org.biojava.bio.program.tagvalue
Class RegexParser

java.lang.Object
  org.biojava.bio.program.tagvalue.RegexParser

All Implemented Interfaces:

TagValueParser

public class RegexParser
extends Object
implements TagValueParser

A TagValueParser that splits a line based upon a regular expression. There are configuration parameters analgous to those in LineSplitParser for configuring parsing details.

Since:

1.3

Author:

Matthew Pocock, Keith James (enabled empty line EOR)

Field Summary

Fields inherited from interface org.biojava.bio.program.tagvalue.TagValueParser

EMPTY_LINE_EOR

Constructor Summary

RegexParser()
Create a new RegexParser with all boolean values set to false.

Method Summary

boolean	getContinueOnEmptyTag() Report whether empty tags will be treated as continuations of the last non -empty tag.
String	getEndOfRecord() Get the explicit end-of-record string.
boolean	getMergeSameTag() Report whether empty tags will be treated as continuations of the last non -empty tag.
Pattern	getPattern() Get the Pattern currently used to split lines.
int	getTagGroup() Get the group number that matches the tag.
boolean	getTrimTag() See if trimming of tags is enabled.
boolean	getTrimValue() See if trimming of values is enabled.
int	getValueGroup() Get the group number that matches the value.
TagValue	parse(Object o)
void	setContinueOnEmptyTag(boolean continueOnEmptyTag) Decide whether to treat empty tags as continuations of the previous non -empty tag.
void	setEndOfRecord(String endOfRecord) Set the explicit end-of-record string.
void	setMergeSameTag(boolean mergeSameTag) Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.
void	setPattern(Pattern pattern) Set the Pattern used to split lines.
void	setTagGroup(int group) Set the group number that will match the tag.
void	setTrimTag(boolean trimTag) Enable trimming of the tag using String.trim().
void	setTrimValue(boolean trimValue) Enable trimming of the value using String.trim().
void	setValueGroup(int group) Set the group number that will match the value.

Methods inherited from class java.lang.Object

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

Constructor Detail

RegexParser

public RegexParser()

Create a new RegexParser with all boolean values set to false.

Method Detail

setPattern

public void setPattern(Pattern pattern)

Set the Pattern used to split lines.

Parameters:

pattern - the Pattern used to split lines

getPattern

public Pattern getPattern()

Get the Pattern currently used to split lines.

Returns:

the current Pattern

setTagGroup

public void setTagGroup(int group)

Set the group number that will match the tag.

Parameters:

group - the tag group number

getTagGroup

public int getTagGroup()

Get the group number that matches the tag.

Returns:

the tag group number

setValueGroup

public void setValueGroup(int group)

Set the group number that will match the value.

Parameters:

group - the value group number

getValueGroup

public int getValueGroup()

Get the group number that matches the value.

Returns:

the value group number

setEndOfRecord

public void setEndOfRecord(String endOfRecord)

Set the explicit end-of-record string.

Parameters:

endOfRecord - the new endOfRecord String

getEndOfRecord

public String getEndOfRecord()

Get the explicit end-of-record string.

Returns:

the current endOfRecord String

setTrimTag

public void setTrimTag(boolean trimTag)

Enable trimming of the tag using String.trim().

Parameters:

trimTag - true if tags should be trimmed, false otherwise

getTrimTag

public boolean getTrimTag()

See if trimming of tags is enabled.

Returns:

true if tag trimming is enabled, false otherwise

setTrimValue

public void setTrimValue(boolean trimValue)

Enable trimming of the value using String.trim().

Parameters:

trimValue - true if values should be trimmed, false otherwise

getTrimValue

public boolean getTrimValue()

See if trimming of values is enabled.

Returns:

true if value trimming is enabled, false otherwise

setContinueOnEmptyTag

public void setContinueOnEmptyTag(boolean continueOnEmptyTag)

Decide whether to treat empty tags as continuations of the previous non -empty tag.

Parameters:

continueOnEmptyTag - true if empty tags should be replaced, false otherwise

getContinueOnEmptyTag

public boolean getContinueOnEmptyTag()

Report whether empty tags will be treated as continuations of the last non -empty tag.

Returns:

true if empty tags will be replaced, false otherwise

setMergeSameTag

public void setMergeSameTag(boolean mergeSameTag)

Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.

Parameters:

mergeSameTag - true if tags will be merged, false otherwise

getMergeSameTag

public boolean getMergeSameTag()

Report whether empty tags will be treated as continuations of the last non -empty tag.

Returns:

true if tags will be merged, false otherwise

parse

public TagValue parse(Object o)
               throws ParserException

Specified by:

parse in interface TagValueParser

Throws:

ParserException