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java.lang.Objectorg.biojava.bio.seq.db.GenbankSequenceDB
public class GenbankSequenceDB
This class contains functions accessing DNA sequences in Genbank format.
Field Summary | |
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protected boolean |
ExceptionFound
|
protected boolean |
IOExceptionFound
|
protected static java.lang.String |
urlBatchSequences
|
Constructor Summary | |
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GenbankSequenceDB()
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Method Summary | |
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boolean |
checkException()
|
boolean |
checkIOException()
|
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()
|
java.lang.String |
getName()
|
Sequence |
getSequence(java.lang.String id)
|
protected SequenceFormat |
getSequenceFormat()
|
SequenceDB |
getSequences(java.util.Set list)
Retrieve sequences from a Genbank |
SequenceDB |
getSequences(java.util.Set list,
SequenceDB database)
Retrieve sequences from a Genbank |
protected java.lang.String |
makeBatchRequest(java.net.URL url,
java.util.Set list)
Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected boolean IOExceptionFound
protected boolean ExceptionFound
protected static final java.lang.String urlBatchSequences
Constructor Detail |
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public GenbankSequenceDB()
Method Detail |
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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()
protected java.lang.String makeBatchRequest(java.net.URL url, java.util.Set list)
url
- URL of the requestlist
- List of sequence identifier
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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