Field Detail

• BASE_UNIPROT_URL

  public static final java.lang.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 java.lang.String EMBL_DBS_REFSEQ_N

  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_GENBANK

  public static final java.lang.String EMBL_GENBANK

  See Also:

  Constant Field Values

• EMBL_REFSEQ

  public static final java.lang.String EMBL_REFSEQ

  See Also:

  Constant Field Values

• EMBL_EMBL

  public static final java.lang.String EMBL_EMBL

  See Also:

  Constant Field Values

Constructor Detail

• SequenceDbWsTools

  public SequenceDbWsTools()

Method Detail

• 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

• 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

• obtainEmblEntry

  public static SequenceDatabaseEntry obtainEmblEntry​(Accession acc)
                                               throws java.io.IOException

  Throws:

  java.io.IOException

• obtainEmblEntry

  public static SequenceDatabaseEntry obtainEmblEntry​(Accession acc,
                                                      int max_lines_to_return)
                                               throws java.io.IOException

  Throws:

  java.io.IOException

• obtainEntry

  public static SequenceDatabaseEntry obtainEntry​(java.lang.String acc_str)
                                           throws java.io.IOException

  Throws:

  java.io.IOException

• obtainRefSeqEntryFromEmbl

  public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl​(Accession acc)
                                                         throws java.io.IOException

  Throws:

  java.io.IOException

• obtainRefSeqEntryFromEmbl

  public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl​(Accession acc,
                                                                int max_lines_to_return)
                                                         throws java.io.IOException

  Throws:

  java.io.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,
                                                java.util.SortedSet<java.lang.String> not_found,
                                                PhylogenyNode node)
                                         throws java.io.IOException

  Throws:

  java.io.IOException

• obtainSeqInformation

  public static final void obtainSeqInformation​(boolean allow_to_set_taxonomic_data,
                                                java.util.SortedSet<java.lang.String> not_found,
                                                PhylogenyNode node)
                                         throws java.io.IOException

  Throws:

  java.io.IOException

• obtainSeqInformation

  public static final java.util.SortedSet<java.lang.String> obtainSeqInformation​(Phylogeny phy,
                                                                                 boolean ext_nodes_only,
                                                                                 boolean allow_to_set_taxonomic_data,
                                                                                 int lines_to_return)
                                                                          throws java.io.IOException

  Throws:

  java.io.IOException

• obtainSeqInformation

  public static final void obtainSeqInformation​(PhylogenyNode node)
                                         throws java.io.IOException

  Throws:

  java.io.IOException

• obtainUniProtEntry

  public static SequenceDatabaseEntry obtainUniProtEntry​(java.lang.String query)
                                                  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

• 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

• queryEmblDb

  public static java.util.List<java.lang.String> queryEmblDb​(Accession acc,
                                                             int max_lines_to_return)
                                                      throws java.io.IOException

  Throws:

  java.io.IOException

• queryEmblDbForRefSeqEntry

  public static java.util.List<java.lang.String> queryEmblDbForRefSeqEntry​(Accession 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