public final class SequenceDbWsTools
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
SequenceDbWsTools.Db |
Modifier and Type | Field and Description |
---|---|
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 and Description |
---|
SequenceDbWsTools() |
Modifier and Type | Method and Description |
---|---|
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) |
public static final java.lang.String BASE_UNIPROT_URL
public static final java.lang.String BASE_EMBL_DB_URL
public static final java.lang.String EMBL_DBS_EMBL
public static final java.lang.String EMBL_DBS_REFSEQ_P
public static final java.lang.String EMBL_DBS_REFSEQ_N
public static java.lang.String parseUniProtAccessor(java.lang.String query)
query
- db
- public static java.util.List<UniProtTaxonomy> getTaxonomiesFromCommonName(java.lang.String cn, int max_taxonomies_return) throws java.io.IOException
java.io.IOException
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> getTaxonomiesFromScientificName(java.lang.String sn, 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 java.util.List<java.lang.String> queryEmblDb(Identifier 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
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 SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Identifier id, int max_lines_to_return) throws java.io.IOException
java.io.IOException
public static SequenceDatabaseEntry obtainEmblEntry(Identifier id, int max_lines_to_return) throws java.io.IOException
java.io.IOException