Package org.biojava.bio.seq.db
Class GenbankSequenceDB
java.lang.Object
org.biojava.bio.seq.db.GenbankSequenceDB
This class contains functions accessing DNA sequences in Genbank format.
- Author:
- Lei Lai, Matthew Pocock, Laurent Jourdren, Shuvankar Mukherjee, Mark Schreiber, Richard Holland
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected boolean
protected static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
boolean
protected URL
getAddress
(String id) Get the URL object for locating sequence object using eutils.protected URL
getAddress
(String id, String format) Get the URL object for locating sequence object using eutils.protected Alphabet
getName()
getSequence
(String id) protected SequenceFormat
getSequences
(Set list) Retrieve sequences from a GenbankgetSequences
(Set list, SequenceDB database) Retrieve sequences from a Genbankprotected String
makeBatchRequest
(URL url, Set list) Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
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Field Details
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IOExceptionFound
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ExceptionFound
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urlBatchSequences
- See Also:
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Constructor Details
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GenbankSequenceDB
public GenbankSequenceDB()
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Method Details
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getSequenceFormat
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getAlphabet
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getAddress
Get the URL object for locating sequence object using eutils. The default value of the return format of the sequence object is text.- Throws:
MalformedURLException
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getAddress
Get the URL object for locating sequence object using eutils. User could specify the return format of the sequence object.- Throws:
MalformedURLException
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getName
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getSequence
- Throws:
Exception
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checkIOException
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checkException
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makeBatchRequest
Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.- Parameters:
url
- URL of the requestlist
- List of sequence identifier- Returns:
- The Post request.
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getSequences
Retrieve sequences from a Genbank- Parameters:
list
- List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.- Returns:
- The database object (HashSequenceDB) with downloaded sequences.
- Throws:
BioException
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getSequences
Retrieve sequences from a Genbank- Parameters:
list
- List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.database
- Where to store sequences. if database is null, use an HashSequenceDB Objet.- Returns:
- The database object with downloaded sequences.
- Throws:
BioException
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