Package org.forester.ws.seqdb
Class SequenceDbWsTools
- java.lang.Object
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- org.forester.ws.seqdb.SequenceDbWsTools
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public final class SequenceDbWsTools extends java.lang.Object
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Field Summary
Fields 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
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Constructor Summary
Constructors Constructor Description SequenceDbWsTools()
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Method Summary
All Methods Static Methods Concrete Methods 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)
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Field Detail
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BASE_UNIPROT_URL
public static final java.lang.String BASE_UNIPROT_URL
- See Also:
- Constant Field Values
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DEFAULT_LINES_TO_RETURN
public static final int DEFAULT_LINES_TO_RETURN
- See Also:
- Constant Field Values
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EMBL_DBS_REFSEQ_N
public static final java.lang.String EMBL_DBS_REFSEQ_N
- See Also:
- Constant Field Values
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EMBL_DBS_REFSEQ_P
public static final java.lang.String EMBL_DBS_REFSEQ_P
- See Also:
- Constant Field Values
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EMBL_GENBANK
public static final java.lang.String EMBL_GENBANK
- See Also:
- Constant Field Values
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EMBL_REFSEQ
public static final java.lang.String EMBL_REFSEQ
- See Also:
- Constant Field Values
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EMBL_EMBL
public static final java.lang.String EMBL_EMBL
- See Also:
- Constant Field Values
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Method Detail
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getTaxonomiesFromCommonNameStrict
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict(java.lang.String cn, int max_taxonomies_return) throws java.io.IOException
- Throws:
java.io.IOException
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getTaxonomiesFromId
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromId(java.lang.String id, int max_taxonomies_return) throws java.io.IOException
- Throws:
java.io.IOException
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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
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getTaxonomiesFromTaxonomyCode
public static java.util.List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode(java.lang.String code, int max_taxonomies_return) throws java.io.IOException
- Throws:
java.io.IOException
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obtainEmblEntry
public static SequenceDatabaseEntry obtainEmblEntry(Accession acc) throws java.io.IOException
- Throws:
java.io.IOException
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obtainEmblEntry
public static SequenceDatabaseEntry obtainEmblEntry(Accession acc, int max_lines_to_return) throws java.io.IOException
- Throws:
java.io.IOException
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obtainEntry
public static SequenceDatabaseEntry obtainEntry(java.lang.String acc_str) throws java.io.IOException
- Throws:
java.io.IOException
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obtainRefSeqEntryFromEmbl
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc) throws java.io.IOException
- Throws:
java.io.IOException
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obtainRefSeqEntryFromEmbl
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc, int max_lines_to_return) throws java.io.IOException
- Throws:
java.io.IOException
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obtainSeqAccession
public static final Accession obtainSeqAccession(PhylogenyNode node)
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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
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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
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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
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obtainSeqInformation
public static final void obtainSeqInformation(PhylogenyNode node) throws java.io.IOException
- Throws:
java.io.IOException
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obtainUniProtEntry
public static SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query) throws java.io.IOException
- Throws:
java.io.IOException
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obtainUniProtEntry
public static SequenceDatabaseEntry obtainUniProtEntry(java.lang.String query, int max_lines_to_return) throws java.io.IOException
- Throws:
java.io.IOException
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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
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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
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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
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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
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