com.hfg.bio.seq.format

Class FASTA<T extends BioSequence>

java.lang.Object

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

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

All Implemented Interfaces:

ReadableSeqFormat<T>, WritableSeqFormat<T>

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

FASTA sequence format. Allowed sequence characters are upper-case letters, lower-case letters, '*' for stop codons, and '-' for gaps. Numbers and spaces will be silently stripped from the sequence and any other characters will cause a SeqFormatException.

Constructor Summary

Constructors

Constructor and Description
FASTA()
FASTA(BioSequenceFactory<T> inSeqFactory)

Method Summary

Modifier and Type	Method and Description
Integer	getLineLength()
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)
T	readRecord(BufferedReader inReader)
FASTA<T>	setLineLength(Integer inValue)
FASTA<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

Constructor Detail

FASTA

public FASTA()

FASTA

public FASTA(BioSequenceFactory<T> inSeqFactory)

Method Detail

getLogger

public static Logger getLogger()

setMaxExceptionsPerRecord

public FASTA<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.

setLineLength

public FASTA<T> setLineLength(Integer inValue)

getLineLength

public Integer getLineLength()

readRecord

public T readRecord(BufferedReader inReader)
             throws SeqIOException

Specified by:

readRecord in interface ReadableSeqFormat<T extends BioSequence>

Throws:

SeqIOException

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

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