Class GenbankReader<S extends AbstractSequence<C>,C extends Compound>
- java.lang.Object
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- org.biojava.nbio.core.sequence.io.GenbankReader<S,C>
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public class GenbankReader<S extends AbstractSequence<C>,C extends Compound> extends Object
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
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Constructor Summary
Constructors Constructor Description GenbankReader(File file, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
boolean
isClosed()
static void
main(String[] args)
LinkedHashMap<String,S>
process()
The parsing is done in this method.
This method tries to process all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results inLinkedHashMap
.
You don't need to callclose()
after calling this method.LinkedHashMap<String,S>
process(int max)
This method tries to parse maximummax
records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.
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Constructor Detail
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GenbankReader
public GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads. InputStreams does not give you the name of the stream to access quickly via file seek. A seek in an inputstream is forced to read all the data so you don't gain anything.- Parameters:
is
-headerParser
-sequenceCreator
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GenbankReader
public GenbankReader(File file, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) throws FileNotFoundException
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.- Parameters:
file
-headerParser
-sequenceCreator
-- Throws:
FileNotFoundException
- if the file does not exist, is a directory rather than a regular file, or for some other reason cannot be opened for reading.SecurityException
- if a security manager exists and its checkRead method denies read access to the file.
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Method Detail
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isClosed
public boolean isClosed()
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process
public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundException
The parsing is done in this method.
This method tries to process all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results inLinkedHashMap
.
You don't need to callclose()
after calling this method.- Returns:
HashMap
containing all the parsed Genbank records present, starting current fileIndex onwards.- Throws:
IOException
CompoundNotFoundException
- See Also:
process(int)
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process
public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotFoundException
This method tries to parse maximummax
records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g. NCBI nr database), which can't fit into memory and will take long time before the first result is available.
N.B.- This method can't be called after calling its NO-ARGUMENT twin.
- remember to close the underlying resource when you are done.
- Parameters:
max
- maximum number of records to return,-1
for infinity.- Returns:
HashMap
containing maximummax
parsed Genbank records present, starting current fileIndex onwards.- Throws:
IOException
CompoundNotFoundException
- Since:
- 3.0.6
- See Also:
process()
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close
public void close()
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