statalign.io.input.plugins
Class FastaReader

java.lang.Object
  statalign.io.input.DataReader
      statalign.io.input.plugins.FastaReader

public class FastaReader
extends DataReader

Class to read files in FASTA format.

Author:

novak

Constructor Summary

FastaReader()

Method Summary

RawSequences	read(java.io.Reader reader) Reads the contents (aligned/non-aligned sequences) of the given data source in Fasta format.
java.util.List<java.lang.String>	supportedExtensions() DataReader plugins must override this to return a list of supported file extensions.

Methods inherited from class statalign.io.input.DataReader

read, read, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReader

public FastaReader()

Method Detail

supportedExtensions

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

Description copied from class: DataReader

DataReader plugins must override this to return a list of supported file extensions.

Specified by:

supportedExtensions in class DataReader

Returns:

a list of all lower case file extensions supported by this plugin

read

public RawSequences read(java.io.Reader reader)
                  throws java.io.IOException

Reads the contents (aligned/non-aligned sequences) of the given data source in Fasta format.

Specified by:

read in class DataReader

Parameters:

reader - Data source

Returns:

RawSequences representation of the contents

Throws:

java.io.IOException - if an I/O error occurs