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java.lang.Objectorg.biojava.bio.seq.db.GenbankSequenceDB
This class contains functions accessing DNA sequences in Genbank format.
Constructor Summary | |
GenbankSequenceDB()
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Method Summary | |
boolean |
checkException()
|
boolean |
checkIOException()
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protected java.net.URL |
getAddress(java.lang.String id)
Get the URL object for locating sequence object using eutils. |
protected java.net.URL |
getAddress(java.lang.String id,
java.lang.String format)
Get the URL object for locating sequence object using eutils. |
protected Alphabet |
getAlphabet()
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java.lang.String |
getName()
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Sequence |
getSequence(java.lang.String id)
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protected SequenceFormat |
getSequenceFormat()
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SequenceDB |
getSequences(java.util.Set list)
Retrieve sequences from a Genbank |
SequenceDB |
getSequences(java.util.Set list,
SequenceDB database)
Retrieve sequences from a Genbank |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public GenbankSequenceDB()
Method Detail |
protected SequenceFormat getSequenceFormat()
protected Alphabet getAlphabet()
protected java.net.URL getAddress(java.lang.String id) throws java.net.MalformedURLException
java.net.MalformedURLException
protected java.net.URL getAddress(java.lang.String id, java.lang.String format) throws java.net.MalformedURLException
java.net.MalformedURLException
public java.lang.String getName()
public Sequence getSequence(java.lang.String id) throws java.lang.Exception
java.lang.Exception
public boolean checkIOException()
public boolean checkException()
public SequenceDB getSequences(java.util.Set list) throws BioException
list
- List of NCBI sequence number (GI), accession, accession.version,
fasta or seqid.
BioException
public SequenceDB getSequences(java.util.Set list, SequenceDB database) throws BioException
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.
BioException
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