calhoun.analysis.crf.io
Class FastaInput

java.lang.Object
  calhoun.analysis.crf.io.FastaInput

All Implemented Interfaces:

InputComponentIO, java.io.Serializable

public class FastaInput
extends java.lang.Object
implements InputComponentIO

See Also:

Serialized Form

Constructor Summary

FastaInput()

Method Summary

java.util.List<java.lang.String>	getComponentNames() A list of names of the components of the InputSequence created by this reader.
java.lang.String	getHeader()
java.lang.Integer	getNumSeqCap()
java.lang.String	getSequence()
void	readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs) reads input sequences from this location.
void	setHeader(java.lang.String header)
void	setNumSeqCap(java.lang.Integer numSeqCap)
void	setSequence(java.lang.String sequence)
void	writeInputSequences(java.lang.String location, java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents) writes input sequences to this location.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaInput

public FastaInput()

Method Detail

getComponentNames

public java.util.List<java.lang.String> getComponentNames()

Description copied from interface: InputComponentIO

A list of names of the components of the InputSequence created by this reader.

Specified by:

getComponentNames in interface InputComponentIO

Returns:

a list of input sequence component names.

readInputSequences

public void readInputSequences(java.lang.String location,
                               java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs)
                        throws java.io.IOException

Description copied from interface: InputComponentIO

reads input sequences from this location. In most cases the location will be a file and this object will read in one or more components of the overall input from that file. Alist of inputs is returned. Each input consists of a set of key-value pairs, where the key is the name of the input component and the value is an (@link InputSequence) object. If this is not the first component to be loaded, this list may already contain entries for the input.

Specified by:

readInputSequences in interface InputComponentIO

Parameters:

location - the location of the data to read. Meaning of the location is implementation dependent, but will usually be a file name.

inputs - a list of input sequences. For each input sequence, a map is returned that maps component names to their associated InputSequence objects.

Throws:

java.io.IOException

writeInputSequences

public void writeInputSequences(java.lang.String location,
                                java.util.List<? extends java.util.Map<java.lang.String,? extends InputSequence<?>>> inputComponents)
                         throws java.io.IOException

Description copied from interface: InputComponentIO

writes input sequences to this location. InputComponentIO optionally can implement this function to provide the ability to write input data as well as read it. This is used by many of the data manipulation tools, such as those for subsetting and creating cross-validation sets.

Specified by:

writeInputSequences in interface InputComponentIO

Parameters:

location - the location of the data to write. Meaning of the location is implementation dependent, but will usually be a file name.

inputComponents - an iterator over input sequences. For each input sequence, a map is returned that maps component names to their associated InputSequence objects. All components of the input are passed, and this object is reponsible for knowing which components it should be writing.

Throws:

java.io.IOException

getHeader

public java.lang.String getHeader()

Returns:

Returns the header.

setHeader

public void setHeader(java.lang.String header)

Parameters:

header - The header to set.

getSequence

public java.lang.String getSequence()

Returns:

Returns the sequence.

setSequence

public void setSequence(java.lang.String sequence)

Parameters:

sequence - The sequence to set.

getNumSeqCap

public java.lang.Integer getNumSeqCap()

setNumSeqCap

public void setNumSeqCap(java.lang.Integer numSeqCap)