Package org.forester.ws.seqdb
Class SequenceDbWsTools
java.lang.Object
org.forester.ws.seqdb.SequenceDbWsTools
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic List<UniProtTaxonomy>getTaxonomiesFromCommonNameStrict(String cn, int max_taxonomies_return) static List<UniProtTaxonomy>getTaxonomiesFromId(String id, int max_taxonomies_return) static List<UniProtTaxonomy>getTaxonomiesFromScientificNameStrict(String sn, int max_taxonomies_return) Does not return "sub-types".static List<UniProtTaxonomy>getTaxonomiesFromTaxonomyCode(String code, int max_taxonomies_return) static SequenceDatabaseEntryobtainEmblEntry(Accession acc) static SequenceDatabaseEntryobtainEmblEntry(Accession acc, int max_lines_to_return) static SequenceDatabaseEntryobtainEntry(String acc_str) static SequenceDatabaseEntrystatic SequenceDatabaseEntryobtainRefSeqEntryFromEmbl(Accession acc, int max_lines_to_return) static final Accessionstatic final voidobtainSeqInformation(boolean allow_to_set_taxonomic_data, int lines_to_return, SortedSet<String> not_found, PhylogenyNode node) static final voidobtainSeqInformation(boolean allow_to_set_taxonomic_data, SortedSet<String> not_found, PhylogenyNode node) static final voidobtainSeqInformation(Phylogeny phy, boolean ext_nodes_only, boolean allow_to_set_taxonomic_data, int lines_to_return) static SequenceDatabaseEntryobtainUniProtEntry(String query) static SequenceDatabaseEntryobtainUniProtEntry(String query, int max_lines_to_return) queryEmblDb(Accession acc, int max_lines_to_return) queryEmblDbForRefSeqEntry(Accession id, int max_lines_to_return) queryUniprot(String query, int max_lines_to_return)
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Field Details
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BASE_UNIPROT_URL
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DEFAULT_LINES_TO_RETURN
public static final int DEFAULT_LINES_TO_RETURN- See Also:
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EMBL_DBS_REFSEQ_N
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EMBL_DBS_REFSEQ_P
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EMBL_GENBANK
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EMBL_REFSEQ
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EMBL_EMBL
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Constructor Details
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SequenceDbWsTools
public SequenceDbWsTools()
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Method Details
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getTaxonomiesFromCommonNameStrict
public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict(String cn, int max_taxonomies_return) throws IOException - Throws:
IOException
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getTaxonomiesFromId
public static List<UniProtTaxonomy> getTaxonomiesFromId(String id, int max_taxonomies_return) throws IOException - Throws:
IOException
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getTaxonomiesFromScientificNameStrict
public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict(String sn, int max_taxonomies_return) throws IOException Does not return "sub-types". For example, for "Mus musculus" only returns "Mus musculus" and not "Mus musculus", "Mus musculus bactrianus", ...- Throws:
IOException
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getTaxonomiesFromTaxonomyCode
public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode(String code, int max_taxonomies_return) throws IOException - Throws:
IOException
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obtainEmblEntry
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IOException
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obtainEmblEntry
public static SequenceDatabaseEntry obtainEmblEntry(Accession acc, int max_lines_to_return) throws IOException - Throws:
IOException
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obtainEntry
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IOException
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obtainRefSeqEntryFromEmbl
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IOException
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obtainRefSeqEntryFromEmbl
public static SequenceDatabaseEntry obtainRefSeqEntryFromEmbl(Accession acc, int max_lines_to_return) throws IOException - Throws:
IOException
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obtainSeqAccession
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obtainSeqInformation
public static final void obtainSeqInformation(boolean allow_to_set_taxonomic_data, int lines_to_return, SortedSet<String> not_found, PhylogenyNode node) throws IOException - Throws:
IOException
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obtainSeqInformation
public static final void obtainSeqInformation(boolean allow_to_set_taxonomic_data, SortedSet<String> not_found, PhylogenyNode node) throws IOException - Throws:
IOException
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obtainSeqInformation
public static final SortedSet<String> obtainSeqInformation(Phylogeny phy, boolean ext_nodes_only, boolean allow_to_set_taxonomic_data, int lines_to_return) throws IOException - Throws:
IOException
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obtainSeqInformation
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IOException
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obtainUniProtEntry
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IOException
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obtainUniProtEntry
public static SequenceDatabaseEntry obtainUniProtEntry(String query, int max_lines_to_return) throws IOException - Throws:
IOException
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queryDb
public static List<String> queryDb(String query, int max_lines_to_return, String base_url) throws IOException - Throws:
IOException
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queryEmblDb
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IOException
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queryEmblDbForRefSeqEntry
public static List<String> queryEmblDbForRefSeqEntry(Accession id, int max_lines_to_return) throws IOException - Throws:
IOException
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queryUniprot
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IOException
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