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.BasicGoTerm;
+import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.sequence.BasicSequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.ForesterUtil;
public final class UniProtEntry implements SequenceDatabaseEntry {
- public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+GO:(\\d+);\\s+([PF]):([^;]+);" );
- private String _ac;
- private String _name;
- private String _symbol;
- private String _gene_name;
- private String _os_scientific_name;
- private String _tax_id;
+ public final static Pattern BindingDB_PATTERN = Pattern.compile( "BindingDB;\\s+([0-9A-Z]+);" );
+ public final static Pattern CTD_PATTERN = Pattern.compile( "CTD;\\s+(\\d+);" );
+ public final static Pattern DrugBank_PATTERN = Pattern.compile( "DrugBank;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PFC]):([^;]+);" );
+ public final static Pattern KEGG_PATTERN = Pattern.compile( "KEGG;\\s+([a-z]+:[0-9]+);" );
+ public final static Pattern MIM_PATTERN = Pattern.compile( "MIM;\\s+(\\d+);" );
+ public final static Pattern NextBio_PATTERN = Pattern.compile( "NextBio;\\s+(\\d+);" );
+ public final static Pattern Orphanet_PATTERN = Pattern.compile( "Orphanet;\\s+(\\d+);\\s+([^\\.]+)" );
+ public final static Pattern PDB_PATTERN = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
+ public final static Pattern PharmGKB_PATTERN = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
+ public final static Pattern Reactome_PATTERN = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ public final static Pattern HGNC_PATTERN = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
+ private String _ac;
+ private SortedSet<Accession> _cross_references;
+ private String _gene_name;
+ private SortedSet<GoTerm> _go_terms;
+ private String _name;
+ private String _os_scientific_name;
+ private String _symbol;
+ private String _tax_id;
+ private MolecularSequence _mol_seq;
private UniProtEntry() {
}
throw new CloneNotSupportedException();
}
+ @Override
+ public String getAccession() {
+ return _ac;
+ }
+
+ @Override
+ public SortedSet<Accession> getCrossReferences() {
+ return _cross_references;
+ }
+
+ @Override
+ public String getGeneName() {
+ return _gene_name;
+ }
+
+ @Override
+ public SortedSet<GoTerm> getGoTerms() {
+ return _go_terms;
+ }
+
+ @Override
+ public String getProvider() {
+ return "uniprot";
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _name;
+ }
+
+ @Override
+ public String getSequenceSymbol() {
+ return _symbol;
+ }
+
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os_scientific_name;
+ }
+
+ @Override
+ public boolean isEmpty() {
+ return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
+ && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
+ && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() )
+ && ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences()
+ .isEmpty() ) );
+ }
+
+ private void addCrossReference( final Accession accession ) {
+ if ( _cross_references == null ) {
+ _cross_references = new TreeSet<Accession>();
+ }
+ _cross_references.add( accession );
+ }
+
+ private void addGoTerm( final BasicGoTerm g ) {
+ if ( _go_terms == null ) {
+ _go_terms = new TreeSet<GoTerm>();
+ }
+ _go_terms.add( g );
+ }
+
+ private void setAc( final String ac ) {
+ if ( _ac == null ) {
+ _ac = ac;
+ }
+ }
+
+ private void setMolecularSequence( final MolecularSequence mol_seq ) {
+ _mol_seq = mol_seq;
+ }
+
+ private void setGeneName( final String gene_name ) {
+ if ( _gene_name == null ) {
+ _gene_name = gene_name;
+ }
+ }
+
+ private void setOsScientificName( final String os_scientific_name ) {
+ if ( _os_scientific_name == null ) {
+ _os_scientific_name = os_scientific_name;
+ }
+ }
+
+ private void setSequenceName( final String name ) {
+ if ( _name == null ) {
+ _name = name;
+ }
+ }
+
+ private void setSequenceSymbol( final String symbol ) {
+ _symbol = symbol;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
final UniProtEntry e = new UniProtEntry();
+ boolean saw_sq = false;
+ final StringBuffer sq_buffer = new StringBuffer();
+ boolean is_aa = false;
for( final String line : lines ) {
//System.out.println( line );
if ( line.startsWith( "AC" ) ) {
- e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
+ e.setAc( SequenceDbWsTools.extractFromTo( line, "AC", ";" ) );
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
+ e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
}
else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
+ e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
}
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
if ( line.indexOf( "Short=" ) > 0 ) {
- e.setSequenceSymbol( DatabaseTools.extract( line, "Short=", ";" ) );
+ e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
}
}
else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
if ( line.indexOf( "Name=" ) > 0 ) {
- e.setGeneName( DatabaseTools.extract( line, "Name=", ";" ) );
+ e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", ";" ) );
}
}
else if ( line.startsWith( "DR" ) ) {
if ( line.indexOf( "GO;" ) > 0 ) {
- Matcher m = GO_PATTERN.matcher( line );
+ final Matcher m = GO_PATTERN.matcher( line );
+ if ( m.find() ) {
+ final String id = m.group( 1 );
+ final String ns_str = m.group( 2 );
+ final String desc = m.group( 3 );
+ String gns = GoNameSpace.BIOLOGICAL_PROCESS_STR;
+ if ( ns_str.equals( "F" ) ) {
+ gns = GoNameSpace.MOLECULAR_FUNCTION_STR;
+ }
+ else if ( ns_str.equals( "C" ) ) {
+ gns = GoNameSpace.CELLULAR_COMPONENT_STR;
+ }
+ e.addGoTerm( new BasicGoTerm( id, desc, gns, false ) );
+ }
+ }
+ else if ( line.indexOf( "PDB;" ) > 0 ) {
+ final Matcher m = PDB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "PDB", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "KEGG;" ) > 0 ) {
+ final Matcher m = KEGG_PATTERN.matcher( line );
if ( m.find() ) {
- String n = m.group( 1 );
- String ns_str = m.group( 2 );
- String desc = m.group( 3 );
- if ( ns_str.equals( "F" ) ) {
-
- System.out.println( "GO:" + n + " " + desc + " " + ns );
- GoTerm go = new BasicGoTerm( n, desc, ns, false );
- // e.setGeneName( DatabaseTools.extract( line, "Name=", ";" ) );
+ e.addCrossReference( new Accession( m.group( 1 ), "KEGG" ) );
+ }
+ }
+ else if ( line.indexOf( "CTD;" ) > 0 ) {
+ final Matcher m = CTD_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "CTD" ) );
+ }
+ }
+ else if ( line.indexOf( "MIM;" ) > 0 ) {
+ final Matcher m = MIM_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "MIM" ) );
+ }
+ }
+ else if ( line.indexOf( "Orphanet;" ) > 0 ) {
+ final Matcher m = Orphanet_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "Orphanet", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "PharmGKB;" ) > 0 ) {
+ final Matcher m = PharmGKB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "PharmGKB" ) );
+ }
+ }
+ else if ( line.indexOf( "BindingDB;" ) > 0 ) {
+ final Matcher m = BindingDB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "BindingDB" ) );
+ }
+ }
+ else if ( line.indexOf( "DrugBank;" ) > 0 ) {
+ final Matcher m = DrugBank_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "DrugBank", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "NextBio;" ) > 0 ) {
+ final Matcher m = NextBio_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "NextBio" ) );
+ }
+ }
+ else if ( line.indexOf( "Reactome;" ) > 0 ) {
+ final Matcher m = Reactome_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "Reactome", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "HGNC;" ) > 0 ) {
+ final Matcher m = HGNC_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "HGNC" ) );
}
}
}
else if ( line.startsWith( "OS" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
- e.setOsScientificName( DatabaseTools.extract( line, "OS", "(" ) );
+ e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
}
else {
- e.setOsScientificName( DatabaseTools.extract( line, "OS", "." ) );
+ e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "." ) );
}
}
else if ( line.startsWith( "OX" ) ) {
if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
- e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
}
}
+ else if ( line.startsWith( "SQ" ) ) {
+ saw_sq = true;
+ if ( line.contains( "AA;" ) ) {
+ is_aa = true;
+ }
+ }
+ else if ( saw_sq && line.startsWith( " " ) ) {
+ sq_buffer.append( line.replaceAll( "\\s+", "" ) );
+ }
}
- return e;
- }
-
- private void setSequenceSymbol( String symbol ) {
- _symbol = symbol;
- }
-
- @Override
- public String getAccession() {
- return _ac;
- }
-
- private void setAc( final String ac ) {
- if ( _ac == null ) {
- _ac = ac;
- }
- }
-
- @Override
- public String getSequenceName() {
- return _name;
- }
-
- private void setSequenceName( final String name ) {
- if ( _name == null ) {
- _name = name;
- }
- }
-
- @Override
- public String getTaxonomyScientificName() {
- return _os_scientific_name;
- }
-
- private void setOsScientificName( final String os_scientific_name ) {
- if ( _os_scientific_name == null ) {
- _os_scientific_name = os_scientific_name;
- }
- }
-
- @Override
- public String getTaxonomyIdentifier() {
- return _tax_id;
- }
-
- private void setTaxId( final String tax_id ) {
- if ( _tax_id == null ) {
- _tax_id = tax_id;
- }
- }
-
- private void setGeneName( final String gene_name ) {
- if ( _gene_name == null ) {
- _gene_name = gene_name;
+ if ( ( sq_buffer.length() > 0 ) && is_aa ) {
+ e.setMolecularSequence( BasicSequence.createAaSequence( e.getAccession(), sq_buffer.toString() ) );
}
+ return e;
}
@Override
- public String getSequenceSymbol() {
- return _symbol;
+ public SortedSet<Annotation> getAnnotations() {
+ return null;
}
@Override
- public boolean isEmpty() {
- return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
- && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
- && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil
- .isEmpty( getSequenceSymbol() ) );
+ public String getMap() {
+ return null;
}
@Override
- public String getProvider() {
- return "uniprot";
+ public String getChromosome() {
+ return null;
}
@Override
- public String getGeneName() {
- return _gene_name;
+ public MolecularSequence getMolecularSequence() {
+ return _mol_seq;
}
}
git://source.jalview.org / jalview.git / blobdiff