Class SequenceDbWsTools


  • public final class SequenceDbWsTools
    extends java.lang.Object
    • 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,
                                                            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
      • 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