broad.core.annotation.BasicGenomicAnnotationReader Class Reference

Inheritance diagram for broad.core.annotation.BasicGenomicAnnotationReader:

Collaboration diagram for broad.core.annotation.BasicGenomicAnnotationReader:

Public Member Functions
	BasicGenomicAnnotationReader ()
	BasicGenomicAnnotationReader (String annotationFile) throws FileNotFoundException
	BasicGenomicAnnotationReader (String annotationFile, String annotationType) throws FileNotFoundException
List< GenomicAnnotation >	getAnnotationList ()
List< GenomicAnnotation >	find (final String chr, final int startPos, final int endPos) throws IOException, ParseException
void	load () throws IOException, ParseException
void	plot (Graphics2D g2d, int start, int end, List< GenomicAnnotation > annots)
GenomicAnnotation	createAnnotation (GenomicAnnotation a)
int	parse (String file, GenomicAnnotationFilter< GenomicAnnotation > filter, AnnotationHandler handler) throws ParseException, IOException
int	parse (BufferedReader br, GenomicAnnotationFilter< GenomicAnnotation > filter, AnnotationHandler handler) throws ParseException, IOException

Static Public Member Functions
static List< GenomicAnnotation >	parseRawRegions (String[] rawRegions)
static List< GenomicAnnotation >	parseRawPointRegions (String[] rawRegions)

Static Public Attributes
static int	RIGHT_MARGIN = 50
static int	VERTICAL_SPACING = 100
static int	INTER_VERTICAL_SPACING = 40
static final Pattern	REG_PATTERN = Pattern.compile("(chr)(\\w{1,2})(:)([0-9]+)(-)([0-9]+)")
static final Pattern	POINT_PATTERN = Pattern.compile("(chr)(\\w{1,2})(:)([0-9]+)")

Protected Member Functions
void	setAnnotationList (List< GenomicAnnotation > list)

Protected Attributes
File	source

Constructor & Destructor Documentation

broad.core.annotation.BasicGenomicAnnotationReader.BasicGenomicAnnotationReader

(

)

broad.core.annotation.BasicGenomicAnnotationReader.BasicGenomicAnnotationReader

(

String

annotationFile

)

throws FileNotFoundException

broad.core.annotation.BasicGenomicAnnotationReader.BasicGenomicAnnotationReader	(	String	annotationFile,
		String	annotationType
	)		throws FileNotFoundException

Member Function Documentation

GenomicAnnotation broad.core.annotation.BasicGenomicAnnotationReader.createAnnotation

(

GenomicAnnotation

a

)

List<GenomicAnnotation> broad.core.annotation.BasicGenomicAnnotationReader.find	(	final String	chr,
		final int	startPos,
		final int	endPos
	)		throws IOException, ParseException

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List<GenomicAnnotation> broad.core.annotation.BasicGenomicAnnotationReader.getAnnotationList

(

)

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void broad.core.annotation.BasicGenomicAnnotationReader.load

(

)

throws IOException, ParseException

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int broad.core.annotation.BasicGenomicAnnotationReader.parse	(	String	file,
		GenomicAnnotationFilter< GenomicAnnotation >	filter,
		AnnotationHandler	handler
	)		throws ParseException, IOException

int broad.core.annotation.BasicGenomicAnnotationReader.parse	(	BufferedReader	br,
		GenomicAnnotationFilter< GenomicAnnotation >	filter,
		AnnotationHandler	handler
	)		throws ParseException, IOException

static List<GenomicAnnotation> broad.core.annotation.BasicGenomicAnnotationReader.parseRawPointRegions ( String[]  rawRegions )

static

static List<GenomicAnnotation> broad.core.annotation.BasicGenomicAnnotationReader.parseRawRegions ( String[]  rawRegions )

static

Parses an array of cannonical region descriptors of the form chrN:start-end

Parameters

rawRegions

Returns

void broad.core.annotation.BasicGenomicAnnotationReader.plot	(	Graphics2D	g2d,
		int	start,
		int	end,
		List< GenomicAnnotation >	annots
	)

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void broad.core.annotation.BasicGenomicAnnotationReader.setAnnotationList ( List< GenomicAnnotation >  list )

protected

Member Data Documentation

int broad.core.annotation.BasicGenomicAnnotationReader.INTER_VERTICAL_SPACING = 40

static

final Pattern broad.core.annotation.BasicGenomicAnnotationReader.POINT_PATTERN = Pattern.compile("(chr)(\\w{1,2})(:)([0-9]+)")

static

final Pattern broad.core.annotation.BasicGenomicAnnotationReader.REG_PATTERN = Pattern.compile("(chr)(\\w{1,2})(:)([0-9]+)(-)([0-9]+)")

static

int broad.core.annotation.BasicGenomicAnnotationReader.RIGHT_MARGIN = 50

static

File broad.core.annotation.BasicGenomicAnnotationReader.source

protected

int broad.core.annotation.BasicGenomicAnnotationReader.VERTICAL_SPACING = 100

static

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The documentation for this class was generated from the following file:

• java/broad/core/annotation/BasicGenomicAnnotationReader.java