org.forester.ws.seqdb

Class SequenceDbWsTools

java.lang.Object

org.forester.ws.seqdb.SequenceDbWsTools

public final class SequenceDbWsTools
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	BASE_UNIPROT_URL
static int	DEFAULT_LINES_TO_RETURN
static String	EMBL_DBS_REFSEQ_N
static String	EMBL_DBS_REFSEQ_P
static String	EMBL_EMBL
static String	EMBL_GENBANK
static String	EMBL_REFSEQ

Constructor Summary

Constructors

Constructor and Description
SequenceDbWsTools()

Method Summary

Modifier and Type	Method and Description
static List<UniProtTaxonomy>	getTaxonomiesFromCommonNameStrict(String cn, int max_taxonomies_return)
static List<UniProtTaxonomy>	getTaxonomiesFromId(String id, int max_taxonomies_return)
static List<UniProtTaxonomy>	getTaxonomiesFromScientificNameStrict(String sn, int max_taxonomies_return) Does not return "sub-types".
static List<UniProtTaxonomy>	getTaxonomiesFromTaxonomyCode(String code, int max_taxonomies_return)
static SequenceDatabaseEntry	obtainEmblEntry(Accession acc)
static SequenceDatabaseEntry	obtainEmblEntry(Accession acc, int max_lines_to_return)
static SequenceDatabaseEntry	obtainEntry(String acc_str)
static SequenceDatabaseEntry	obtainRefSeqEntryFromEmbl(Accession acc)
static SequenceDatabaseEntry	obtainRefSeqEntryFromEmbl(Accession acc, int max_lines_to_return)
static Accession	obtainSeqAccession(PhylogenyNode node)
static void	obtainSeqInformation(boolean allow_to_set_taxonomic_data, int lines_to_return, SortedSet<String> not_found, PhylogenyNode node)
static void	obtainSeqInformation(boolean allow_to_set_taxonomic_data, SortedSet<String> not_found, PhylogenyNode node)
static SortedSet<String>	obtainSeqInformation(Phylogeny phy, boolean ext_nodes_only, boolean allow_to_set_taxonomic_data, int lines_to_return)
static void	obtainSeqInformation(PhylogenyNode node)
static SequenceDatabaseEntry	obtainUniProtEntry(String query)
static SequenceDatabaseEntry	obtainUniProtEntry(String query, int max_lines_to_return)
static List<String>	queryDb(String query, int max_lines_to_return, String base_url)
static List<String>	queryEmblDb(Accession acc, int max_lines_to_return)
static List<String>	queryEmblDbForRefSeqEntry(Accession id, int max_lines_to_return)
static List<String>	queryUniprot(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 String BASE_UNIPROT_URL

See Also:

Constant Field Values

DEFAULT_LINES_TO_RETURN

public static final int DEFAULT_LINES_TO_RETURN

See Also:

Constant Field Values

EMBL_DBS_REFSEQ_N

public static final String EMBL_DBS_REFSEQ_N

See Also:

Constant Field Values

EMBL_DBS_REFSEQ_P

public static final String EMBL_DBS_REFSEQ_P

See Also:

Constant Field Values

EMBL_GENBANK

public static final String EMBL_GENBANK

See Also:

Constant Field Values

EMBL_REFSEQ

public static final String EMBL_REFSEQ

See Also:

Constant Field Values

EMBL_EMBL

public static final String EMBL_EMBL

See Also:

Constant Field Values

Constructor Detail

SequenceDbWsTools

public SequenceDbWsTools()

Method Detail

getTaxonomiesFromCommonNameStrict

public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict(String cn,
                                                                      int max_taxonomies_return)
                                                               throws IOException

Throws:

IOException

getTaxonomiesFromId

public static List<UniProtTaxonomy> getTaxonomiesFromId(String id,
                                                        int max_taxonomies_return)
                                                 throws IOException

Throws:

IOException

getTaxonomiesFromScientificNameStrict

public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict(String sn,
                                                                          int max_taxonomies_return)
                                                                   throws IOException

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

Throws:

IOException

getTaxonomiesFromTaxonomyCode

public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode(String code,
                                                                  int max_taxonomies_return)
                                                           throws IOException

Throws:

IOException

obtainEmblEntry

public static SequenceDatabaseEntry obtainEmblEntry(Accession acc)
                                             throws IOException

Throws:

IOException

obtainEmblEntry

public static SequenceDatabaseEntry obtainEmblEntry(Accession acc,
                                                    int max_lines_to_return)
                                             throws IOException

Throws:

IOException

obtainEntry

public static SequenceDatabaseEntry obtainEntry(String acc_str)
                                         throws IOException

Throws:

IOException

obtainRefSeqEntryFromEmbl

public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc)
                                                       throws IOException

Throws:

IOException

obtainRefSeqEntryFromEmbl

public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc,
                                                              int max_lines_to_return)
                                                       throws IOException

Throws:

IOException

obtainSeqAccession

public static final Accession obtainSeqAccession(PhylogenyNode node)

obtainSeqInformation

public static final void obtainSeqInformation(boolean allow_to_set_taxonomic_data,
                                              int lines_to_return,
                                              SortedSet<String> not_found,
                                              PhylogenyNode node)
                                       throws IOException

Throws:

IOException

obtainSeqInformation

public static final void obtainSeqInformation(boolean allow_to_set_taxonomic_data,
                                              SortedSet<String> not_found,
                                              PhylogenyNode node)
                                       throws IOException

Throws:

IOException

obtainSeqInformation

public static final SortedSet<String> obtainSeqInformation(Phylogeny phy,
                                                           boolean ext_nodes_only,
                                                           boolean allow_to_set_taxonomic_data,
                                                           int lines_to_return)
                                                    throws IOException

Throws:

IOException

obtainSeqInformation

public static final void obtainSeqInformation(PhylogenyNode node)
                                       throws IOException

Throws:

IOException

obtainUniProtEntry

public static SequenceDatabaseEntry obtainUniProtEntry(String query)
                                                throws IOException

Throws:

IOException

obtainUniProtEntry

public static SequenceDatabaseEntry obtainUniProtEntry(String query,
                                                       int max_lines_to_return)
                                                throws IOException

Throws:

IOException

queryDb

public static List<String> queryDb(String query,
                                   int max_lines_to_return,
                                   String base_url)
                            throws IOException

Throws:

IOException

queryEmblDb

public static List<String> queryEmblDb(Accession acc,
                                       int max_lines_to_return)
                                throws IOException

Throws:

IOException

queryEmblDbForRefSeqEntry

public static List<String> queryEmblDbForRefSeqEntry(Accession id,
                                                     int max_lines_to_return)
                                              throws IOException

Throws:

IOException

queryUniprot

public static List<String> queryUniprot(String query,
                                        int max_lines_to_return)
                                 throws IOException

Throws:

IOException