Constant Field Values

Contents

• org.utgenome.*

org.utgenome.*

org.utgenome.format.bed.BEDLexer

public static final int	Attribute	7
public static final int	Description	4
public static final int	Digit	10
public static final int	Dot	9
public static final int	Double	22
public static final int	EOF	-1
public static final int	Eq	8
public static final int	EscapeSequence	13
public static final int	Exp	17
public static final int	Frac	16
public static final int	HexDigit	11
public static final int	Int	15
public static final int	Integer	21
public static final int	Name	5
public static final int	Number	23
public static final int	QName	24
public static final int	String	20
public static final int	StringChar	14
public static final int	StringChars	19
public static final int	UnicodeChar	12
public static final int	Value	6
public static final int	WhiteSpace	18

org.utgenome.format.bed.BEDParser

public static final int	Attribute	7
public static final int	Description	4
public static final int	Digit	10
public static final int	Dot	9
public static final int	Double	22
public static final int	EOF	-1
public static final int	Eq	8
public static final int	EscapeSequence	13
public static final int	Exp	17
public static final int	Frac	16
public static final int	HexDigit	11
public static final int	Int	15
public static final int	Integer	21
public static final int	Name	5
public static final int	Number	23
public static final int	QName	24
public static final int	String	20
public static final int	StringChar	14
public static final int	StringChars	19
public static final int	UnicodeChar	12
public static final int	Value	6
public static final int	WhiteSpace	18

org.utgenome.format.fasta.CompactFASTA

public static final String	PAC_FILE_SUFFIX	".pac"
public static final String	PAC_INDEX_FILE_SUFFIX	".i.silk"
public static final String	PAC_N_FILE_SUFFIX	".pacn"

org.utgenome.format.wig.WIGDatabaseGenerator

public static final int

DATA_SPLIT_UNIT

100000

org.utgenome.format.wig.WIGLexer

public static final int	Attribute	7
public static final int	Description	4
public static final int	Digit	10
public static final int	Dot	9
public static final int	Double	22
public static final int	EOF	-1
public static final int	Eq	8
public static final int	EscapeSequence	13
public static final int	Exp	17
public static final int	Frac	16
public static final int	HexDigit	11
public static final int	Int	15
public static final int	Integer	21
public static final int	Name	5
public static final int	Number	23
public static final int	QName	24
public static final int	String	20
public static final int	StringChar	14
public static final int	StringChars	19
public static final int	UnicodeChar	12
public static final int	Value	6
public static final int	WhiteSpace	18

org.utgenome.format.wig.WIGParser

public static final int	Attribute	7
public static final int	Description	4
public static final int	Digit	10
public static final int	Dot	9
public static final int	Double	22
public static final int	EOF	-1
public static final int	Eq	8
public static final int	EscapeSequence	13
public static final int	Exp	17
public static final int	Frac	16
public static final int	HexDigit	11
public static final int	Int	15
public static final int	Integer	21
public static final int	Name	5
public static final int	Number	23
public static final int	QName	24
public static final int	String	20
public static final int	StringChar	14
public static final int	StringChars	19
public static final int	UnicodeChar	12
public static final int	Value	6
public static final int	WhiteSpace	18

org.utgenome.gwt.utgb.client.bio.SAMReadFlag

public static final int	FLAG_FAILS_QUALITY_CHECK	512
public static final int	FLAG_IS_FIRST_READ	64
public static final int	FLAG_IS_SECOND_READ	128
public static final int	FLAG_MAPPED_IN_A_PROPER_PAIR	2
public static final int	FLAG_MATE_IS_UNMAPPED	8
public static final int	FLAG_NOT_PRIMARY	256
public static final int	FLAG_PAIRED_READ	1
public static final int	FLAG_PCR_OR_OPTICAL_DUPLICATE	1024
public static final int	FLAG_QUERY_IS_UNMAPPED	4
public static final int	FLAG_STRAND_OF_MATE	32
public static final int	FLAG_STRAND_OF_QUERY	16

org.utgenome.gwt.utgb.client.canvas.GWTGraphCanvas.GraphStyle

public static final String	CONFIG_GRAPH_WINDOW	"window function"
public static final String	CONFIG_TRACK_HEIGHT	"trackHeight"

org.utgenome.gwt.utgb.client.canvas.ReadDisplayStyle

public static final String	CONFIG_COVERAGE_STYLE	"coverage.style"
public static final String	CONFIG_DRAW_SHADOW	"draw shadow"
public static final String	CONFIG_HIDE_MATCHED_BASE	"gray matches"
public static final String	CONFIG_LAYOUT	"layout"
public static final String	CONFIG_MIN_READ_HEIGHT	"min read height"
public static final String	CONFIG_NUM_READ_MAX	"num reads to display"
public static final String	CONFIG_PE_OVERLAP	"overlap paired reads"
public static final String	CONFIG_READ_HEIGHT	"read height"
public static final String	CONFIG_READ_MARGIN	"read margin"
public static final String	CONFIG_REVERSE_READ_HISTOGRAM	"reverse read histogram"
public static final String	CONFIG_REVERSE_READ_TRACK	"reverse read track color"
public static final String	CONFIG_SHOW_BASE_QUALITY	"show base quality"
public static final String	CONFIG_SHOW_LABELS	"showLabels"
public static final String	CONFIG_SHOW_STRAND	"show strand"

org.utgenome.gwt.utgb.client.db.DatabaseTable

public static final int

LABEL_ROW

0

org.utgenome.gwt.utgb.client.track.TrackFrame

public static final int	INFOPANEL_WIDTH	250
public static final int	SCROLLBAR_WIDTH	25

org.utgenome.gwt.utgb.client.track.TrackFrameState

public static final int

DEFAULT_MIN_TRACKFRAME_HEIGHT

18

org.utgenome.gwt.utgb.client.track.UTGBProperty

public static final String	DB_GROUP	"dbGroup"
public static final String	DB_NAME	"dbName"
public static final String	GROUP	"group"
public static final String	REVISION	"revision"
public static final String	SEQUENCE_SIZE	"sequenceSize"
public static final String	SPECIES	"species"
public static final String	TARGET	"target"

org.utgenome.gwt.utgb.client.track.lib.BEDTrack

protected final String

CONFIG_FILENAME

"fileName"

org.utgenome.gwt.utgb.client.track.lib.GenomeTrack

public static final String	CONFIG_TRACK_BASE_URL	"trackBaseURL"
public static final String	CONFIG_TRACK_TYPE	"type"

org.utgenome.gwt.utgb.client.track.lib.NavigatorTrack

public static final int

MINIMUM_WINDOW_SIZE

10

org.utgenome.gwt.utgb.client.track.lib.old.OldUTGBProperty

public static final String	REVISION	"revision"
public static final String	SPECIES	"species"
public static final String	TARGET	"target"

org.utgenome.gwt.utgb.client.ui.Border

protected static final int	LEFT	0
public static final int	LOWER	2
protected static final int	RIGHT	1
public static final int	UPPER	0

org.utgenome.gwt.utgb.client.ui.DraggableTable

public static final String

TABLE_STYLE

"dg-table"

org.utgenome.gwt.utgb.client.ui.Frame

public static final int	BUTTON_ADJUST	2
public static final int	BUTTON_CLOSE	8
public static final int	BUTTON_CONFIG	1
public static final int	BUTTON_MINIMIZE	4

org.utgenome.gwt.utgb.client.ui.RoundCornerFrame

public static final int	BORDER_FULL	15
public static final int	EAST	2
public static final int	NORTH	1
public static final int	SOUTH	8
public static final int	WEST	4

org.utgenome.gwt.utgb.client.util.TableData

public static final String

DEFAULT_KEY_COLUMN_NAME

"id"

org.utgenome.gwt.utgb.server.JDBCService.HSQLDBAccess

public static final String	ADDRESS_PREFIX	"jdbc:hsqldb:"
public static final String	DRIVER_NAME	"org.hsqldb.jdbcDriver"

org.utgenome.gwt.utgb.server.app.CSEGViewer

public static final int	DEFAULT_HEIGHT	800
public static final int	DEFAULT_HEIGHT_PER_SAMPLE	4

org.utgenome.gwt.utgb.server.app.Sequence.GraphicalOutput

public static final int	DEFAULT_HEIGHT	12
public static final float	FONT_SIZE	10.5f

org.utgenome.gwt.widget.client.FrameBorder

public static final int	BORDER_FULL	15
public static final int	EAST	2
public static final int	NORTH	1
public static final int	SOUTH	8
public static final int	WEST	4

org.utgenome.gwt.widget.client.HorizontalBorder

protected static final int	LEFT	0
public static final int	LOWER	2
protected static final int	RIGHT	1
public static final int	UPPER	0

org.utgenome.gwt.widget.client.Style

public static final String	BORDER_DASHED	"dashed"
public static final String	BORDER_INSET	"inset"
public static final String	BORDER_OUTSET	"outset"
public static final String	BORDER_SOLID	"solid"
public static final String	COLOR_BLACK	"black"
public static final String	COLOR_GRAY	"gray"
public static final String	COLOR_RED	"red"
public static final String	COLOR_SKYBLUE	"#99CCFF"
public static final String	COLOR_WHITE	"white"
public static final String	CSS_BACKGROUND_COLOR	"backgroundColor"
public static final String	CSS_BACKGROUND_IMAGE	"backgroundImage"
public static final String	CSS_BACKGROUND_POSITION	"backgroundPosition"
public static final String	CSS_BACKGROUND_REPEAT	"backgroundRepeat"
public static final String	CSS_BORDER	"border"
public static final String	CSS_BORDER_COLLAPSE	"borderCollapse"
public static final String	CSS_CURSOR	"cursor"
public static final String	CSS_DISPLAY	"display"
public static final String	CSS_FONT_COLOR	"color"
public static final String	CSS_FONT_FAMILY	"fontFamily"
public static final String	CSS_FONT_SIZE	"fontSize"
public static final String	CSS_FONT_WEIGHT	"fontWeight"
public static final String	CSS_MARGIN	"margin"
public static final String	CSS_NOWRAP	"nowrap"
public static final String	CSS_OVERFLOW_X	"overflowX"
public static final String	CSS_OVERFLOW_Y	"overflowY"
public static final String	CSS_PADDING	"padding"
public static final String	CSS_VERTICAL_ALIGN	"verticalAlign"
public static final String	CSS_WHITESPACE	"whiteSpace"
public static final String	CSS_Z_INDEX	"zIndex"
public static final String	CURSOR_AUTO	"auto"
public static final String	CURSOR_CROSSHAIR	"crosshair"
public static final String	CURSOR_HELP	"help"
public static final String	CURSOR_MOVE	"move"
public static final String	CURSOR_POINTER	"pointer"
public static final String	CURSOR_RESIZE_E	"e-resize"
public static final String	CURSOR_RESIZE_N	"n-resize"
public static final String	CURSOR_RESIZE_SE	"se-resize"
public static final String	CURSOR_TEXT	"text"
public static final String	DISPLAY_BLOCK	"block"
public static final String	OVERFLOW_AUTO	"auto"
public static final String	OVERFLOW_HIDDEN	"hidden"

org.utgenome.gwt.widget.client.TrackFrame

public static final int	BUTTON_ADJUSTHEIGHT	4
public static final int	BUTTON_ALL	31
public static final int	BUTTON_CLOSE	16
public static final int	BUTTON_CONFIG	2
public static final int	BUTTON_MINIMIZE	8
public static final int	BUTTON_RELOAD	1

org.utgenome.gwt.widget.client.UTGBDesignFactory

public static final String

TRACKFRAME_BACKGROUND

"trackframe-bg.png"

org.utgenome.gwt.widget.client.VerticalDraggableTrackPanel

public static final String

TABLE_STYLE

"dg-table"

org.utgenome.gwt.widget.client.impl.PathElement

public static final String	ARC	" ar"
public static final String	CLOSE	" x"
public static final String	CUBIC	" qb"
public static final String	END	" e"
public static final String	LINETO	" l"
public static final String	MOVETO	" m"
public static final String	QUADRATIC	" qb"

org.utgenome.shell.UTGBShellCommand

public static final String	APP_FOLDER	"app"
public static final String	EXPLODED_WEBAPP_DIR	"target/utgb"
public static final String	SRC_FOLDER	"src/main/java"
public static final String	WEBAPP_FOLDER	"src/main/webapp"