// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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.util.ForesterUtil;
public final class EbiDbEntry implements SequenceDatabaseEntry {
+ 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;
+ // FIXME actually this is NCBI entry
//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 String _pa;
+ private String _provider;
+ private String _symbol;
+ private String _tax_id;
+ // TODO PUBMED 15798186
+ //TODO (FEATURES)
+ // source /db_xref="taxon:9606"
+ // gene 1..2881
+ // /gene="RBM39"
+ //
+ // /db_xref="MIM:604739"
+ // CDS
+ // /gene="RBM39"
+ // /db_xref="MIM:604739"
+ // /db_xref="InterPro:IPR002475"
+ // /product="Bcl-2"
+ // /db_xref="UniProtKB/TrEMBL:Q5J7V1" <- reparse?
+ //
+ // Protein
+ /*
+ LOCUS NM_184234 2881 bp mRNA linear PRI 16-JUN-2013
+ DEFINITION Homo sapiens RNA binding motif protein 39 (RBM39), transcript
+ variant 1, mRNA.
+ ACCESSION NM_184234
+ VERSION NM_184234.2 GI:336176061
+ KEYWORDS RefSeq.
+ SOURCE Homo sapiens (human)
+ ORGANISM Homo sapiens
+ Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+ Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
+ Catarrhini; Hominidae; Homo.
+ REFERENCE 1 (bases 1 to 2881)
+ AUTHORS Sillars-Hardebol,A.H., Carvalho,B., Belien,J.A., de Wit,M.,
+ Delis-van Diemen,P.M., Tijssen,M., van de Wiel,M.A., Ponten,F.,
+ Meijer,G.A. and Fijneman,R.J.
+ TITLE CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma
+ progression
+ JOURNAL Cell Oncol (Dordr) 35 (4), 293-300 (2012)
+ PUBMED 22711543
+ REMARK GeneRIF: Data show that CSE1L, DIDO1 and RBM39 mRNA expression
+ levels correlated with chromosome 20q DNA copy number status.
+ REFERENCE 2 (bases 1 to 2881)
+ AUTHORS Huang,G., Zhou,Z., Wang,H. and Kleinerman,E.S.
+ TITLE CAPER-alpha alternative splicing regulates the expression of
+ vascular endothelial growth factor(1)(6)(5) in Ewing sarcoma cells
+ JOURNAL Cancer 118 (8), 2106-2116 (2012)
+ PUBMED 22009261
+ REMARK GeneRIF: Increased VEGF(165) expression is secondary to the
+ down-regulation of CAPER-alpha by EWS/FLI-1. CAPER-alpha mediates
+ alternative splicing and controls the shift from VEGF(189) to
+ VEGF(165) .
+ REFERENCE 3 (bases 1 to 2881)
+ AUTHORS Han,B., Stockwin,L.H., Hancock,C., Yu,S.X., Hollingshead,M.G. and
+ Newton,D.L.
+ TITLE Proteomic analysis of nuclei isolated from cancer cell lines
+ treated with indenoisoquinoline NSC 724998, a novel topoisomerase I
+ inhibitor
+ JOURNAL J. Proteome Res. 9 (8), 4016-4027 (2010)
+ PUBMED 20515076
+ REMARK Erratum:[J Proteome Res. 2011 Apr 1;10(4):2128]
+ REFERENCE 4 (bases 1 to 2881)
+ AUTHORS Zhang,J.Y., Looi,K.S. and Tan,E.M.
+ TITLE Identification of tumor-associated antigens as diagnostic and
+ predictive biomarkers in cancer
+ JOURNAL Methods Mol. Biol. 520, 1-10 (2009)
+ PUBMED 19381943
+ REFERENCE 5 (bases 1 to 2881)
+ AUTHORS Dutta,J., Fan,G. and Gelinas,C.
+ TITLE CAPERalpha is a novel Rel-TAD-interacting factor that inhibits
+ lymphocyte transformation by the potent Rel/NF-kappaB oncoprotein
+ v-Rel
+ JOURNAL J. Virol. 82 (21), 10792-10802 (2008)
+ PUBMED 18753212
+ REMARK GeneRIF: this study identifies CAPERalpha (RNA binding motif
+ protein 39) as a new transcriptional coregulator for v-Rel and
+ reveals an important role in modulating Rel's oncogenic activity.
+ REFERENCE 6 (bases 1 to 2881)
+ AUTHORS Cazalla,D., Newton,K. and Caceres,J.F.
+ TITLE A novel SR-related protein is required for the second step of
+ Pre-mRNA splicing
+ JOURNAL Mol. Cell. Biol. 25 (8), 2969-2980 (2005)
+ PUBMED 15798186
+ REFERENCE 7 (bases 1 to 2881)
+ AUTHORS Dowhan,D.H., Hong,E.P., Auboeuf,D., Dennis,A.P., Wilson,M.M.,
+ Berget,S.M. and O'Malley,B.W.
+ TITLE Steroid hormone receptor coactivation and alternative RNA splicing
+ by U2AF65-related proteins CAPERalpha and CAPERbeta
+ JOURNAL Mol. Cell 17 (3), 429-439 (2005)
+ PUBMED 15694343
+ REFERENCE 8 (bases 1 to 2881)
+ AUTHORS Sun,N.N., Fastje,C.D., Wong,S.S., Sheppard,P.R., Macdonald,S.J.,
+ Ridenour,G., Hyde,J.D. and Witten,M.L.
+ TITLE Dose-dependent transcriptome changes by metal ores on a human acute
+ lymphoblastic leukemia cell line
+ JOURNAL Toxicol Ind Health 19 (7-10), 157-163 (2003)
+ PUBMED 15747776
+ REMARK GeneRIF: 10 genes were down-regulated following treatment of the
+ T-ALL cells with 0.15 and 1.5 microg/mL of metal ores at 72 h
+ REFERENCE 9 (bases 1 to 2881)
+ AUTHORS Jung,D.J., Na,S.Y., Na,D.S. and Lee,J.W.
+ TITLE Molecular cloning and characterization of CAPER, a novel
+ coactivator of activating protein-1 and estrogen receptors
+ JOURNAL J. Biol. Chem. 277 (2), 1229-1234 (2002)
+ PUBMED 11704680
+ REMARK GeneRIF: This paper describes the mouse gene.
+ REFERENCE 10 (bases 1 to 2881)
+ AUTHORS Imai,H., Chan,E.K., Kiyosawa,K., Fu,X.D. and Tan,E.M.
+ TITLE Novel nuclear autoantigen with splicing factor motifs identified
+ with antibody from hepatocellular carcinoma
+ JOURNAL J. Clin. Invest. 92 (5), 2419-2426 (1993)
+ PUBMED 8227358
+ COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
+ reference sequence was derived from DC346351.1, BC141835.1 and
+ C75555.1.
+ On Jun 16, 2011 this sequence version replaced gi:35493810.
+
+ Summary: This gene encodes a member of the U2AF65 family of
+ proteins. The encoded protein is found in the nucleus, where it
+ co-localizes with core spliceosomal proteins. It has been shown to
+ play a role in both steroid hormone receptor-mediated transcription
+ and alternative splicing, and it is also a transcriptional
+ coregulator of the viral oncoprotein v-Rel. Multiple transcript
+ variants have been observed for this gene. A related pseudogene has
+ been identified on chromosome X. [provided by RefSeq, Aug 2011].
+
+ Transcript Variant: This variant (1) encodes the longest isoform
+ (a, also called CC1.4).
+
+ Publication Note: This RefSeq record includes a subset of the
+ publications that are available for this gene. Please see the Gene
+ record to access additional publications.
+
+ ##Evidence-Data-START##
+ Transcript exon combination :: BC141835.1, L10911.1 [ECO:0000332]
+ RNAseq introns :: mixed/partial sample support
+ ERS025081, ERS025082 [ECO:0000350]
+ ##Evidence-Data-END##
+ COMPLETENESS: complete on the 3' end.
+ PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
+ 1-578 DC346351.1 3-580
+ 579-2872 BC141835.1 429-2722
+ 2873-2881 C75555.1 1-9 c
+ FEATURES Location/Qualifiers
+ source 1..2881
+ /organism="Homo sapiens"
+ /mol_type="mRNA"
+ /db_xref="taxon:9606"
+ /chromosome="20"
+ /map="20q11.22"
+ gene 1..2881
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /note="RNA binding motif protein 39"
+ /db_xref="GeneID:9584"
+ /db_xref="HGNC:15923"
+ /db_xref="HPRD:09201"
+ /db_xref="MIM:604739"
+ exon 1..396
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ STS 35..262
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="REN58946"
+ /db_xref="UniSTS:383746"
+ misc_feature 221..223
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /note="upstream in-frame stop codon"
+ STS 299..453
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="G64285"
+ /db_xref="UniSTS:158667"
+ exon 397..460
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ CDS 410..2002
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /note="isoform a is encoded by transcript variant 1;
+ coactivator of activating protein-1 and estrogen
+ receptors; functional spliceosome-associated protein 59;
+ RNA-binding region (RNP1, RRM) containing 2;
+ hepatocellular carcinoma protein 1; splicing factor HCC1"
+ /codon_start=1
+ /product="RNA-binding protein 39 isoform a"
+ /protein_id="NP_909122.1"
+ /db_xref="GI:35493811"
+ /db_xref="CCDS:CCDS13266.1"
+ /db_xref="GeneID:9584"
+ /db_xref="HGNC:15923"
+ /db_xref="HPRD:09201"
+ /db_xref="MIM:604739"
+ /translation="MADDIDIEAMLEAPYKKDENKLSSANGHEERSKKRKKSKSRSRS
+ HERKRSKSKERKRSRDRERKKSKSRERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGP
+ KFNSAIRGKIGLPHSIKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQL
+ AARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRV
+ LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRI
+ ESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASS
+ ASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAE
+ FSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDV
+ IEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL
+ PTYHNLFPDSMTATQLLVPSRR"
+ misc_feature 413..415
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="N-acetylalanine; propagated from
+ UniProtKB/Swiss-Prot (Q14498.2); acetylation site"
+
+ exon 461..510
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+
+ exon 1902..2874
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ STS 1956..2182
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="REN58786"
+ /db_xref="UniSTS:383586"
+ STS 2104..2148
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="D19S1033"
+ /db_xref="UniSTS:154759"
+ STS 2145..2400
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="REN58785"
+ /db_xref="UniSTS:383585"
+
+ polyA_signal 2851..2856
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ polyA_site 2874
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ ORIGIN
+ 1 atttggagct tggggcagct tctcgcgaga gcccgtgctg agggctctgt gaggccccgt
+ 61 gtgtttgtgt gtgtgtatgt gtgctggtga atgtgagtac agggaagcag cggccgccat
+ 121 ttcagggagc ttgtcgacgc tgtcgcaggg gtggatcctg agctgccgaa gccgccgtcc
+ 181 tgctctcccg cgtgggcttc tctaattcca ttgttttttt tagattctct cgggcctagc
+ 241 cgtccttgga acccgatatt cgggctgggc ggttccgcgg cctgggccta ggggcttaac
+
+
+
+ */
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" ) ) {
- // if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- e.setDe( DatabaseTools.extract( line, "DE" ) );
- //}
- }
- // else if ( line.startsWith( "GN" ) ) {
- // if ( ( line.indexOf( "Name=" ) > 0 ) ) {
- // e.setSymbol( extract( line, "Name=", ";" ) );
- // }
- // }
- 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
return _symbol;
}
- private void setSymbol( final String symbol ) {
- if ( _symbol == null ) {
- _symbol = symbol;
- }
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os;
}
@Override
&& ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
}
- @Override
- public String getProvider() {
- return _provider;
- }
-
public void setProvider( final String provider ) {
_provider = provider;
}
+
+ private void addAnnotation( final Annotation annotation ) {
+ if ( _annotations == null ) {
+ _annotations = new TreeSet<Annotation>();
+ }
+ _annotations.add( annotation );
+ }
+
+ private void addCrossReference( final Accession accession ) {
+ if ( _cross_references == null ) {
+ _cross_references = new TreeSet<Accession>();
+ }
+ System.out.println( "XREF ADDED: " + accession );
+ _cross_references.add( accession );
+ }
+
+ private void setAccession( final String pa ) {
+ if ( _pa == null ) {
+ _pa = pa;
+ }
+ }
+
+ private void setChromosome( final String chromosome ) {
+ _chromosome = chromosome;
+ }
+
+ 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;
+ }
+ }
+
+ // public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
+ // final EbiDbEntry e = new EbiDbEntry();
+ // for( final String line : lines ) {
+ // if ( line.startsWith( "PA" ) ) {
+ // e.setPA( SequenceDbWsTools.extractFrom( line, "PA" ) );
+ // }
+ // else if ( line.startsWith( "DE" ) ) {
+ // e.setDe( SequenceDbWsTools.extractFrom( line, "DE" ) );
+ // }
+ // else if ( line.startsWith( "OS" ) ) {
+ // if ( line.indexOf( "(" ) > 0 ) {
+ // e.setOs( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
+ // }
+ // else {
+ // e.setOs( SequenceDbWsTools.extractFrom( line, "OS" ) );
+ // }
+ // }
+ // else if ( line.startsWith( "OX" ) ) {
+ // if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
+ // e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
+ // }
+ // }
+ // }
+ // return e;
+ // }
+ public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
+ final Pattern X_PATTERN = Pattern.compile( "^[A-Z]+" );
+ final Pattern chromosome_PATTERN = Pattern.compile( "\\s+/chromosome=\"(\\w+)\"" );
+ final Pattern map_PATTERN = Pattern.compile( "\\s+/map=\"([\\w+\\.])\"" );
+ final Pattern gene_PATTERN = Pattern.compile( "\\s+/gene=\"(.+)\"" );
+ final Pattern mim_PATTERN = Pattern.compile( "\\s+/db_xref=\"MIM:(\\d+)\"" );
+ final Pattern taxon_PATTERN = Pattern.compile( "\\s+/db_xref=\"taxon:(\\d+)\"" );
+ final Pattern interpro_PATTERN = Pattern.compile( "\\s+/db_xref=\"InterPro:([A-Z0-9]+)\"" );
+ final Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/[A-Za-z-]*:(\\w+)\"" );
+ final Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
+ final Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
+ final Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
+ final Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
+ final Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
+ 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 ) {
+ x( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) ) );
+ }
+ else {
+ x( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "[" ) ) );
+ }
+ }
+ else if ( line.indexOf( "." ) > 0 ) {
+ if ( definiton ) {
+ x( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) ) );
+ }
+ else {
+ x( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "." ) ) );
+ }
+ }
+ else {
+ if ( definiton ) {
+ x( def, ( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) ) );
+ }
+ else {
+ x( 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" ) );
+ }
+ // in_def = false;
+ }
+ 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 " ) && X_PATTERN.matcher( line ).find() ) {
+ in_features = false;
+ in_source = false;
+ in_gene = false;
+ in_cds = false;
+ in_mrna = false;
+ in_protein = false;
+ // in_def = 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;
+ }
+
+ private static void x( final StringBuilder sb, final String s ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( s.trim() );
+ }
}
git://source.jalview.org / jalview.git / blobdiff