Package ca.ualberta.stothard.cgview

Class CgviewFactoryPtt

java.lang.Object

ca.ualberta.stothard.cgview.CgviewFactoryPtt

All Implemented Interfaces:

CgviewConstants

public class CgviewFactoryPtt
extends Object
implements CgviewConstants

This class reads a tab-delimited feature file and creates a Cgview object.

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
CgviewFactoryPtt()	Constructs a new CgviewFactoryPtt object.

Method Summary

Modifier and Type	Method	Description
void	addFeature(String strand, int slot, int start, int stop, float opacity, float thickness, float radius, String type, String label, String mouseover, String hyperlink)	Add a feature to this map.
Cgview	createCgviewFromFile(String filename)	Generates a Cgview object from an tab-delimited feature file.
Cgview	createCgviewFromURL(URL url)	Generates a Cgview object from an tab-delimited feature file.
void	setHeight(int height)	Sets the height of the map.
void	setLabelFontSize(int size)	Sets the font size of feature labels.
void	setLegendFontSize(int size)	Sets the font size of legends.
void	setMapItemSizeAdjustment(float adjustment)
void	setReadDimension(boolean readDimension)	Sets whether or not canvas dimension information should be read from the input file.
void	setRulerFontSize(int size)	Sets the font size of the sequence ruler.
void	setTickDensity(double density)	Sets the tick density.
void	setWidth(int width)	Sets the width of the map.

Methods inherited from class java.lang.Object

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

Constructor Details

CgviewFactoryPtt

public CgviewFactoryPtt()

Constructs a new CgviewFactoryPtt object.

Method Details

createCgviewFromFile

public Cgview createCgviewFromFile(String filename)
                            throws Exception,
IOException

Generates a Cgview object from an tab-delimited feature file.

Parameters:

filename - the file to read.

Returns:

the newly created Cgview object.

Throws:

Exception

IOException

createCgviewFromURL

public Cgview createCgviewFromURL(URL url)
                           throws Exception,
IOException

Generates a Cgview object from an tab-delimited feature file.

Parameters:

url - the URL of the tab-delimited file to read.

Returns:

the newly created Cgview object.

Throws:

Exception

IOException

addFeature

public void addFeature(String strand,
 int slot,
 int start,
 int stop,
 float opacity,
 float thickness,
 float radius,
 String type,
 String label,
 String mouseover,
 String hyperlink)
                throws Exception

Add a feature to this map. Note that the start of the feature should be a smaller number than the stop of the feature, regardless of the strand. The only case where start is larger than the stop is when the feature runs across the start/stop boundary, for example 6899-10 on a 7000bp plasmid.

Parameters:

strand - one of the following: forward, reverse.

slot - one of the following: 1, 2, 3, 4, 5, 6.

start - the start position of the feature. Must be between 1 and the length of the plasmid.

stop - the end position of the feature. Must be between 1 and the length of the plasmid.

opacity - the opacity of the feature.

thickness - the thickness of the feature.

radius - the radius of the feature.

type - one of the following: origin_of_replication, promoter, terminator, regulatory_sequence, unique_restriction_site, restriction_site, open_reading_frame, gene, predicted_gene, sequence_similarity, score, primer.

label - the label to show or empty String.

mouseover - the mouseover to show or empty String.

hyperlink - the label hyperlink or empty String.

Throws:

Exception

setReadDimension

public void setReadDimension(boolean readDimension)

Sets whether or not canvas dimension information should be read from the input file.

Parameters:

readDimension - whether or not to read the canvas dimension from the input file.

setWidth

public void setWidth(int width)

Sets the width of the map. Use this method before calling createCgviewFromURL() or createCgviewFromFile() to specify the default image width.

Parameters:

width - the width of the map.

setHeight

public void setHeight(int height)

Sets the height of the map. Use this method before calling createCgviewFromURL() or createCgviewFromFile() to specify the default image height.

Parameters:

height - the height of the map.

setMapItemSizeAdjustment

public void setMapItemSizeAdjustment(float adjustment)

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.

setTickDensity

public void setTickDensity(double density)

Sets the tick density.

Parameters:

density - a double between 0.0 and 1.0, with 1.0 being more dense.