de.jstacs.io

Class AbstractStringExtractor

java.lang.Object

de.jstacs.io.AbstractStringExtractor

All Implemented Interfaces:

Enumeration<String>

Direct Known Subclasses:

InfixStringExtractor, LimitedStringExtractor, SimpleStringExtractor, SparseStringExtractor, StringExtractor

public abstract class AbstractStringExtractor
extends Object
implements Enumeration<String>

This class implements the reader that extracts strings. The class ignores lines starting with a given character, since those lines are treated as comments. If the user does not specify this character, it is set to "#" internally. If the user specifies this character as ">", the file or String will be treated as in FastA-format, i.e. lines beginning with ">" will be stripped and the lines between two ">" (or until the end of the file) will be appended to form a new String.

Author:

Jan Grau, Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected String	annotation The annotation of the source.
static char	FASTA The comment character for FastA-formatted files is ">".
protected char	ignore The internal comment character.
protected Pattern	ignorePattern The pattern for ignoring comment lines.
static char	USUALLY The usual comment character is "#".

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractStringExtractor(char ignore) Creates a new AbstractStringExtractor with the specified character as start of each comment line.

Method Summary

Methods

Modifier and Type	Method and Description
String	getAnnotation() Returns the annotation of the source.
SequenceAnnotation[]	getCurrentSequenceAnnotations() Returns the SequenceAnnotation or null if no SequenceAnnotation is available.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Enumeration

hasMoreElements, nextElement

Field Detail

USUALLY

public static final char USUALLY

The usual comment character is "#". Lines beginning with this sign will be ignored.

See Also:

Constant Field Values

FASTA

public static final char FASTA

The comment character for FastA-formatted files is ">". If ">" is specified as the comment character, the file or String will be interpreted as in FastA format.

See Also:

Constant Field Values

annotation

protected String annotation

The annotation of the source.

ignorePattern

protected Pattern ignorePattern

The pattern for ignoring comment lines.

ignore

protected char ignore

The internal comment character.

Constructor Detail

AbstractStringExtractor

protected AbstractStringExtractor(char ignore)

Creates a new AbstractStringExtractor with the specified character as start of each comment line.

Parameters:

ignore - the comment character

See Also:

Pattern

Method Detail

getAnnotation

public final String getAnnotation()

Returns the annotation of the source.

Returns:

the annotation

getCurrentSequenceAnnotations

public SequenceAnnotation[] getCurrentSequenceAnnotations()

Returns the SequenceAnnotation or null if no SequenceAnnotation is available.

Returns:

the SequenceAnnotation or null if no SequenceAnnotation is available.