Package ca.ualberta.stothard.cgview

Class CgviewFactory

java.lang.Object

org.xml.sax.helpers.DefaultHandler

ca.ualberta.stothard.cgview.CgviewFactory

All Implemented Interfaces:

CgviewConstants, ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class CgviewFactory
extends DefaultHandler
implements CgviewConstants

This class reads an XML document and creates a Cgview object. The various elements and attributes in the file are used to describe sequence features (position, type, name, color, label font, and opacity). Optional XML attributes can be included, to control global map characteristics, and to add legends, a title, and footnotes.

Author:

Paul Stothard

Field Summary

Fields inherited from interface ca.ualberta.stothard.cgview.CgviewConstants

BASES, BOUNDS_BUTTON, BOUNDS_FEATURE, BOUNDS_RULER, CENTISOMES, DECORATION_CLOCKWISE_ARROW, DECORATION_COUNTERCLOCKWISE_ARROW, DECORATION_HIDDEN, DECORATION_STANDARD, DIRECT_STRAND, INNER_LABELS_AUTO, INNER_LABELS_NO_SHOW, INNER_LABELS_SHOW, LABEL, LABEL_FORCE, LABEL_NONE, LABEL_ZOOMED, LEGEND_DRAW_ZOOMED, LEGEND_ITEM_ALIGN_CENTER, LEGEND_ITEM_ALIGN_LEFT, LEGEND_ITEM_ALIGN_RIGHT, LEGEND_LOWER_CENTER, LEGEND_LOWER_LEFT, LEGEND_LOWER_RIGHT, LEGEND_MIDDLE_CENTER, LEGEND_MIDDLE_LEFT, LEGEND_MIDDLE_LEFT_OF_CENTER, LEGEND_MIDDLE_RIGHT, LEGEND_MIDDLE_RIGHT_OF_CENTER, LEGEND_NO_DRAW_ZOOMED, LEGEND_UPPER_CENTER, LEGEND_UPPER_LEFT, LEGEND_UPPER_RIGHT, POSITIONS_AUTO, POSITIONS_NO_SHOW, POSITIONS_SHOW, REVERSE_STRAND, SWATCH_NO_SHOW, SWATCH_SHOW

Constructor Summary

Constructors

Constructor	Description
CgviewFactory()	Constructs a new CgviewFactory object.

Method Summary

Modifier and Type	Method	Description
void	addToCgviewFromFile(Cgview cgview, String filename)	Adds FeatureSlot, Feature, and FeatureRange objects described in an XML file to an existing Cgview object.
void	addToCgviewFromString(Cgview cgview, String xml)	Adds FeatureSlot, Feature, and FeatureRange objects described in a String of XML to an existing Cgview object.
void	characters(char[] ch, int start, int length)
Cgview	createCgviewFromFile(String filename)	Generates a Cgview object from an XML file.
Cgview	createCgviewFromString(String xml)	Generates a Cgview object from a String of XML content.
void	endDocument()
void	endElement(String uri, String name, String qName)
void	setDocumentLocator(Locator loc)
void	setLabelFontSize(int size)	Sets the font size of feature labels.
void	setLegendFontSize(int size)	Sets the font size of legends.
void	setRulerFontSize(int size)	Sets the font size of the sequence ruler.
void	startDocument()
void	startElement(String uri, String name, String qName, Attributes atts)

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.xml.sax.ContentHandler

declaration

Constructor Details

CgviewFactory

public CgviewFactory()

Constructs a new CgviewFactory object.

Method Details

createCgviewFromFile

public Cgview createCgviewFromFile(String filename)
                            throws SAXException,
IOException

Generates a Cgview object from an XML file.

Parameters:

filename - the XML file to read.

Returns:

the newly created Cgview object.

Throws:

SAXException

IOException

createCgviewFromString

public Cgview createCgviewFromString(String xml)
                              throws SAXException,
IOException

Generates a Cgview object from a String of XML content.

Parameters:

xml - the XML content to read.

Returns:

the newly created Cgview object.

Throws:

SAXException

IOException

addToCgviewFromFile

public void addToCgviewFromFile(Cgview cgview,
 String filename)
                         throws SAXException,
IOException

Adds FeatureSlot, Feature, and FeatureRange objects described in an XML file to an existing Cgview object. Any Legend and LegendItem objects in the XML are ignored, as are attributes in the cgview element.

Parameters:

cgview - the Cgview object to modify.

filename - the XML file to supply the additional map content.

Throws:

SAXException

IOException

addToCgviewFromString

public void addToCgviewFromString(Cgview cgview,
 String xml)
                           throws SAXException,
IOException

Adds FeatureSlot, Feature, and FeatureRange objects described in a String of XML to an existing Cgview object. Any Legend and LegendItem objects in the XML are ignored, as are attributes in the cgview element.

Parameters:

cgview - the Cgview object to modify.

xml - the XML content to read.

Throws:

SAXException

IOException

setLabelFontSize

public void setLabelFontSize(int size)

Sets the font size of feature labels. Use this method before calling createCgviewFromURL() or createCgviewFromFile().

Parameters:

size - the font size of feature labels.

setRulerFontSize

public void setRulerFontSize(int size)

Sets the font size of the sequence ruler. Use this method before calling createCgviewFromURL() or createCgviewFromFile().

Parameters:

size - the font size of the sequence ruler.

setLegendFontSize

public void setLegendFontSize(int size)

Sets the font size of legends. Use this method before calling createCgviewFromURL() or createCgviewFromFile().

Parameters:

size - the font size of legends.

setDocumentLocator

public void setDocumentLocator(Locator loc)

Specified by:

setDocumentLocator in interface ContentHandler

Overrides:

setDocumentLocator in class DefaultHandler

startDocument

public void startDocument()

Specified by:

startDocument in interface ContentHandler

Overrides:

startDocument in class DefaultHandler

endDocument

public void endDocument()

Specified by:

endDocument in interface ContentHandler

Overrides:

endDocument in class DefaultHandler

startElement

public void startElement(String uri,
 String name,
 String qName,
 Attributes atts)
                  throws SAXException

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class DefaultHandler

Throws:

SAXException

characters

public void characters(char[] ch,
 int start,
 int length)

Specified by:

characters in interface ContentHandler

Overrides:

characters in class DefaultHandler

endElement

public void endElement(String uri,
 String name,
 String qName)
                throws SAXException

Specified by:

endElement in interface ContentHandler

Overrides:

endElement in class DefaultHandler

Throws:

SAXException