calhoun.analysis.crf.io
Class FastaAlignmentInput

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

All Implemented Interfaces:

InputComponentIO, java.io.Serializable

public class FastaAlignmentInput
extends java.lang.Object
implements InputComponentIO

See Also:

Serialized Form

Constructor Summary

FastaAlignmentInput()

Method Summary

java.lang.String	getComponent()
java.util.List<java.lang.String>	getComponentNames() A list of names of the components of the InputSequence created by this reader.
void	readInputSequences(java.lang.String location, java.util.List<java.util.Map<java.lang.String,InputSequence<?>>> inputs) reads input sequences from this location.
void	setComponent(java.lang.String header)
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

FastaAlignmentInput

public FastaAlignmentInput()

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

getComponent

public java.lang.String getComponent()

Returns:

Returns the header.

setComponent

public void setComponent(java.lang.String header)

Parameters:

header - The header to set.