith( "FT " ) ) {
+ in_features = true;
+ }
+ if ( in_features && ( line.startsWith( " source " ) || line.startsWith( "FT source " ) ) ) {
+ in_source = true;
+ in_gene = false;
+ in_cds = false;
+ in_mrna = false;
+ in_protein = false;
+ }
+ if ( in_features && ( line.startsWith( " gene " ) || line.startsWith( "FT gene " ) ) ) {
+ in_source = false;
+ in_gene = true;
+ in_cds = false;
+ in_mrna = false;
+ in_protein = false;
+ }
+ if ( in_features && ( line.startsWith( " CDS " ) || line.startsWith( "FT CDS " ) ) ) {
+ in_source = false;
+ in_gene = false;
+ in_cds = true;
+ in_mrna = false;
+ in_protein = false;
+ }
+ if ( in_features && ( line.startsWith( " Protein " ) || line.startsWith( "FT Protein " ) ) ) {
+ in_source = false;
+ in_gene = false;
+ in_cds = false;
+ in_mrna = false;
+ in_protein = true;
+ }
+ if ( in_features && ( line.startsWith( " mRNA " ) || line.startsWith( "FT mRNA " ) ) ) {
+ in_source = false;
+ in_gene = false;
+ in_cds = false;
+ in_mrna = true;
+ in_protein = false;
+ }
+ if ( in_source ) {
+ final Matcher ti = taxon_PATTERN.matcher( line );
+ if ( ti.find() ) {
+ e.setTaxId( ti.group( 1 ) );
+ }
+ final Matcher chr = chromosome_PATTERN.matcher( line );
+ if ( chr.find() ) {
+ e.setChromosome( chr.group( 1 ) );
+ }
+ final Matcher map = map_PATTERN.matcher( line );
+ if ( map.find() ) {
+ e.setMap( map.group( 1 ) );
+ }
+ }
+ if ( in_cds || in_gene ) {
+ final Matcher hgnc = hgnc_PATTERN.matcher( line );
+ if ( hgnc.find() ) {
+ e.addCrossReference( new Accession( hgnc.group( 1 ), "hgnc" ) );
+ }
+ final Matcher geneid = geneid_PATTERN.matcher( line );
+ if ( geneid.find() ) {
+ e.addCrossReference( new Accession( geneid.group( 1 ), "geneid" ) );
+ }
+ }
+ if ( in_protein || in_cds || in_gene || in_mrna ) {
+ final Matcher ec = ec_PATTERN.matcher( line );
+ if ( ec.find() ) {
+ e.addAnnotation( new Annotation( "EC", ec.group( 1 ) ) );
+ }
+ final Matcher gene = gene_PATTERN.matcher( line );
+ if ( gene.find() ) {
+ e.setGeneName( gene.group( 1 ) );
+ }
+ final Matcher uniprot = uniprot_PATTERN.matcher( line );
+ if ( uniprot.find() ) {
+ e.addCrossReference( new Accession( uniprot.group( 1 ), "uniprot" ) );
+ }
+ final Matcher interpro = interpro_PATTERN.matcher( line );
+ if ( interpro.find() ) {
+ e.addCrossReference( new Accession( interpro.group( 1 ), "interpro" ) );
+ }
+ final Matcher mim = mim_PATTERN.matcher( line );
+ if ( mim.find() ) {
+ e.addCrossReference( new Accession( mim.group( 1 ), "mim" ) );
+ }
+ final Matcher product = product_PATTERN.matcher( line );
+ if ( product.find() ) {
+ e.setSequenceSymbol( product.group( 1 ) );
+ }
+ final Matcher pdb = pdb_PATTERN.matcher( line );
+ if ( pdb.find() ) {
+ e.addCrossReference( new Accession( pdb.group( 1 ), "pdb" ) );
+ }
+ }
+ }
+ if ( def.length() > 0 ) {
+ e.setSequenceName( def.toString().trim() );
+ }
+ return e;
}
+
}
git://source.jalview.org / jalview.git / blobdiff