calhoun.analysis.crf.io
Class MultipleAlignmentInput

java.lang.Object
  calhoun.analysis.crf.io.InterleavedInputComponentBase
      calhoun.analysis.crf.io.MultipleAlignmentInput

All Implemented Interfaces:

InputComponentIO, InterleavedInputComponent, java.io.Serializable

public class MultipleAlignmentInput
extends InterleavedInputComponentBase

an input component that reads in multiple alignment sequences. Creates MultipleAlignmentInputSequence objects for each sequence. Can be used as a regular input or as part of an interleaved input file.

See Also:

Serialized Form

Constructor Summary

MultipleAlignmentInput()

Method Summary

boolean	read(java.io.BufferedReader r, java.util.Map<java.lang.String,InputSequence<?>> output) Read the contents of the sequence in from a reader.
void	write(java.io.Writer w, java.util.Map<java.lang.String,? extends InputSequence<?>> data) Output this sequence to the given writer.

Methods inherited from class calhoun.analysis.crf.io.InterleavedInputComponentBase

getComponentNames, getName, readInputSequences, setName, writeInputSequences

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleAlignmentInput

public MultipleAlignmentInput()

Method Detail

read

public boolean read(java.io.BufferedReader r,
                    java.util.Map<java.lang.String,InputSequence<?>> output)
             throws java.io.IOException

Description copied from interface: InterleavedInputComponent

Read the contents of the sequence in from a reader. Return false if the end of file was reached.

Parameters:

r - the buffered reader from which the next sequence should be read.

output - a map to which new components for this input sequence should be added.

Returns:

true if a sequence was read in and the map was populated. false if the end of the sequence was reached.

Throws:

java.io.IOException

write

public void write(java.io.Writer w,
                  java.util.Map<java.lang.String,? extends InputSequence<?>> data)
           throws java.io.IOException

Description copied from interface: InterleavedInputComponent

Output this sequence to the given writer.

Parameters:

w - a writer to which this sequence should be written

data - a map containing the data for the sequence to be written

Throws:

java.io.IOException