Index (cgview 2.0.3-SNAPSHOT API)

A B C D E F G H I L M O P R S T U W
All Classes and Interfaces|All Packages|Constant Field Values

A

addBreak() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a br tag to this CgviewHTMLDocument.
addButton(String, String, String) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an image of a button to this CgviewHTMLDocument and links the button to another file.
addButtonNoLink(String, String) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an image of a button to this CgviewHTMLDocument.
addFeature(Feature) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Adds a Feature object to this FeatureSlot.
addFeature(String, int, int, int, float, float, float, String, String, String, String) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Add a feature to this map.
addFeature(String, int, int, int, float, float, float, String, String, String, String) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Add a feature to this map.
addFeature(String, String, int, int, int) - Method in class ca.ualberta.stothard.cgview.Plasmid: Add a feature to this map.
addFooter() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds body and html closing tags to this CgviewHTMLDocument.
addHeader(String, String, String, String, Boolean, Boolean) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds header information to this CgviewHTMLDocument, including an html opening tag.
addImage(String, int, int) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an image to this CgviewHTMLDocument.
addImage(String, int, int, String) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an image to this CgviewHTMLDocument.
addImageMap(String, int, int, ArrayList, Boolean) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an image with an image map to this CgviewHTMLDocument, to implement mouseovers and hyperlinks associated with Cgview Feature objects and FeatureRange objects.
addInnerLabel(Label) - Method in class ca.ualberta.stothard.cgview.Cgview: Adds an InnerLabel object to this cgview object.
addLegendItem(LegendItem) - Method in class ca.ualberta.stothard.cgview.Legend: Adds a LegendItem object to this Legend.
addLink(String, String) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a hyperlink to this CgviewHTMLDocument.
addOuterLabel(Label) - Method in class ca.ualberta.stothard.cgview.Cgview: Adds an outerLabel object to this cgview object.
addRange(FeatureRange) - Method in class ca.ualberta.stothard.cgview.Feature: Adds a FeatureRange to this Feature.
addSpace() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a non-breaking space to this CgviewHTMLDocument.
addSpanEnd() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a span closing tag to this CgviewHTMLDocument.
addSpanFileSizeStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a span opening tag with the 'fileSize' style to this CgviewHTMLDocument.
addSpanNoteStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a span opening tag with the 'note' style to this CgviewHTMLDocument.
addSpanValidStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a span opening tag with the 'validInfo' style to this CgviewHTMLDocument.
addSpanWarningStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds a span opening tag with the 'warning' style to this CgviewHTMLDocument.
addSVG(String, int, int) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds an SVG image to this CgviewHTMLDocument.
addTableColumnCenterStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds td opening tag with center alignment to this CgviewHTMLDocument.
addTableColumnEnd() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds td closing tag to this CgviewHTMLDocument.
addTableColumnLeftStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds td opening tag with left alignment to this CgviewHTMLDocument.
addTableColumnRightStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds td opening tag with right alignment to this CgviewHTMLDocument.
addTableColumnStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds td opening tag to this CgviewHTMLDocument.
addTableEnd() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds table and tbody closing tags to this CgviewHTMLDocument.
addTableRowEnd() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds tr closing tag to this CgviewHTMLDocument.
addTableRowStart() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds tr opening tag to this CgviewHTMLDocument.
addTableStart(int) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds table and tbody opening tags to this CgviewHTMLDocument.
addTableStart(int, int) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds table and tbody opening tags to this CgviewHTMLDocument.
addText(String) - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds text to this CgviewHTMLDocument.
addToCgviewFromFile(Cgview, String) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Adds FeatureSlot, Feature, and FeatureRange objects described in an XML file to an existing Cgview object.
addToCgviewFromString(Cgview, String) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Adds FeatureSlot, Feature, and FeatureRange objects described in a String of XML to an existing Cgview object.
addValidationInfo() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Adds text to this CgviewHTMLDocument stating that the document is valid XHTML 1.0 and valid CSS.
adjustZoom(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Checks the zoomMultiplier value and makes adjustments if necessary
allowedRadiansDelta - Variable in class ca.ualberta.stothard.cgview.Label
almostInZoomRangeOne(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the first zoom range, or if it is one base less than the start.
ascent - Variable in class ca.ualberta.stothard.cgview.Label

B

baseIsDrawable(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the visible region of the map.
BASES - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Cgview sequence ruler should be shown in base pair units.
BOUNDS_BUTTON - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the labelBounds encloses a button.
BOUNDS_FEATURE - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the labelBounds encloses a feature label.
BOUNDS_RULER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LabelBounds encloses a tick mark.

C

ca.ualberta.stothard.cgview - package ca.ualberta.stothard.cgview
CENTISOMES - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Cgview sequence ruler should be shown in centisome units.
cgview - Variable in class ca.ualberta.stothard.cgview.Label
Cgview - Class in ca.ualberta.stothard.cgview: Represents a circular map of a DNA sequence.
Cgview(int) - Constructor for class ca.ualberta.stothard.cgview.Cgview: Constructs a new Cgview object.
CgviewConstants - Interface in ca.ualberta.stothard.cgview: The CgviewConstants interface provides constants for use in the ca.ualberta.stothard.cgview package.
CgviewFactory - Class in ca.ualberta.stothard.cgview: This class reads an XML document and creates a Cgview object.
CgviewFactory() - Constructor for class ca.ualberta.stothard.cgview.CgviewFactory: Constructs a new CgviewFactory object.
CgviewFactoryPtt - Class in ca.ualberta.stothard.cgview: This class reads a tab-delimited feature file and creates a Cgview object.
CgviewFactoryPtt() - Constructor for class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Constructs a new CgviewFactoryPtt object.
CgviewFactoryTab - Class in ca.ualberta.stothard.cgview: This class reads a tab-delimited feature file and creates a Cgview object.
CgviewFactoryTab() - Constructor for class ca.ualberta.stothard.cgview.CgviewFactoryTab: Constructs a new CgviewFactoryTab object.
CgviewHTMLDocument - Class in ca.ualberta.stothard.cgview: This class contains methods for constructing HTML pages that contain Cgview maps.
CgviewHTMLDocument() - Constructor for class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Constructs a new CgviewHTMLDocument object.
CgviewIO - Class in ca.ualberta.stothard.cgview: This class contains static methods for converting Cgview objects to image files.
CgviewIO() - Constructor for class ca.ualberta.stothard.cgview.CgviewIO
characters(char[], int, int) - Method in class ca.ualberta.stothard.cgview.CgviewFactory
clashes(Label) - Method in class ca.ualberta.stothard.cgview.Label: Returns a boolean specifying whether or not this Label clashes with the supplied Label.
clashesWithAny() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Returns a boolean specifying whether or not this Label currently clashes with other Label objects in the Cgview object containing this Label.
clashesWithAny() - Method in class ca.ualberta.stothard.cgview.Label
clashesWithAny() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Returns a boolean specifying whether or not this Label clashes with other Label objects in the Cgview object containing this Label.
clashesWithAny(ArrayList) - Method in class ca.ualberta.stothard.cgview.Label: Returns a boolean specifying whether or not this Label clashes with any of the labels in the supplied ArrayList.
color - Variable in class ca.ualberta.stothard.cgview.Label
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.Feature.SortFeatureRangesByStart
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.FeatureSlot.SortFeaturesByStart
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByForceLabel
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadians
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadiansShift
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadius
compare(Object, Object) - Method in class ca.ualberta.stothard.cgview.SortSeriesImageByZoomCenter
createCgviewFromFile(String) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Generates a Cgview object from an XML file.
createCgviewFromFile(String) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Generates a Cgview object from an tab-delimited feature file.
createCgviewFromFile(String) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Generates a Cgview object from an tab-delimited feature file.
createCgviewFromString(String) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Generates a Cgview object from a String of XML content.
createCgviewFromURL(URL) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Generates a Cgview object from an tab-delimited feature file.
createCgviewFromURL(URL) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Generates a Cgview object from an tab-delimited feature file.

D

DECORATION_CLOCKWISE_ARROW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Feature or FeatureRange should be drawn as an arc with an arrowhead at the end.
DECORATION_COUNTERCLOCKWISE_ARROW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Feature or FeatureRange should be drawn as an arc with an arrowhead at the beginning.
DECORATION_HIDDEN - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Feature or FeatureRange should not be drawn.
DECORATION_STANDARD - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Feature or FeatureRange should be drawn as a simple arc.
descent - Variable in class ca.ualberta.stothard.cgview.Label
DIRECT_STRAND - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Represents the direct strand.
draw() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Draws the contents of this FeatureSlot.
draw() - Method in class ca.ualberta.stothard.cgview.Legend: Draws the contents of this Legend.
draw(Cgview, double, double, double) - Method in class ca.ualberta.stothard.cgview.LegendItem: Draws the contents of this LegendItem.
draw(Cgview, double, float, double) - Method in class ca.ualberta.stothard.cgview.Feature: Draws this Feature and creates labels if necessary.
draw(Cgview, double, float, double) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Draws this FeatureRange and creates a label if necessary.
draw(Graphics2D) - Method in class ca.ualberta.stothard.cgview.Cgview: Draws this Cgview map into the specified Graphics2D context
draw(Graphics2D, boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Draws this Cgview map into the specified Graphics2D context
drawLabelLine() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Draws a line joining the feature to this Label.
drawLabelLine() - Method in class ca.ualberta.stothard.cgview.Label
drawLabelLine() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Draws a line joining the feature to this Label.
drawLabelText() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Draws the text portion of this Label.
drawLabelText() - Method in class ca.ualberta.stothard.cgview.Label
drawLabelText() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Draws the text portion of this Label.
drawLine(double, double, double, double) - Method in class ca.ualberta.stothard.cgview.Label: Draws a line between two points described by radius and radian values.
drawLine(double, double, double, double, Area) - Method in class ca.ualberta.stothard.cgview.Label: Draws a line between two points described by radius and radian values.
drawZoomed(Graphics2D, double, int) - Method in class ca.ualberta.stothard.cgview.Cgview: Draws this Cgview map into the specified Graphics2D context.
drawZoomed(Graphics2D, double, int, boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Draws this Cgview map into the specified Graphics2D context.

E

endDocument() - Method in class ca.ualberta.stothard.cgview.CgviewFactory
endElement(String, String, String) - Method in class ca.ualberta.stothard.cgview.CgviewFactory
equals(Object) - Method in class ca.ualberta.stothard.cgview.Feature.SortFeatureRangesByStart
equals(Object) - Method in class ca.ualberta.stothard.cgview.FeatureSlot.SortFeaturesByStart
equals(Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByForceLabel
equals(Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadians
equals(Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadiansShift
equals(Object) - Method in class ca.ualberta.stothard.cgview.SortLabelsByRadius
equals(Object) - Method in class ca.ualberta.stothard.cgview.SortSeriesImageByZoomCenter
extendedLineEndRadius - Variable in class ca.ualberta.stothard.cgview.Label
extendedLineStartRadius - Variable in class ca.ualberta.stothard.cgview.Label
extendedRadius - Variable in class ca.ualberta.stothard.cgview.Label
extendRadius() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Attempts to move this Label by increasing its radius value.
extendRadius() - Method in class ca.ualberta.stothard.cgview.Label
extendRadius() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Attempts to move this Label by extending its radius value.

F

Feature - Class in ca.ualberta.stothard.cgview: This class represents a sequence feature.
Feature() - Constructor for class ca.ualberta.stothard.cgview.Feature: Constructs a new Feature object.
Feature(boolean) - Constructor for class ca.ualberta.stothard.cgview.Feature: Constructs a new Feature object.
Feature(FeatureSlot) - Constructor for class ca.ualberta.stothard.cgview.Feature: Constructs a new Feature object.
Feature(FeatureSlot, String) - Constructor for class ca.ualberta.stothard.cgview.Feature: Constructs a new Feature object.
Feature.SortFeatureRangesByStart - Class in ca.ualberta.stothard.cgview
FeatureRange - Class in ca.ualberta.stothard.cgview: This class is used to assign sequence features, which are described using the Feature object, to specific bases of a DNA sequence.
FeatureRange(Feature, int, int) - Constructor for class ca.ualberta.stothard.cgview.FeatureRange: Constructs a new FeatureRange object.
FeatureSlot - Class in ca.ualberta.stothard.cgview: Represents a slot of space on the Cgview map.
FeatureSlot(int) - Constructor for class ca.ualberta.stothard.cgview.FeatureSlot: Constructs a new FeatureSlot object.
FeatureSlot(int, boolean) - Constructor for class ca.ualberta.stothard.cgview.FeatureSlot: Constructs a new FeatureSlot object.
FeatureSlot(Cgview, int) - Constructor for class ca.ualberta.stothard.cgview.FeatureSlot: Constructs a new FeatureSlot object.
FeatureSlot.SortFeaturesByStart - Class in ca.ualberta.stothard.cgview
FileMover - Class in ca.ualberta.stothard.cgview: This class contains methods for moving jar resources to the output directory.
FileMover() - Constructor for class ca.ualberta.stothard.cgview.FileMover
fitsInBackground() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Returns a boolean specifying whether or not this Label can fit inside of the map canvas.
fitsInBackground() - Method in class ca.ualberta.stothard.cgview.Label
fitsInBackground() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Returns a boolean specifying whether or not this Label can completely fit inside of the map canvas.
fixedInPlace - Variable in class ca.ualberta.stothard.cgview.Label
font - Variable in class ca.ualberta.stothard.cgview.Label
forceLabel - Variable in class ca.ualberta.stothard.cgview.Label

G

getAlignment() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the alignment of legendItems in this Legend.
getAllowLabelClash() - Method in class ca.ualberta.stothard.cgview.Legend: Returns whether or not feature labels are allowed to clash with this Legend.
getArrowheadLength() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the length of the arrowheads used for features that are drawn as arrows.
getBackboneColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the circle that represents the DNA sequence.
getBackboneRadius() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the radius of the circle that represents the DNA sequence.
getBackboneThickness() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the thickness of the line used to draw the circle that represents the DNA sequence.
getBackgroundColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the background color of the map.
getBackgroundColor() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the color of the background of this Legend when drawn.
getBackgroundOpacity() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the opacity of the background of this Legend when drawn.
getBackgroundRectangle() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a rectangle corresponding to the visible portion of the map.
getBase() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns the sequence position closest to this LabelBounds.
getBasesPerMinFeature(double) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns the minimum feature length in bases that can be drawn accurately in this FeatureSlot, at the given zoom value.
getBorderColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the map border.
getBounds() - Method in class ca.ualberta.stothard.cgview.Label: Returns a rectangle that represents the bounds of this Label.
getBounds() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns a rectangle that represents the bounds of this LabelBounds.
getBounds() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the bounds of this Legend.
getCenter() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a Point2D specifying the center of this cgview.
getClockwiseFilePrefix(ArrayList) - Method in class ca.ualberta.stothard.cgview.SeriesImage: Determines which SeriesImage is adjacent to this SeriesImage in the clockwise direction.
getColor() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the default color that will be assigned to FeatureRange objects added to this Feature.
getColor() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the color of this FeatureRange when drawn.
getContents() - Method in class ca.ualberta.stothard.cgview.CgviewHTMLDocument: Returns the contents of this CgviewHTMLDocument.
getCounterclockwiseFilePrefix(ArrayList) - Method in class ca.ualberta.stothard.cgview.SeriesImage: Determines which SeriesImage is adjacent to this SeriesImage in the counterclockwise direction.
getDecoration() - Method in class ca.ualberta.stothard.cgview.Feature: Returns an integer indicating what type of decoration will be added to this Feature when drawn.
getDecoration() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns an integer indicating what type of decoration will be added to this FeatureRange when drawn.
getDegrees(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a degrees representation of the given base.
getDesiredNumberOfTicks() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the approximate number of long tick marks to be drawn in the sequence ruler.
getDesiredZoom() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the zoom value stored using the setDesiredZoom() method.
getDesiredZoomCenter() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the zoomCenter value stored using the setDesiredZoomCenter() method.
getDrawEntirePlasmid() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the entire plasmid should be drawn.
getDrawLegends() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns boolean indicating whether or not legends should be drawn on this map.
getDrawSwatch() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns whether or not a color swatch should be drawn for this LegendItem.
getDrawTickMarks() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if tick marks are to be drawn.
getDrawWhenZoomed() - Method in class ca.ualberta.stothard.cgview.Legend: Returns whether or not this Legend is drawn when a zoomed Cgview map is generated.
getExtendedLineEndRadius() - Method in class ca.ualberta.stothard.cgview.Label: Returns the radius of the outermost point in the second line (the extended line) extending from the feature to this Label.
getFeatureSlots() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an arrayList containing the FeatureSlot objects associated with this Cgview.
getFeatureSlotSpacing() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the amount of blank space placed between the concentric feature rings (FeatureSlot objects).
getFeatureThickness() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the default thickness of the line used to represent sequence features.
getFeatureThickness() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns the thickness of the arc used to represent sequence features in this FeatureSlot.
getFirstInnerFeatureRadius() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the radius of the first (nearest to the backbone) reverse strand FeatureSlot in this Cgview.
getFirstOuterFeatureRadius() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the radius of the first (nearest to the backbone) direct strand FeatureSlot in this Cgview.
getFont() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the font used for labels generated for this Feature.
getFont() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the font used for the label generated for this FeatureRange.
getFont() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the font used for text in this Legend.
getFont() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the font used for this LegendItem.
getFontColor() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the default color that will be used for the text in this Legend.
getFontColor() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the color that will be used for the text in this LegendItem.
getForceLabel() - Method in class ca.ualberta.stothard.cgview.Feature: Returns a boolean specifying whether or not labels created for this Feature should be drawn even if they cannot be placed such that they do not clash with other labels.
getForceLabel() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns a boolean specifying whether or not labels created for this FeatureRange should be drawn even if they cannot be placed such that they do not clash with other labels.
getForceLabel() - Method in class ca.ualberta.stothard.cgview.Label: Returns a boolean specifying whether or not this label should be drawn even if it cannot be placed such that it does not clash with other labels.
getGiveFeaturePositions() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the feature position labelling behaviour of this Cgview.
getGlobalLabel() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not feature labels should be shown on this map.
getGlobalLabelColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of all labels, or null if the labels are colored based on the feature they represent.
getGraphics() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the Graphics2D object for this Cgview.
getHeight() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the height of the map.
getHeight(Cgview) - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the height of the text in this LegendItem.
getHighlightOpacity() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the opacity of the highlighting added to map items.
getHyperlink() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the hyperlink to be associated with this Feature.
getHyperlink() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the hyperlink to be associated with this Feature.
getHyperlink() - Method in class ca.ualberta.stothard.cgview.Label: Returns the hyperlink to be associated with this Label.
getHyperlink() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns the hyperlink associated with this LabelBounds.
getImageHeight() - Method in class ca.ualberta.stothard.cgview.Plasmid: Returns the height of this map.
getImageWidth() - Method in class ca.ualberta.stothard.cgview.Plasmid: Returns the width of this map.
getInnerLabels() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an arrayList of InnerLabel objects associated with this Cgview.
getIsLinear() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not the map should be drawn with a broken backbone line to indicate a linear molecule.
getKeepLastLabels() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the existing labels (those generated by the previous draw operation) are to be drawn.
getLabel() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the label text for this Feature.
getLabel() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the label text for this FeatureRange.
getLabel() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns the text that gave rise to this LabelBounds.
getLabel() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the text to be used for this LegendItem.
getLabelBounds() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an arrayList of LabelBounds objects associated with this Cgview.
getLabelFont() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the font of the feature labels.
getLabelLineLength() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the length of the line that extends from the feature to the feature label.
getLabelLineThickness() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the thickness of the line that extends from features to feature labels.
getLabelShuffle() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if labels are to be randomly shuffled before removing excess labels.
getLabelsToKeep() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the maximum number of labels to attempt to arrange for display.
getLabelText() - Method in class ca.ualberta.stothard.cgview.Label: Returns the text of this Label.
getLastInnerFeatureRadius() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the radius of the last (furthest from the backbone) reverse strand FeatureSlot in this Cgview.
getLastOuterFeatureRadius() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the radius of the last (furthest from the backbone) direct strand FeatureSlot in this Cgview.
getLegendFont() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the default font used for text in Legend objects added to this Cgview.
getLegends() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an arrayList of the Legend objects in this Cgview.
getLegendTextColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the default color of the text used for Legend objects.
getLengthRectangle() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a rectangle that covers the length portion of the map title.
getLinearBreakText() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the text to draw at the sequence start/end boundary if this is a linear molecule.
getLineAsArea(double, double, double, double) - Method in class ca.ualberta.stothard.cgview.Label: Returns an Area representing a line between two points described by radius and radian values.
getLineEndRadians() - Method in class ca.ualberta.stothard.cgview.Label: Returns the radians of the outermost point in the line extending from the feature to this Label.
getLineEndRadius() - Method in class ca.ualberta.stothard.cgview.Label: Returns the radius of the outermost point in the line extending from the feature to this Label.
getLineStart() - Method in class ca.ualberta.stothard.cgview.Label: Returns the starting point of the line drawn to this Label.
getLineStartRadians() - Method in class ca.ualberta.stothard.cgview.Label: Returns the radians of the innermost point in the line extending from the feature to this Label.
getLineStartRadius() - Method in class ca.ualberta.stothard.cgview.Label: Returns the radius of the innermost point in the line extending from the feature to this Label.
getLongTickColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the tick marks in the sequence ruler.
getMinimumFeatureLength() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the minimum feature length to use when drawing sequence features.
getMinimumFeatureLength() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns the minimum feature length to use when drawing sequence features.
getMouseover() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the mouseover to be associated with this Feature.
getMouseover() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the mouseover to be associated with this FeatureRange.
getMouseover() - Method in class ca.ualberta.stothard.cgview.Label: Returns the mouseover to be associated with this Label.
getMouseover() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns the mouseover associated with this LabelBounds.
getMoveInnerLabelsToOuter() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not inner labels should be moved from the inside of the backbone circle to the outside of the backbone circle when there is insufficient room on the inside of the backbone circle.
getOpacity() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the opacity of this Feature when drawn.
getOpacity() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the opacity of this FeatureRange when drawn.
getOrigin() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the number of degrees that the origin is to be moved in the counterclockwise direction from the three o'clock position.
getOuterLabels() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an arrayList of OuterLabel objects associated with this Cgview.
getPosition() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the position of this Legend relative to the Cgview map canvas.
getProportionOfThickness() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the thickness of this Feature when drawn, as a proportion of the thickness of the FeatureSlot containing this Feature.
getProportionOfThickness() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the thickness of this FeatureRange when drawn, as a proportion of the thickness of the FeatureSlot containing this FeatureRange.
getRadians(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a radians representation of the given base.
getRadians(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a radians representation of the given base.
getRadiansShiftConstant() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a constant that controls label movement along the map backbone.
getRadiusAdjustment() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the position of this Feature relative to the FeatureSlot object that contains it.
getRadiusAdjustment() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the position of this FeatureRange relative to the FeatureSlot object that contains it.
getRadiusShiftAmount() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the distance moved by the labels each time they are moved away from the map backbone during label repositioning.
getRanges() - Method in class ca.ualberta.stothard.cgview.Feature: Returns an ArrayList of FeatureRange objects contained by this Feature.
getRulerFont() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the font of the number labels in the sequence ruler.
getRulerFontColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the text used for the sequence ruler.
getRulerTextPadding() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the spacing between the ruler number labels and the tick marks.
getRulerUnits() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the units to be used for the sequence ruler.
getSequenceLength() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the length of the sequence to be mapped.
getShadingProportion() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the proportion of the width of the features to be redrawn for highlighting and shadowing purposes.
getShadowOpacity() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the opacity of the shadowing added to map items.
getShiftSmallFeatures() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the alignment behavior of small features when they are drawn.
getShortTickColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the short tick marks in the sequence ruler.
getShortTickThickness() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the thickness of the short tick marks in the sequence ruler.
getShowBorder() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not a border should be drawn around the map.
getShowLabel() - Method in class ca.ualberta.stothard.cgview.Feature: Returns whether or not a label should be generated for this Feature when drawn.
getShowLabel() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns whether or not a label should be generated for this FeatureRange when drawn.
getShowShading() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not items on the map should be drawn with shading.
getShowShading() - Method in class ca.ualberta.stothard.cgview.Feature: Returns whether or not this Feature should be drawn with shading.
getShowShading() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns whether or not this FeatureRange should be drawn with shading.
getShowShading() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns whether or not items in this FeatureSlot should be drawn with shading.
getShowWarning() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns whether or not the message set using setWarningText() should be drawn at the bottom of the figure.
getSmallestDimension() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the width or the height of the map, whichever is smaller.
getStart() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the smallest start value from the featureRanges in this Feature, or -1 if there are no featureRanges.
getStart() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the position of the first base in this FeatureRange.
getStop() - Method in class ca.ualberta.stothard.cgview.FeatureRange: Returns the position of the last base in this FeatureRange.
getStrand() - Method in class ca.ualberta.stothard.cgview.Feature: Returns the strand of this Feature, which is determined by the FeatureSlot that contains this Feature.
getStrand() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns the strand of this FeatureSlot.
getSwatchColor() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the swatch color that will be used for this LegendItem.
getSwatchHeight() - Method in class ca.ualberta.stothard.cgview.Legend: Returns the height that is suitable for any LegendItem swatches drawn in this Legend.
getSwatchOpacity() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the opacity of the swatch drawn for this LegendItem.
getTextAlignment() - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the alignment of this legendItem, relative to the Legend object that contains it.
getTickDensity() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the tick density, with 0 being the minimum, 1 being the maximum.
getTickLength() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the length of the tick marks in the sequence ruler.
getTickThickness() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the thickness of the tick marks in the sequence ruler.
getTitle() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the title of the map.
getTitleFont() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the font of the map title.
getTitleFontColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the text used for the sequence title.
getTitleRectangle() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a rectangle that covers the map title.
getType() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns the type of this LabelBounds.
getUse() - Method in class ca.ualberta.stothard.cgview.LabelBounds: Returns whether or not this LabelBounds should be used.
getUseColoredLabelBackgrounds() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if labels are to be drawn with a colored background.
getUseInnerLabels() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the inner label behaviour of this Cgview.
getWarningFont() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the font used for any warnings that appear at the bottom of the map.
getWarningFontColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the text used for warnings that appear at the bottom of the figure.
getWarningText() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns a warning message to appear at the bottom of the map.
getWidestLegendItem(double) - Method in class ca.ualberta.stothard.cgview.Legend: Returns the width of the widest LegendItem in this Legend.
getWidth() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the width of the map.
getWidth(Cgview, double) - Method in class ca.ualberta.stothard.cgview.LegendItem: Returns the width of the text in this LegendItem.
getZeroTickColor() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the color of the tick mark drawn at the boundary between the end and beginning of the sequence.
getZoomCenter() - Method in class ca.ualberta.stothard.cgview.SeriesImage: Returns the zoom center value of this SeriesImage.
getZoomInFilePrefix(ArrayList, int) - Method in class ca.ualberta.stothard.cgview.SeriesImage: Examines the ArrayList of LabelBounds objects of type BOUNDS_RULER and determines which is the middle one.
getZoomMax() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns an estimate of the maximum suitable zoom value for this map.
getZoomMultiplier() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the zoom multiplier for the map, as set using the drawZoomed() method.
getZoomOutFilePrefix(ArrayList, int) - Method in class ca.ualberta.stothard.cgview.SeriesImage: Determines which SeriesImage should be linked to this SeriesImage using a zoom out button.
getZoomRangeOneStart() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the number of the first base inside the first zoom range.
getZoomRangeOneStop() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the number of the last base inside the first zoom range.
getZoomRangeTwoStart() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the number of the first base inside the second zoom range.
getZoomRangeTwoStop() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the number of the last base inside the second zoom range.
getZoomShift() - Method in class ca.ualberta.stothard.cgview.Cgview: Returns the minimum zoom value necessary for labels to be drawn below the backbone.
getZoomValue() - Method in class ca.ualberta.stothard.cgview.SeriesImage: Returns the zoom value of this SeriesImage.

H

hyperlink - Variable in class ca.ualberta.stothard.cgview.Label

I

INNER_LABELS_AUTO - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels should be shown be drawn on the inside of the backbone if they are in a reverse-strand FeatureSlot and a zoomed map is generated.
INNER_LABELS_NO_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that all labels should be drawn on the outside of the backbone.
INNER_LABELS_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels should be drawn on the inside of the backbone if they are in a reverse-strand FeatureSlot.
InnerLabel - Class in ca.ualberta.stothard.cgview: This class is used by Cgview objects to facilitate label layout and drawing.
InnerLabel(Cgview, String, String, String, Font, Color, boolean, double, int) - Constructor for class ca.ualberta.stothard.cgview.InnerLabel: Constructs a new InnerLabel object.
inZoomRange(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the first zoom range or the second zoom range.
inZoomRange(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the first zoom range or the second zoom range.
inZoomRangeOne(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the first zoom range.
inZoomRangeOne(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the first zoom range.
inZoomRangeTwo(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the second zoom range.
inZoomRangeTwo(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Returns true if the base is located within the second zoom range.
isEqual(SeriesImage) - Method in class ca.ualberta.stothard.cgview.SeriesImage: Compares a SeriesImage object to this SeriesImage and returns true if they are equal.
isExtendedRadius() - Method in class ca.ualberta.stothard.cgview.Label: Returns a boolean specifying whether or not the line between the feature and this Label has been extended to prevent label clashes.
isRoom(Feature) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Returns a boolean specifying whether or not the supplied Feature object can fit in this FeatureSlot without overlapping with Feature objects already present in this FeatureSlot.

L

Label - Class in ca.ualberta.stothard.cgview: This class is used by Cgview objects to facilitate label layout and drawing.
Label(Cgview, String, String, String, Font, Color, boolean, double, int) - Constructor for class ca.ualberta.stothard.cgview.Label: Constructs a new Label object.
LABEL - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels are to be created.
LABEL_FORCE - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that a label is to be drawn even if there is insufficient space.
LABEL_NONE - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that no labels are to be created.
LABEL_ZOOMED - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels are to be drawn only when a zoomed map is generated.
LabelBounds - Class in ca.ualberta.stothard.cgview: This class is used to store bounds information about text already drawn on a Cgview map.
LabelBounds(Cgview) - Constructor for class ca.ualberta.stothard.cgview.LabelBounds: Constructs a new LabelBounds object.
labelText - Variable in class ca.ualberta.stothard.cgview.Label
Legend - Class in ca.ualberta.stothard.cgview: This class is used add legends to a Cgview map.
Legend(Cgview) - Constructor for class ca.ualberta.stothard.cgview.Legend: Constructs a new Legend object.
LEGEND_DRAW_ZOOMED - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn when zoomed.
LEGEND_ITEM_ALIGN_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LegendItem text should be aligned to the center.
LEGEND_ITEM_ALIGN_LEFT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LegendItem text should be aligned to the left.
LEGEND_ITEM_ALIGN_RIGHT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LegendItem text should be aligned to the right.
LEGEND_LOWER_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the lower center portion of the map.
LEGEND_LOWER_LEFT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the lower left portion of the map.
LEGEND_LOWER_RIGHT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the lower right portion of the map.
LEGEND_MIDDLE_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the middle center portion of the map.
LEGEND_MIDDLE_LEFT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the middle left portion of the map.
LEGEND_MIDDLE_LEFT_OF_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn left of the middle left portion of the map.
LEGEND_MIDDLE_RIGHT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the middle right portion of the map.
LEGEND_MIDDLE_RIGHT_OF_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn right of the middle right portion of the map.
LEGEND_NO_DRAW_ZOOMED - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should not be drawn when zoomed.
LEGEND_UPPER_CENTER - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the upper center portion of the map.
LEGEND_UPPER_LEFT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the upper left portion of the map.
LEGEND_UPPER_RIGHT - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the Legend should be drawn in the upper right portion of the map.
LegendItem - Class in ca.ualberta.stothard.cgview: This class is used to add text entries to Legend objects.
LegendItem(Legend) - Constructor for class ca.ualberta.stothard.cgview.LegendItem: Constructs a new LegendItem object.
lineEndRadians - Variable in class ca.ualberta.stothard.cgview.Label
lineEndRadius - Variable in class ca.ualberta.stothard.cgview.Label
lineStartRadians - Variable in class ca.ualberta.stothard.cgview.Label
lineStartRadius - Variable in class ca.ualberta.stothard.cgview.Label

M

main(String[]) - Static method in class ca.ualberta.stothard.cgview.Cgview
main(String[]) - Static method in class ca.ualberta.stothard.cgview.CgviewIO
main(String[]) - Static method in class ca.ualberta.stothard.cgview.Plasmid
mouseover - Variable in class ca.ualberta.stothard.cgview.Label
moveFile(String, String, String) - Method in class ca.ualberta.stothard.cgview.FileMover

O

OuterLabel - Class in ca.ualberta.stothard.cgview: This class is used by Cgview objects to facilitate label layout and drawing.
OuterLabel(Cgview, String, String, String, Font, Color, boolean, double, int) - Constructor for class ca.ualberta.stothard.cgview.OuterLabel: Constructs a new OuterLabel object.
OuterLabel(InnerLabel) - Constructor for class ca.ualberta.stothard.cgview.OuterLabel: Constructs a new OuterLabel object from an InnerLabel object, and adds the new OuterLabel to the parent Cgview object.

P

PADDING - Static variable in class ca.ualberta.stothard.cgview.Legend
placedBounds - Variable in class ca.ualberta.stothard.cgview.Label
Plasmid - Class in ca.ualberta.stothard.cgview
Plasmid(int) - Constructor for class ca.ualberta.stothard.cgview.Plasmid: Create a new Plasmid.
Plasmid(String, int) - Constructor for class ca.ualberta.stothard.cgview.Plasmid: Create a new Plasmid.
POSITIONS_AUTO - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels should be shown with position information only when a zoomed map is generated.
POSITIONS_NO_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels should not be shown with position information.
POSITIONS_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that labels should be shown with position information.

R

RADIAN_SHIFT_PADDING - Static variable in class ca.ualberta.stothard.cgview.Label
radiansShiftAmount - Static variable in class ca.ualberta.stothard.cgview.Label
radiusShiftAmount - Static variable in class ca.ualberta.stothard.cgview.Label
removeLabels() - Method in class ca.ualberta.stothard.cgview.Cgview: Removes labels from this Cgview.
removeLegends() - Method in class ca.ualberta.stothard.cgview.Cgview: Removes legends from this Cgview.
REVERSE_STRAND - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Represents the reverse strand.

S

SeriesImage - Class in ca.ualberta.stothard.cgview: This class is used to encapsulate Cgview map information when a series of images is linked together.
SeriesImage(int, int) - Constructor for class ca.ualberta.stothard.cgview.SeriesImage: Constructs a SeriesImage object.
setAddCategoryInfo(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether a category is added to certain labels to provide more information.
setAlignment(int) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the alignment of the LegendItems in this Legend.
setAllowLabelClash(boolean) - Method in class ca.ualberta.stothard.cgview.Legend: Sets whether or not feature labels are allowed to clash with this Legend.
setArrowheadLength(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the length of the arrowheads used for features that are drawn as arrows.
setBackboneColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the circle that represents the DNA sequence.
setBackboneRadius(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the radius of the circle that represents the DNA sequence.
setBackboneThickness(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the thickness of the line used to draw the circle that represents the DNA sequence.
setBackboneThickness(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the thickness of the arc used to draw the backbone.
setBackgroundColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the background color of the map.
setBackgroundColor(Color) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the color of the background of this Legend when drawn.
setBackgroundOpacity(float) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the opacity of the background of this Legend when drawn.
setBase(int) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies which sequence position this LabelBounds is closest to.
setBorderColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the map border.
setBounds() - Method in class ca.ualberta.stothard.cgview.Legend: Calculates the bounds of this Legend.
setBounds(double, double) - Method in class ca.ualberta.stothard.cgview.Legend: Calculates the bounds of this Legend.
setBounds(Rectangle2D) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies the bounds of this LabelBounds.
setCgview(Cgview) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Adds this FeatureSlot to a Cgview object.
setColor(Color) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the default color that will be assigned to FeatureRange objects added to this Feature.
setColor(Color) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the color of this FeatureRange when drawn.
setColorScheme(int) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether the overall color scheme.
setDecoration(int) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the type of decoration added to this Feature when drawn.
setDecoration(int) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the type of decoration added to this FeatureRange when drawn.
setDesiredNumberOfTicks(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the approximate number of long tick marks to be drawn in the sequence ruler.
setDesiredZoom(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Can be used to store a zoom value when a Cgview object is read from XML data.
setDesiredZoomCenter(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Can be used to store a zoom center value when a Cgview object is read from XML data.
setDocumentLocator(Locator) - Method in class ca.ualberta.stothard.cgview.CgviewFactory
setDrawLegends(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not legends should be drawn on this map.
setDrawSwatch(int) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets whether or not a color swatch should be drawn for this LegendItem.
setDrawTickMarks(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not tick marks are drawn.
setDrawTickMarks(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether tick marks are drawn.
setDrawWhenZoomed(int) - Method in class ca.ualberta.stothard.cgview.Legend: Sets whether or not this Legend is drawn when a zoomed Cgview map is generated.
setFeatureSlot(FeatureSlot) - Method in class ca.ualberta.stothard.cgview.Feature: Places this Feature into a FeatureSlot.
setFeatureSlotSpacing(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the amount of blank space placed between the concentric feature rings (FeatureSlot objects).
setFeatureThickness(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the default thickness of the line used to represent sequence features.
setFeatureThickness(float) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Sets the thickness of the arc used to represent sequence features in this FeatureSlot.
setFeatureThickness(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the thickness of the arc used to draw features.
setFont(Font) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the font used for labels generated for this Feature.
setFont(Font) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the font used for the label generated for this FeatureRange.
setFont(Font) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the font used for text in this Legend.
setFont(Font) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the font used for this LegendItem.
setFontColor(Color) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the default color that will be used for the text in this Legend.
setFontColor(Color) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the color that will be used for the text in this LegendItem.
setForceLabel(boolean) - Method in class ca.ualberta.stothard.cgview.Feature: Specifies whether or not labels created for this Feature should be drawn even if they cannot be placed such that they do not clash with other labels.
setForceLabel(boolean) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Specifies whether or not labels created for this FeatureRange should be drawn even if they cannot be placed such that they do not clash with other labels.
setGiveFeaturePositions(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Specifies under what circumstances feature position information should be added to the label text.
setGlobalLabel(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not feature labels should be shown on this map.
setGlobalLabelColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: By default, feature labels are colored to match the color of the feature they represent.
setHeight(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the height of the map.
setHeight(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the height of the map.
setHeight(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the height of the map.
setHighlightOpacity(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the opacity of the highlighting added to map items.
setHyperlink(String) - Method in class ca.ualberta.stothard.cgview.Feature: Specifies a hyperlink to be associated with this Feature.
setHyperlink(String) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Specifies a hyperlink to be associated with this FeatureRange.
setHyperlink(String) - Method in class ca.ualberta.stothard.cgview.Label: Specifies the hyperlink to be associated with this Label.
setHyperlink(String) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies a hyperlink to be associated with this LabelBounds.
setImageHeight(int) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the height of this map.
setImageWidth(int) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the width of this map.
setIsLinear(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not the map should be drawn with a broken backbone line to indicate a linear molecule.
setLabel(String) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the label text for this Feature.
setLabel(String) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the label text for this FeatureRange.
setLabel(String) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies the text that gave rise to this LabelBounds.
setLabel(String) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the text to be used for this LegendItem.
setLabelFont(Font) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the default font of the feature labels.
setLabelFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Sets the font size of feature labels.
setLabelFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the font size of feature labels.
setLabelFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the font size of feature labels.
setLabelLineLength(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the length of the line that extends from the feature to the feature label.
setLabelLineThickness(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the thickness of the line that extends from features to feature labels.
setLabelPlacementQuality(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Specifies how carefully labels placed on the map.
setLabelShuffle(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not labels should be randomly shuffled before removing excess labels.
setLabelsToKeep(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the maximum number of labels to attempt to arrange for display.
setLegendFont(Font) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the default font used for text in Legend objects added to this Cgview.
setLegendFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Sets the font size of legends.
setLegendFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the font size of legends.
setLegendFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the font size of legends.
setLegendPosition(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the legend position.
setLegendTextColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the default color of the text used for Legend objects.
setLinearBreakText(String) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the text to draw at the sequence start/end boundary if this is a linear molecule.
setLineStartRadius(double) - Method in class ca.ualberta.stothard.cgview.InnerLabel: Specifies radius of the innermost point in the line extending from the feature to this Label.
setLineStartRadius(double) - Method in class ca.ualberta.stothard.cgview.Label
setLineStartRadius(double) - Method in class ca.ualberta.stothard.cgview.OuterLabel: Specifies radius of the innermost point in the line extending from the feature to this Label.
setLongTickColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the tick marks in the sequence ruler.
setMapItemSizeAdjustment(float) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt
setMapItemSizeAdjustment(float) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab
setMessage(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the map message.
setMinimumFeatureLength(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the minimum feature length to use when drawing sequence features.
setMinimumFeatureLength(double) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Sets the minimum feature length to use when drawing sequence features.
setMouseover(String) - Method in class ca.ualberta.stothard.cgview.Feature: Specifies a mouseover to be associated with this Feature.
setMouseover(String) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Specifies a mouseover to be associated with this FeatureRange.
setMouseover(String) - Method in class ca.ualberta.stothard.cgview.Label: The mouseover to be associated with this Label.
setMouseover(String) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies a mouseover to be associated with this LabelBounds.
setMoveInnerLabelsToOuter(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not inner labels should be moved from the inside of the backbone circle to the outside of the backbone circle when there is insufficient room on the inside of the backbone circle.
setOpacity(float) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the opacity of this Feature when drawn.
setOpacity(float) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the opacity of this FeatureRange when drawn.
setOrigin(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the origin of the sequence in relation to the backbone drawing.
setPosition(int) - Method in class ca.ualberta.stothard.cgview.Legend: Sets the position of this Legend relative to the Cgview map canvas.
setProportionOfThickness(float) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the thickness of this Feature when drawn, as a proportion of the thickness of the FeatureSlot containing this Feature.
setProportionOfThickness(float) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the thickness of this FeatureRange when drawn, as a proportion of the thickness of the FeatureSlot containing this Feature.
setRadiansShiftConstant(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Controls label movement along the map backbone.
setRadius() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Sets the radius of this FeatureSlot.
setRadiusAdjustment(float) - Method in class ca.ualberta.stothard.cgview.Feature: Sets the position of this Feature relative to the FeatureSlot object that contains it.
setRadiusAdjustment(float) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets the position of this FeatureRange relative to the FeatureSlot object that contains it.
setReadDimension(boolean) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets whether or not canvas dimension information should be read from the input file.
setReadDimension(boolean) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets whether or not canvas dimension information should be read from the input file.
setRulerFont(Font) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the font of the number labels in the sequence ruler.
setRulerFontColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the text used for the sequence ruler.
setRulerFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactory: Sets the font size of the sequence ruler.
setRulerFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the font size of the sequence ruler.
setRulerFontSize(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the font size of the sequence ruler.
setRulerTextPadding(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the spacing between the ruler number labels and the tick marks.
setRulerUnits(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the units to be used for the sequence ruler.
setSequenceLength(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the length of the sequence to be mapped.
setShadingProportion(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the proportion of the width of the features to be redrawn for highlighting and shadowing purposes.
setShadowOpacity(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the opacity of the shadowing added to map items.
setShiftSmallFeatures(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the alignment behavior of small features when they are drawn.
setShortTickColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the short tick marks in the sequence ruler.
setShortTickThickness(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the thickness of the short tick marks in the sequence ruler.
setShowBorder(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not a border should be drawn around the map.
setShowBorder(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether this map is drawn with a border.
setShowInnerLabels(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether labels are allowed to be drawn on the inside of the plasmid.
setShowLabel(int) - Method in class ca.ualberta.stothard.cgview.Feature: Sets whether or not a label should be drawn for this Feature.
setShowLabel(int) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets whether or not a label a should be drawn for this FeatureRange.
setShowLabels(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether labels are drawn on this map.
setShowLegend(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether a legend is drawn on this map.
setShowMessage(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether a message is drawn on this map.
setShowShading(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not items on the map should be drawn with shading.
setShowShading(boolean) - Method in class ca.ualberta.stothard.cgview.Feature: Sets whether or not this Feature should be drawn with shading.
setShowShading(boolean) - Method in class ca.ualberta.stothard.cgview.FeatureRange: Sets whether or not this FeatureRange should be drawn with shading.
setShowShading(boolean) - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Sets whether or not items in this FeatureSlot should be drawn with shading.
setShowShading(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether items on the map are drawn with shading.
setShowTitle(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether a title is drawn on this map.
setShowWarning(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not the message set using setWarningText() should be drawn at the bottom of the figure.
setShowWarning(boolean) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets whether or not a warning is shown.
setSwatchColor(Color) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the swatch color that will be used for this LegendItem.
setSwatchOpacity(float) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the opacity of the swatch drawn for this LegendItem.
setTextAlignment(int) - Method in class ca.ualberta.stothard.cgview.LegendItem: Sets the alignment of this LegendItem, relative to the Legend object that contains it.
setTickDensity(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Adjusts the tick density, with 0 being the minimum, 1 being the maximum.
setTickDensity(double) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the tick density.
setTickDensity(double) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the tick density.
setTickLength(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the length of the tick marks in the sequence ruler.
setTickThickness(float) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the thickness of the tick marks in the sequence ruler.
setTitle(String) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the title of of the map.
setTitle(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets the title of of the map.
setTitleFont(Font) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the font of the map title.
setTitleFontColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the text used for the sequence title.
setType(int) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Specifies what map object this LabelBounds represents.
setUse(boolean) - Method in class ca.ualberta.stothard.cgview.LabelBounds: Sets whether or not this LabelBounds should be used.
setUseArrows(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether arrows are drawn on this map (true) or just arcs (false).
setUseColoredLabelBackground(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether labels are drawn with a colored box surrounding them.
setUseColoredLabelBackgrounds(boolean) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets whether or not labels should be drawn with a colored background.
setUseColoredLabels(boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Sets whether labels are drawn using color (true), or just black and white (false).
setUseInnerLabels(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Specifies under what circumstances labels should be drawn on the inside of the backbone circle.
setWarningFont(Font) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the font used for any warnings that appear at the bottom of the map.
setWarningFontColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the text used for warnings that appear at the bottom of the figure.
setWarningText(String) - Method in class ca.ualberta.stothard.cgview.Cgview: Specifies a warning message to appear at the bottom of the map.
setWidth(int) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the width of the map.
setWidth(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryPtt: Sets the width of the map.
setWidth(int) - Method in class ca.ualberta.stothard.cgview.CgviewFactoryTab: Sets the width of the map.
setZeroTickColor(Color) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the color of the tick mark drawn at the boundary between the end and beginning of the sequence.
setZoomShift(double) - Method in class ca.ualberta.stothard.cgview.Cgview: Sets the minimum zoom value necessary for labels to be drawn below the backbone.
shiftRadiansHigher() - Method in class ca.ualberta.stothard.cgview.Label: Attempts to move this Label by increasing its radians value.
shiftRadiansLower() - Method in class ca.ualberta.stothard.cgview.Label: Attempts to move this Label by decreasing its radians value.
shiftRadiansToOriginal(ArrayList) - Method in class ca.ualberta.stothard.cgview.Label: Attempts to move this Label by adjusting its radians value such that it is closer to its original radians value.
smallestDimension - Static variable in class ca.ualberta.stothard.cgview.Label
SortFeatureRangesByStart() - Constructor for class ca.ualberta.stothard.cgview.Feature.SortFeatureRangesByStart
sortFeaturesByStart() - Method in class ca.ualberta.stothard.cgview.FeatureSlot: Sorts the features in this FeatureSlot by start base.
SortFeaturesByStart() - Constructor for class ca.ualberta.stothard.cgview.FeatureSlot.SortFeaturesByStart
SortLabelsByForceLabel - Class in ca.ualberta.stothard.cgview: Sorts Label objects so that those where Label.getForceLabel() returns true are last.
SortLabelsByForceLabel() - Constructor for class ca.ualberta.stothard.cgview.SortLabelsByForceLabel
SortLabelsByRadians - Class in ca.ualberta.stothard.cgview: Sorts Label objects so that those with smaller Label.getLineStartRadians() values are first.
SortLabelsByRadians() - Constructor for class ca.ualberta.stothard.cgview.SortLabelsByRadians
SortLabelsByRadiansShift - Class in ca.ualberta.stothard.cgview: Sorts Label objects so that those that those with the smallest absolute difference between Label.getLineStartRadians() and Label.getLineEndRadians() are first.
SortLabelsByRadiansShift() - Constructor for class ca.ualberta.stothard.cgview.SortLabelsByRadiansShift
SortLabelsByRadius - Class in ca.ualberta.stothard.cgview: Sorts Label objects so that those that those furthest from the sequence backbone are first.
SortLabelsByRadius() - Constructor for class ca.ualberta.stothard.cgview.SortLabelsByRadius
SortSeriesImageByZoomCenter - Class in ca.ualberta.stothard.cgview: Sorts SeriesImage objects so that those with the lowest zoom center value are first.
SortSeriesImageByZoomCenter() - Constructor for class ca.ualberta.stothard.cgview.SortSeriesImageByZoomCenter
startDocument() - Method in class ca.ualberta.stothard.cgview.CgviewFactory
startElement(String, String, String, Attributes) - Method in class ca.ualberta.stothard.cgview.CgviewFactory
strand - Variable in class ca.ualberta.stothard.cgview.Label
SWATCH_NO_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LegendItem should be drawn without a color swatch.
SWATCH_SHOW - Static variable in interface ca.ualberta.stothard.cgview.CgviewConstants: Indicates that the LegendItem should be drawn with a color swatch.

T

translateCanvas() - Method in class ca.ualberta.stothard.cgview.Cgview: Translates the canvas.
translateZeroCenter() - Method in class ca.ualberta.stothard.cgview.Cgview: Translates the canvas so that point (0,0) is in the center.

U

unplacedBounds - Variable in class ca.ualberta.stothard.cgview.Label
untranslateCanvas() - Method in class ca.ualberta.stothard.cgview.Cgview: Undoes the canvas translation, so that point(0,0) is in upper left.
untranslateZeroCenter() - Method in class ca.ualberta.stothard.cgview.Cgview: Undoes the translation of the canvas that was done to place point (0,0) at the center, so that point(0,0) becomes upper left.
updateBounds() - Method in class ca.ualberta.stothard.cgview.InnerLabel: Recalculates the rectangle that represents the bounds of this Label.
updateBounds() - Method in class ca.ualberta.stothard.cgview.Label
updateBounds() - Method in class ca.ualberta.stothard.cgview.OuterLabel: Recalculates the rectangle that represents the bounds of this Label.
updateBounds(double) - Method in class ca.ualberta.stothard.cgview.InnerLabel: Recalculates the rectangle that represents the bounds of this Label.
updateBounds(double) - Method in class ca.ualberta.stothard.cgview.Label
updateBounds(double) - Method in class ca.ualberta.stothard.cgview.OuterLabel: Recalculates the rectangle that represents the bounds of this Label.

W

writeHTMLFile(Cgview, String, String, String) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Creates an HTML file that links to a Cgview map.
writeHTMLFile(Cgview, String, String, String, boolean) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Creates an HTML file that links to a Cgview map.
writeToJPGFile(Cgview, String) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a JPG file.
writeToJPGFile(Cgview, String, boolean) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a JPG file.
writeToJPGFile(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Writes this map to a JPG file.
writeToPNGFile(Cgview, String) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a PNG file.
writeToPNGFile(Cgview, String, boolean) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a PNG file.
writeToPNGFile(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Writes this map to a PNG file.
writeToSVGFile(Cgview, String, boolean) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a SVG or a SVGZ file.
writeToSVGFile(Cgview, String, boolean, boolean) - Static method in class ca.ualberta.stothard.cgview.CgviewIO: Writes a Cgview object to a SVG or a SVGZ file.
writeToSVGFile(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Writes this map to an SVG file.
writeToSVGFile(String, boolean, boolean) - Method in class ca.ualberta.stothard.cgview.Plasmid: Writes this map to an SVG file.
writeToSVGZFile(String) - Method in class ca.ualberta.stothard.cgview.Plasmid: Writes this map to an SVGZ file (a zipped SVG file).

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