calhoun.seq
Class FastaWriter

java.lang.Object
  calhoun.seq.FastaWriter

public class FastaWriter
extends java.lang.Object

Used for writing fasta files. Formats sequences to a specific line length. Allows multiple sequences to be to the same file.

Field Summary

static int

DEFAULT_LINE_LENGTH

Constructor Summary

FastaWriter(java.io.File file, boolean append)
Opens a fasta file for writing.

FastaWriter(java.io.File file, boolean append, int lineLength)
Opens a fasta file for writing.

FastaWriter(java.lang.String file, boolean append)
Opens a fasta file for writing.

FastaWriter(java.lang.String file, boolean append, int lineLength)
Opens a fasta file for writing.

FastaWriter(java.io.Writer w, int lineLength)

Method Summary

void	close() Closes the file.
java.lang.String	getFilename()
void	writeSeq(FastaSequence seq) Writes a sequence to the file, which may have been previously read from a different file.
void	writeSeq(java.lang.String header, java.lang.String content) Writes a sequence to the file.
void	writeSeq(java.lang.String header, java.lang.String string, java.lang.Integer start, java.lang.Integer stop) Writes a portion of the sequence to the file.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_LINE_LENGTH

public static final int DEFAULT_LINE_LENGTH

See Also:

Constant Field Values

Constructor Detail

FastaWriter

public FastaWriter(java.lang.String file,
                   boolean append)

Opens a fasta file for writing. Uses the default line length.

Parameters:

file - Filename of the file to open

append - true if sequences should be appended to this file, false if it should be replaced.

FastaWriter

public FastaWriter(java.lang.String file,
                   boolean append,
                   int lineLength)

Opens a fasta file for writing.

Parameters:

file - Filename of the file to open

append - true if sequences should be appended to this file, false if it should be replaced.

lineLength - Allows the length of a sequence line to be set.

FastaWriter

public FastaWriter(java.io.File file,
                   boolean append)

Opens a fasta file for writing. Uses the default line length

Parameters:

file - Filename of the file to open

append - true if sequences should be appended to this file, false if it should be replaced.

FastaWriter

public FastaWriter(java.io.File file,
                   boolean append,
                   int lineLength)

Opens a fasta file for writing.

Parameters:

file - Filename of the file to open

append - true if sequences should be appended to this file, false if it should be replaced.

lineLength - Allows the length of a sequence line to be set.

FastaWriter

public FastaWriter(java.io.Writer w,
                   int lineLength)

Method Detail

writeSeq

public void writeSeq(java.lang.String header,
                     java.lang.String content)

Writes a sequence to the file.

Parameters:

header - The fasta header for the sequence. Should not include '>'.

content - The actual sequence. It will be broken up into lines based on linelength as it is written out.

writeSeq

public void writeSeq(java.lang.String header,
                     java.lang.String string,
                     java.lang.Integer start,
                     java.lang.Integer stop)

Writes a portion of the sequence to the file.

Parameters:

header - The fasta header for the sequence. Should not include '>'.

content - The actual sequence. It will be broken up into lines based on linelength as it is written out.

start - 1-based index of the first base to write. If null, writing will start from the beginning of the sequence.

stop - 1-based index of the last base to write. If null, writing will continue until the end of the sequence.

writeSeq

public void writeSeq(FastaSequence seq)

Writes a sequence to the file, which may have been previously read from a different file.

close

public void close()

Closes the file. Once it is closed, no more sequences may be written. Open a new FastaWriter to append more sequences into the file.

getFilename

public java.lang.String getFilename()