public final class SequenceDbWsTools
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
BASE_UNIPROT_URL |
|
static int |
DEFAULT_LINES_TO_RETURN |
|
static java.lang.String |
EMBL_DBS_REFSEQ_N |
|
static java.lang.String |
EMBL_DBS_REFSEQ_P |
|
static java.lang.String |
EMBL_EMBL |
|
static java.lang.String |
EMBL_GENBANK |
|
static java.lang.String |
EMBL_REFSEQ |
Constructor | Description |
---|---|
SequenceDbWsTools() |
Modifier and Type | Method | Description |
---|---|---|
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> |
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(Accession acc) |
|
static SequenceDatabaseEntry |
obtainEmblEntry(Accession acc,
int max_lines_to_return) |
|
static SequenceDatabaseEntry |
obtainEntry(java.lang.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,
java.util.SortedSet<java.lang.String> not_found,
PhylogenyNode node) |
|
static void |
obtainSeqInformation(boolean allow_to_set_taxonomic_data,
java.util.SortedSet<java.lang.String> not_found,
PhylogenyNode node) |
|
static void |
obtainSeqInformation(PhylogenyNode node) |
|
static java.util.SortedSet<java.lang.String> |
obtainSeqInformation(Phylogeny phy,
boolean ext_nodes_only,
boolean allow_to_set_taxonomic_data,
int lines_to_return) |
|
static SequenceDatabaseEntry |
obtainUniProtEntry(java.lang.String query) |
|
static SequenceDatabaseEntry |
obtainUniProtEntry(java.lang.String query,
int max_lines_to_return) |
|
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(Accession acc,
int max_lines_to_return) |
|
static java.util.List<java.lang.String> |
queryEmblDbForRefSeqEntry(Accession id,
int max_lines_to_return) |
|
static java.util.List<java.lang.String> |
queryUniprot(java.lang.String query,
int max_lines_to_return) |
public static final java.lang.String BASE_UNIPROT_URL
public static final int DEFAULT_LINES_TO_RETURN
public static final java.lang.String EMBL_DBS_REFSEQ_N
public static final java.lang.String EMBL_DBS_REFSEQ_P
public static final java.lang.String EMBL_GENBANK
public static final java.lang.String EMBL_REFSEQ
public static final java.lang.String EMBL_EMBL
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict(java.lang.String cn, int max_taxonomies_return) throws java.io.IOException
java.io.IOException
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromId(java.lang.String id, int max_taxonomies_return) throws java.io.IOException
java.io.IOException
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict(java.lang.String sn, int max_taxonomies_return) throws java.io.IOException
java.io.IOException
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode(java.lang.String code, int max_taxonomies_return) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainEmblEntry(Accession acc) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainEmblEntry(Accession acc, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainEntry(java.lang.String acc_str) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static final Accession obtainSeqAccession(PhylogenyNode node)
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
java.io.IOException
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
java.io.IOException
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
java.io.IOException
public static final void obtainSeqInformation(PhylogenyNode node) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query, int max_lines_to_return) throws java.io.IOException
java.io.IOException
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
java.io.IOException
public static java.util.List<java.lang.String> queryEmblDb(Accession acc, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static java.util.List<java.lang.String> queryEmblDbForRefSeqEntry(Accession id, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static java.util.List<java.lang.String> queryUniprot(java.lang.String query, int max_lines_to_return) throws java.io.IOException
java.io.IOException