org.dishevelled.bio.tools

Class FilterFasta

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterFasta

All Implemented Interfaces:

Callable<Integer>

public final class FilterFasta
extends AbstractFilter

Filter DNA or protein sequences in FASTA format.

Since:

1.3.3

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterFasta.Filter Filter.
static class	FilterFasta.LengthFilter Length filter.
static class	FilterFasta.ScriptFilter Script filter.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static String	DEFAULT_ALPHABET
(package private) static int	DEFAULT_LINE_WIDTH
(package private) static String	DESCRIPTION_LINE

Constructor Summary

Constructors

Constructor and Description
FilterFasta(List<FilterFasta.Filter> filters, File inputFastaFile, File outputFastaFile, int lineWidth) Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter> filters, File inputFastaFile, File outputFastaFile, String alphabet, int lineWidth) Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter> filters, Path inputFastaPath, File outputFastaFile, int lineWidth) Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter> filters, Path inputFastaPath, File outputFastaFile, String alphabet, int lineWidth) Filter DNA or protein sequences in FASTA format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) static String	describeSequence(org.biojava.bio.seq.Sequence sequence)
(package private) boolean	isProteinAlphabet()
static void	main(String[] args) Main.
(package private) static void	writeSequence(org.biojava.bio.seq.Sequence sequence, int lineWidth, PrintWriter writer)

Methods inherited from class org.dishevelled.bio.tools.AbstractFilter

createScriptEngine

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_ALPHABET

static final String DEFAULT_ALPHABET

See Also:

Constant Field Values

DEFAULT_LINE_WIDTH

static final int DEFAULT_LINE_WIDTH

See Also:

Constant Field Values

DESCRIPTION_LINE

static final String DESCRIPTION_LINE

See Also:

Constant Field Values

Constructor Detail

FilterFasta

public FilterFasta(List<FilterFasta.Filter> filters,
                   File inputFastaFile,
                   File outputFastaFile,
                   int lineWidth)

Filter DNA or protein sequences in FASTA format.

Parameters:

filters - list of filters, must not be null

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

FilterFasta

public FilterFasta(List<FilterFasta.Filter> filters,
                   Path inputFastaPath,
                   File outputFastaFile,
                   int lineWidth)

Filter DNA or protein sequences in FASTA format.

Parameters:

filters - list of filters, must not be null

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

Since:

2.1

FilterFasta

public FilterFasta(List<FilterFasta.Filter> filters,
                   File inputFastaFile,
                   File outputFastaFile,
                   String alphabet,
                   int lineWidth)

Filter DNA or protein sequences in FASTA format.

Parameters:

filters - list of filters, must not be null

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

alphabet - input FASTA file alphabet { dna, protein }, if any

lineWidth - line width

Since:

2.0

FilterFasta

public FilterFasta(List<FilterFasta.Filter> filters,
                   Path inputFastaPath,
                   File outputFastaFile,
                   String alphabet,
                   int lineWidth)

Filter DNA or protein sequences in FASTA format.

Parameters:

filters - list of filters, must not be null

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

alphabet - input FASTA file alphabet { dna, protein }, if any

lineWidth - line width

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

isProteinAlphabet

boolean isProteinAlphabet()

describeSequence

static String describeSequence(org.biojava.bio.seq.Sequence sequence)

writeSequence

static void writeSequence(org.biojava.bio.seq.Sequence sequence,
                          int lineWidth,
                          PrintWriter writer)
                   throws IOException

Throws:

IOException

main

public static void main(String[] args)

Main.

Parameters:

args - command line args