de.jstacs.io
Class StringExtractor

java.lang.Object
  de.jstacs.io.AbstractStringExtractor
      de.jstacs.io.StringExtractor

All Implemented Interfaces:

Enumeration<String>

public class StringExtractor
extends AbstractStringExtractor

This class implements the reader that extracts Strings from either a File or a String. Internally the Strings are extracted and stored in an array when creating a new instance.

Author:

Jan Grau, Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.io.AbstractStringExtractor

annotation, FASTA, ignore, ignorePattern, USUALLY

Constructor Summary

StringExtractor(File file, int initSize)
A constructor that reads the lines from file.

StringExtractor(File file, int initSize, char ignore)
A constructor that reads the lines from file and ignores those starting with the comment character ignore.

StringExtractor(File file, int initSize, char ignore, String annotation)
A constructor that reads the lines from file, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.

StringExtractor(File file, int initSize, String annotation)
A constructor that reads the lines from file and sets the annotation of the source to annotation.

StringExtractor(String content, int initSize, char ignore, String annotation)
A constructor that reads the lines from a String content, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.

StringExtractor(String content, int initSize, String annotation)
A constructor that reads the lines from a String content and sets the annotation of the source to annotation.

Method Summary

String	getElement(int idx) Returns String number idx that has been extracted.
int	getNumberOfElements() Returns the number of Strings that have been read.
boolean	hasMoreElements()
String	nextElement()

Methods inherited from class de.jstacs.io.AbstractStringExtractor

getAnnotation, getCurrentSequenceAnnotations

Methods inherited from class java.lang.Object

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

Constructor Detail

StringExtractor

public StringExtractor(File file,
                       int initSize)
                throws IOException,
                       FileNotFoundException

A constructor that reads the lines from file.

Parameters:

file - the File to be read from

initSize - the initial number of lines that can be handled

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

See Also:

StringExtractor(File, int, char)

StringExtractor

public StringExtractor(File file,
                       int initSize,
                       char ignore)
                throws IOException,
                       FileNotFoundException

A constructor that reads the lines from file and ignores those starting with the comment character ignore.

Parameters:

file - the File to be read from

initSize - the initial number of lines that can be handled

ignore - the first character of lines that should be treated as comments

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

See Also:

StringExtractor(File, int, char, String)

StringExtractor

public StringExtractor(File file,
                       int initSize,
                       String annotation)
                throws IOException,
                       FileNotFoundException

A constructor that reads the lines from file and sets the annotation of the source to annotation.

Parameters:

file - the File to be read from

initSize - the initial number of lines that can be handled

annotation - the annotation for the source

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

See Also:

StringExtractor(File, int, char, String)

StringExtractor

public StringExtractor(File file,
                       int initSize,
                       char ignore,
                       String annotation)
                throws IOException,
                       FileNotFoundException

A constructor that reads the lines from file, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.

Parameters:

file - the File to be read from

initSize - the initial number of lines that can be handled

ignore - the first character of lines that should be treated as comments

annotation - the annotation for the source

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

StringExtractor

public StringExtractor(String content,
                       int initSize,
                       String annotation)

A constructor that reads the lines from a String content and sets the annotation of the source to annotation.

Parameters:

content - the complete String with all lines

initSize - the initial number of lines that can be handled

annotation - some annotation for the content

See Also:

StringExtractor(String, int, char, String)

StringExtractor

public StringExtractor(String content,
                       int initSize,
                       char ignore,
                       String annotation)

A constructor that reads the lines from a String content, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.

Parameters:

content - the complete String with all lines

initSize - the initial number of lines that can be handled

ignore - the first character of lines that should be treated as comments

annotation - some annotation for the content

Method Detail

nextElement

public String nextElement()

hasMoreElements

public boolean hasMoreElements()

getNumberOfElements

public int getNumberOfElements()

Returns the number of Strings that have been read.

Returns:

the number of Strings that have been read

getElement

public String getElement(int idx)

Returns String number idx that has been extracted.

Parameters:

idx - the number of the String

Returns:

String number idx