org.forester.ws.seqdb
Class SequenceDbWsTools

java.lang.Object
  org.forester.ws.seqdb.SequenceDbWsTools

public final class SequenceDbWsTools
extends java.lang.Object

Nested Class Summary

static class

SequenceDbWsTools.Db

Field Summary

static java.lang.String	BASE_EMBL_DB_URL
static java.lang.String	BASE_UNIPROT_URL
static java.lang.String	EMBL_DBS_EMBL
static java.lang.String	EMBL_DBS_REFSEQ_N
static java.lang.String	EMBL_DBS_REFSEQ_P

Constructor Summary

SequenceDbWsTools()

Method Summary

static java.util.List<UniProtTaxonomy>	getTaxonomiesFromCommonName(java.lang.String cn, int max_taxonomies_return)
static java.util.List<UniProtTaxonomy>	getTaxonomiesFromCommonNameStrict(java.lang.String cn, int max_taxonomies_return)
static java.util.List<UniProtTaxonomy>	getTaxonomiesFromId(java.lang.String id, int max_taxonomies_return)
static java.util.List<UniProtTaxonomy>	getTaxonomiesFromScientificName(java.lang.String sn, int max_taxonomies_return)
static java.util.List<UniProtTaxonomy>	getTaxonomiesFromScientificNameStrict(java.lang.String sn, int max_taxonomies_return) Does not return "sub-types".
static java.util.List<UniProtTaxonomy>	getTaxonomiesFromTaxonomyCode(java.lang.String code, int max_taxonomies_return)
static SequenceDatabaseEntry	obtainEmblEntry(Identifier id, int max_lines_to_return)
static SequenceDatabaseEntry	obtainRefSeqEntryFromEmbl(Identifier id, int max_lines_to_return)
static SequenceDatabaseEntry	obtainUniProtEntry(java.lang.String query, int max_lines_to_return)
static java.lang.String	parseUniProtAccessor(java.lang.String query) Returns null if no match.
static java.util.List<java.lang.String>	queryDb(java.lang.String query, int max_lines_to_return, java.lang.String base_url)
static java.util.List<java.lang.String>	queryEmblDb(Identifier id, int max_lines_to_return)
static java.util.List<java.lang.String>	queryUniprot(java.lang.String query, int max_lines_to_return)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BASE_UNIPROT_URL

public static final java.lang.String BASE_UNIPROT_URL

See Also:

Constant Field Values

BASE_EMBL_DB_URL

public static final java.lang.String BASE_EMBL_DB_URL

See Also:

Constant Field Values

EMBL_DBS_EMBL

public static final java.lang.String EMBL_DBS_EMBL

See Also:

Constant Field Values

EMBL_DBS_REFSEQ_P

public static final java.lang.String EMBL_DBS_REFSEQ_P

See Also:

Constant Field Values

EMBL_DBS_REFSEQ_N

public static final java.lang.String EMBL_DBS_REFSEQ_N

See Also:

Constant Field Values

Constructor Detail

SequenceDbWsTools

public SequenceDbWsTools()

Method Detail

parseUniProtAccessor

public static java.lang.String parseUniProtAccessor(java.lang.String query)

Returns null if no match.

Parameters:

query -

db -

Returns:

getTaxonomiesFromCommonName

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromCommonName(java.lang.String cn,
                                                                          int max_taxonomies_return)
                                                                   throws java.io.IOException

Throws:

java.io.IOException

getTaxonomiesFromCommonNameStrict

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict(java.lang.String cn,
                                                                                int max_taxonomies_return)
                                                                         throws java.io.IOException

Throws:

java.io.IOException

getTaxonomiesFromId

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromId(java.lang.String id,
                                                                  int max_taxonomies_return)
                                                           throws java.io.IOException

Throws:

java.io.IOException

getTaxonomiesFromScientificName

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromScientificName(java.lang.String sn,
                                                                              int max_taxonomies_return)
                                                                       throws java.io.IOException

Throws:

java.io.IOException

getTaxonomiesFromScientificNameStrict

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict(java.lang.String sn,
                                                                                    int max_taxonomies_return)
                                                                             throws java.io.IOException

Does not return "sub-types". For example, for "Mus musculus" only returns "Mus musculus" and not "Mus musculus", "Mus musculus bactrianus", ...

Throws:

java.io.IOException

getTaxonomiesFromTaxonomyCode

public static java.util.List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode(java.lang.String code,
                                                                            int max_taxonomies_return)
                                                                     throws java.io.IOException

Throws:

java.io.IOException

queryEmblDb

public static java.util.List<java.lang.String> queryEmblDb(Identifier id,
                                                           int max_lines_to_return)
                                                    throws java.io.IOException

Throws:

java.io.IOException

queryUniprot

public static java.util.List<java.lang.String> queryUniprot(java.lang.String query,
                                                            int max_lines_to_return)
                                                     throws java.io.IOException

Throws:

java.io.IOException

queryDb

public static java.util.List<java.lang.String> queryDb(java.lang.String query,
                                                       int max_lines_to_return,
                                                       java.lang.String base_url)
                                                throws java.io.IOException

Throws:

java.io.IOException

obtainUniProtEntry

public static SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query,
                                                       int max_lines_to_return)
                                                throws java.io.IOException

Throws:

java.io.IOException

obtainRefSeqEntryFromEmbl

public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Identifier id,
                                                              int max_lines_to_return)
                                                       throws java.io.IOException

Throws:

java.io.IOException

obtainEmblEntry

public static SequenceDatabaseEntry obtainEmblEntry(Identifier id,
                                                    int max_lines_to_return)
                                             throws java.io.IOException

Throws:

java.io.IOException