Package pt.ist.phylolib.data.dataset

Class DatasetParser

java.lang.Object

pt.ist.phylolib.data.dataset.DatasetParser

All Implemented Interfaces:

IReader<Dataset>

Direct Known Subclasses:

FASTA, ML, SNP

public abstract class DatasetParser
extends Object
implements IReader<Dataset>

Responsible for parsing phylogenetic datasets from Strings.

Field Summary

Fields inherited from interface pt.ist.phylolib.data.IReader

FAILED, FINISHED, log, READ, STARTED

Constructor Summary

Constructors

Constructor	Description
DatasetParser()

Method Summary

Modifier and Type	Method	Description
protected void	init(Iterator<String> iterator)	Initializes the state of the processor by parsing the first lines of the dataset.
protected abstract Profile	parse(Iterator<String> iterator)	Parses one profile from the given Strings.
Dataset	parse(Stream<String> data, Options options)	Parses the input data into an object.

Methods inherited from class java.lang.Object

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

Constructor Details

DatasetParser

public DatasetParser()

Method Details

parse

public Dataset parse(Stream<String> data,
 Options options)

Description copied from interface: IReader

Parses the input data into an object.

Specified by:

parse in interface IReader<Dataset>

Parameters:

data - the input data to parse

Returns:

the object resultant from parsing the input data

init

protected void init(Iterator<String> iterator)

Initializes the state of the processor by parsing the first lines of the dataset.

By default, does not parse anything.

Parameters:

iterator - the iterator containing the lines of the dataset

parse

protected abstract Profile parse(Iterator<String> iterator)

Parses one profile from the given Strings.

Parameters:

iterator - the iterator containing the lines of the dataset

Returns:

a new profile resultant from parsing lines of the dataset