com.hfg.bio.seq.format

Class GenBank<T extends BioSequence>

java.lang.Object

com.hfg.bio.seq.format.ReadableSeqFormatBase<T>

com.hfg.bio.seq.format.GenBank<T>

All Implemented Interfaces:

ReadableSeqFormat<T>, WritableSeqFormat<T>

public class GenBank<T extends BioSequence>
extends ReadableSeqFormatBase<T>
implements WritableSeqFormat<T>

GenBank sequence format.

See ftp://ftp.ncbi.nlm.nih.gov/genbank/gbrel.txt

See http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

Field Summary

Fields

Modifier and Type	Field and Description
static String	COMMENT_ATTR
static String	CONTIG_ATTR
static String	NCBI_GI_ATTR

Constructor Summary

Constructors

Constructor and Description
GenBank(BioSequenceFactory<T> inSeqFactory)

Method Summary

Modifier and Type	Method and Description
static Logger	getLogger()
boolean	hasJanusDelimiter() A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record.
boolean	isEndOfRecord(String inLine)
protected List<String>	parsePatentApplicants(String inApplicantString)
T	readRecord(BufferedReader inReader)
GenBank<T>	setMaxExceptionsPerRecord(int inValue) Specify the maximum number of Exceptions to tolerate per record.
String	write(Collection<T> inSeqs)
String	write(T inSeq)
void	write(T inSeq, OutputStream inStream)
void	write(T inSeq, Writer inWriter)

Methods inherited from class com.hfg.bio.seq.format.ReadableSeqFormatBase

getBioSequenceFactory, read, read, readRecord

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

COMMENT_ATTR

public static final String COMMENT_ATTR

See Also:

Constant Field Values

NCBI_GI_ATTR

public static final String NCBI_GI_ATTR

See Also:

Constant Field Values

CONTIG_ATTR

public static final String CONTIG_ATTR

See Also:

Constant Field Values

Constructor Detail

GenBank

public GenBank(BioSequenceFactory<T> inSeqFactory)

Method Detail

getLogger

public static Logger getLogger()

isEndOfRecord

public boolean isEndOfRecord(String inLine)

Specified by:

isEndOfRecord in interface ReadableSeqFormat<T extends BioSequence>

hasJanusDelimiter

public boolean hasJanusDelimiter()

Description copied from interface: ReadableSeqFormat

A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record. Will return true for formats like FASTA.

Specified by:

hasJanusDelimiter in interface ReadableSeqFormat<T extends BioSequence>

Returns:

whether or not this format's record delimiter is also part of the next record

setMaxExceptionsPerRecord

public GenBank<T> setMaxExceptionsPerRecord(int inValue)

Specify the maximum number of Exceptions to tolerate per record. Defaults to zero. This mechanism will only work with sequences objects that implement the BioSequencePlus interface. If a record produces less than the specified maximum number of Exceptions, the Exceptions can be retrieved via the getParseExceptions() method on the BioSequencePlus sequence object.

Parameters:

inValue - the maximum number of Exceptions to tolerate per record

Returns:

this format object to facilitate method chaining.

readRecord

public T readRecord(BufferedReader inReader)
             throws SeqIOException

Specified by:

readRecord in interface ReadableSeqFormat<T extends BioSequence>

Throws:

SeqIOException

write

public String write(Collection<T> inSeqs)
             throws SeqIOException

Throws:

SeqIOException

write

public String write(T inSeq)
             throws SeqIOException

Specified by:

write in interface WritableSeqFormat<T extends BioSequence>

Throws:

SeqIOException

write

public void write(T inSeq,
                  OutputStream inStream)
           throws SeqIOException

Throws:

SeqIOException

write

public void write(T inSeq,
                  Writer inWriter)
           throws SeqIOException

Specified by:

write in interface WritableSeqFormat<T extends BioSequence>

Throws:

SeqIOException

parsePatentApplicants

protected List<String> parsePatentApplicants(String inApplicantString)