2 // forester -- software libraries and applications
3 // for genomics and evolutionary biology research.
5 // Copyright (C) 2010 Christian M Zmasek
6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.ws.seqdb;
28 import java.util.List;
29 import java.util.SortedSet;
30 import java.util.TreeSet;
31 import java.util.regex.Matcher;
32 import java.util.regex.Pattern;
34 import org.forester.go.BasicGoTerm;
35 import org.forester.go.GoNameSpace;
36 import org.forester.go.GoTerm;
37 import org.forester.phylogeny.data.Accession;
38 import org.forester.phylogeny.data.Annotation;
39 import org.forester.sequence.BasicSequence;
40 import org.forester.sequence.MolecularSequence;
41 import org.forester.util.ForesterUtil;
43 public final class UniProtEntry implements SequenceDatabaseEntry {
45 public final static Pattern BindingDB_PATTERN = Pattern.compile( "BindingDB;\\s+([0-9A-Z]+);" );
46 public final static Pattern CTD_PATTERN = Pattern.compile( "CTD;\\s+(\\d+);" );
47 public final static Pattern DrugBank_PATTERN = Pattern.compile( "DrugBank;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
48 public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PFC]):([^;]+);" );
49 public final static Pattern KEGG_PATTERN = Pattern.compile( "KEGG;\\s+([a-z]+:[0-9]+);" );
50 public final static Pattern MIM_PATTERN = Pattern.compile( "MIM;\\s+(\\d+);" );
51 public final static Pattern NextBio_PATTERN = Pattern.compile( "NextBio;\\s+(\\d+);" );
52 public final static Pattern Orphanet_PATTERN = Pattern.compile( "Orphanet;\\s+(\\d+);\\s+([^\\.]+)" );
53 public final static Pattern PDB_PATTERN = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
54 public final static Pattern PharmGKB_PATTERN = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
55 public final static Pattern Reactome_PATTERN = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
56 public final static Pattern HGNC_PATTERN = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
57 public final static Pattern NCBI_TAXID_PATTERN = Pattern.compile( "NCBI_TaxID=(\\d+)" );
59 private SortedSet<Accession> _cross_references;
60 private String _gene_name;
61 private SortedSet<GoTerm> _go_terms;
63 private String _os_scientific_name;
64 private String _symbol;
65 private String _tax_id;
66 private MolecularSequence _mol_seq;
68 private UniProtEntry() {
72 public Object clone() throws CloneNotSupportedException {
73 throw new CloneNotSupportedException();
77 public String getAccession() {
82 public SortedSet<Accession> getCrossReferences() {
83 return _cross_references;
87 public String getGeneName() {
92 public SortedSet<GoTerm> getGoTerms() {
97 public String getProvider() {
102 public String getSequenceName() {
107 public String getSequenceSymbol() {
112 public String getTaxonomyIdentifier() {
117 public String getTaxonomyScientificName() {
118 return _os_scientific_name;
122 public boolean isEmpty() {
123 return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
124 && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
125 && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() )
126 && ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences()
131 public String getMap() {
136 public String getChromosome() {
141 public MolecularSequence getMolecularSequence() {
145 private void addCrossReference( final Accession accession ) {
146 if ( _cross_references == null ) {
147 _cross_references = new TreeSet<Accession>();
149 _cross_references.add( accession );
152 private void addGoTerm( final BasicGoTerm g ) {
153 if ( _go_terms == null ) {
154 _go_terms = new TreeSet<GoTerm>();
159 private void setAc( final String ac ) {
165 private void setMolecularSequence( final MolecularSequence mol_seq ) {
169 private void setGeneName( final String gene_name ) {
170 if ( _gene_name == null ) {
171 _gene_name = gene_name;
175 private void setOsScientificName( final String os_scientific_name ) {
176 if ( _os_scientific_name == null ) {
177 _os_scientific_name = os_scientific_name;
181 private void setSequenceName( final String name ) {
182 if ( _name == null ) {
187 private void setSequenceSymbol( final String symbol ) {
191 private void setTaxId( final String tax_id ) {
192 if ( _tax_id == null ) {
200 public SortedSet<Annotation> getAnnotations() {
204 public final static SequenceDatabaseEntry createInstance( final List<String> lines ) {
205 final UniProtEntry e = new UniProtEntry();
206 boolean saw_sq = false;
207 final StringBuffer sq_buffer = new StringBuffer();
208 boolean is_aa = false;
209 for( final String line : lines ) {
210 if ( line.startsWith( "AC" ) ) {
211 e.setAc( SequenceDbWsTools.extractFromTo( line, "AC", ";" ) );
213 else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
214 if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
215 if ( line.indexOf( "{" ) > 0 ) {
216 e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
219 e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
222 else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
223 if ( line.indexOf( "{" ) > 0 ) {
224 e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
227 e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
231 else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
232 if ( line.indexOf( "Short=" ) > 0 ) {
233 if ( line.indexOf( "{" ) > 0 ) {
234 e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", "{" ) );
237 e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
241 else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
242 if ( line.indexOf( "Name=" ) > 0 ) {
243 if ( line.indexOf( "{" ) > 0 ) {
244 e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", "{" ) );
247 e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", ";" ) );
251 else if ( line.startsWith( "DR" ) ) {
252 if ( line.indexOf( "GO;" ) > 0 ) {
253 final Matcher m = GO_PATTERN.matcher( line );
255 final String id = m.group( 1 );
256 final String ns_str = m.group( 2 );
257 final String desc = m.group( 3 );
258 String gns = GoNameSpace.BIOLOGICAL_PROCESS_STR;
259 if ( ns_str.equals( "F" ) ) {
260 gns = GoNameSpace.MOLECULAR_FUNCTION_STR;
262 else if ( ns_str.equals( "C" ) ) {
263 gns = GoNameSpace.CELLULAR_COMPONENT_STR;
265 e.addGoTerm( new BasicGoTerm( id, desc, gns, false ) );
268 else if ( line.indexOf( "PDB;" ) > 0 ) {
269 final Matcher m = PDB_PATTERN.matcher( line );
271 e.addCrossReference( new Accession( m.group( 1 ), "PDB", m.group( 2 ) ) );
274 else if ( line.indexOf( "KEGG;" ) > 0 ) {
275 final Matcher m = KEGG_PATTERN.matcher( line );
277 e.addCrossReference( new Accession( m.group( 1 ), "KEGG" ) );
280 else if ( line.indexOf( "CTD;" ) > 0 ) {
281 final Matcher m = CTD_PATTERN.matcher( line );
283 e.addCrossReference( new Accession( m.group( 1 ), "CTD" ) );
286 else if ( line.indexOf( "MIM;" ) > 0 ) {
287 final Matcher m = MIM_PATTERN.matcher( line );
289 e.addCrossReference( new Accession( m.group( 1 ), "MIM" ) );
292 else if ( line.indexOf( "Orphanet;" ) > 0 ) {
293 final Matcher m = Orphanet_PATTERN.matcher( line );
295 e.addCrossReference( new Accession( m.group( 1 ), "Orphanet", m.group( 2 ) ) );
298 else if ( line.indexOf( "PharmGKB;" ) > 0 ) {
299 final Matcher m = PharmGKB_PATTERN.matcher( line );
301 e.addCrossReference( new Accession( m.group( 1 ), "PharmGKB" ) );
304 else if ( line.indexOf( "BindingDB;" ) > 0 ) {
305 final Matcher m = BindingDB_PATTERN.matcher( line );
307 e.addCrossReference( new Accession( m.group( 1 ), "BindingDB" ) );
310 else if ( line.indexOf( "DrugBank;" ) > 0 ) {
311 final Matcher m = DrugBank_PATTERN.matcher( line );
313 e.addCrossReference( new Accession( m.group( 1 ), "DrugBank", m.group( 2 ) ) );
316 else if ( line.indexOf( "NextBio;" ) > 0 ) {
317 final Matcher m = NextBio_PATTERN.matcher( line );
319 e.addCrossReference( new Accession( m.group( 1 ), "NextBio" ) );
322 else if ( line.indexOf( "Reactome;" ) > 0 ) {
323 final Matcher m = Reactome_PATTERN.matcher( line );
325 e.addCrossReference( new Accession( m.group( 1 ), "Reactome", m.group( 2 ) ) );
328 else if ( line.indexOf( "HGNC;" ) > 0 ) {
329 final Matcher m = HGNC_PATTERN.matcher( line );
331 e.addCrossReference( new Accession( m.group( 1 ), "HGNC" ) );
335 else if ( line.startsWith( "OS" ) ) {
336 if ( line.indexOf( "(" ) > 0 ) {
337 e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
340 e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "." ) );
343 else if ( line.startsWith( "OX" ) ) {
344 if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
345 final Matcher m = NCBI_TAXID_PATTERN.matcher( line );
347 e.setTaxId( m.group( 1 ) );
351 else if ( line.startsWith( "SQ" ) ) {
353 if ( line.contains( "AA;" ) ) {
357 else if ( saw_sq && line.startsWith( " " ) ) {
358 sq_buffer.append( line.replaceAll( "\\s+", "" ) );
361 if ( sq_buffer.length() > 0 ) {
363 e.setMolecularSequence( BasicSequence.createAaSequence( e.getAccession(), sq_buffer.toString() ) );
366 e.setMolecularSequence( BasicSequence.createDnaSequence( e.getAccession(), sq_buffer.toString() ) );