Programs of the NMRPipe System
NMRDraw: Display and Analysis of NMRPipe-Format Spectral Data and Images

Flag	Argument	Default	Description
`-in`	`inName`	`test.ft2`	First Input Name.
`-dir`	`dirName`	`.`	Default Input Directory.
`-file`	`fileExp`	`"*"`	Directory List Filter.
`-name`	`defName`	`test.ft2`	Default Input Name.
`-text`	`textDir`	`.`	Help Text Directory.
`-read`		`no`	Auto-Read on Startup.

General Flags:

`-square`		Square Display Area.
`-track`		Default Loc Tracks Mouse.
`-focus`		Allow focus grab.
`-panel`		Use Stand-Alone Panel.
`-scroll`		Use Scrollable Panel.
`-verb`		Verbose Mode On.
`-noverb`		Verbose Mode Off (Default).
`-noxvwarn`		XView Warnings OFF (Default).
`-xvwarn`		XView Warnings ON.
`-dbg`	`0`	Debug Message Level.

2D Display:

`-draw`			Auto-Draw with Read.
`-clear`			Auto-Clear when Drawing.
`-frzLevels`		`Sometimes`	Freeze Contour Levels: Always Sometimes Never
`-frzZoom`		`Sometimes`	Freeze 2D Zoom Region: Always Sometimes Never
`-autoScale`			Auto-Calc Contour Level.
`-grid`			Draw Grid Lines.
`-pix`			PixMap Display is Default.
`-useTitle`			Display Title from Header.Window Parameter Set-Up:
`-cellX`	`xPix`	`0`	Character Cell Width.
`-cellY`	`yPix`	`0`	Character Cell Height.
`-xAdj`	`xPix`	`0`	X Width Border Adjustment.
`-yAdj`	`yPix`	`0`	Y Width Border Adjustment.
`-dct`	`msec`	`1500`	Double-Click Time, msec.
`-repaint`			Force Manual Repaint Mode.
`-norepaint`			Avoid Manual Repaint Mode (Default).
`-frp`		`3`	First Repaint Count.
`-depth`	`dbits`	`8`	Window Depth. Requires use of the -visual option.
`-type1`	`size`		Size for Regular Font: Small Medium Large
`-type2`	`size`		Size for Large Font: Small Medium Large
`-visual`	`class`		Visual Class Keyword: PseudoColor StaticColor StaticGray GrayScale DirectColor TrueColor

Default (PseudoColor)
Special Application Set-Up:

`-peak`	`filtName`	Peak Analysis Setup.
`-image`		Image Display Setup.
`-dev`		Development Setup.
`-tk`		Use Tk-Style IPC.

1D Display:

`-lw1d`	`0`	1D Drawing Width, Pixels.
`-vert`		Enable Vertical Plots.
`-zero`		Draw 1D Zero Level Line.
`-cursor`		Draw 1D Position Cursor.
`-relative`		Use Relative 1D Scaling.
`-compress`		Use 1D Display Compression.

Coordinates:

`-iz`		`1`	Z-Plane Number.
`-ia`		`1`	A-Plane Number.

Script Execution and External Commands:

`-sh`	`shName`	`csh`	Command interpreter name.
`-ext`	`extName`	`com`	File extension for scripts.
`-bin`	`binPath`		NMRPipe Binary Path.
`-exec`	`execCmnd`		Command for executing scripts.
`-sys`			Use System Call Via system().
`-nosys`			Use System Call Via \| csh.
`-fork`			Use System Call Via fork().
`-save1D`			Suppress pipeline processing. Use explicit 1D save instead.

Processing:

`-func`	`fnTab`	`func.tab`	Function Table Name.
`-proc`	`script`	`proc1d.com`	1D Processing Script.
`-zfht`			Temporary Zero Fill (ZF) with Hilbert Transform.
`-nozfht`			Suppress Temporary ZF with Hilbert Transform. (Default)

Contours:

`-mult`	`contFactor`	`1.3`	Contour Level Factor.
`-plev`	`numLevels`	`10`	Number of Positive Levels.
`-nlev`	`numLevels`	`10`	Number of Negative Levels.
`-hi`	`firstHeight`		First Contour Height. (Old Option)
`-fhi`	`firstHeight`		First Contour Height.
`-lhi`	`lastHeight`		Last Contour Height.

Positive Level HSV Color Vector:

`-pcc`	`numColors`	`12`	Positive Color Count.
`-pHue1`	`hue`	`0.5`	First Hue, 0.0 to 1.0.
`-pHue2`	`hue`	`0.7`	Last Hue, 0.0 to 1.0.
`-pSat1`	`saturation`	`0.8`	First Saturation, 0.0 to 1.0.
`-pSat2`	`saturation`	`1.0`	Last Saturation, 0.0 t 1.0.
`-pVal1`	`value`	`1.0`	First Value (Brightness) 0.0 to 1.0.
`-pVal2`	`value`	`1.0`	Last Value (Brightness) 0.0 to 1.0.

Negative Level HSV Color Vector:

`-ncc`	`numColors`	`12`	Negative Color Count.
`-nHue1`	`hue`	`0.5`	First Hue, 0.0 to 1.0.
`-nHue2`	`hue`	`0.7`	Last Hue, 0.0 to 1.0.
`-nSat1`	`saturation`	`0.8`	First Saturation, 0.0 to 1.0.
`-nSat2`	`saturation`	`1.0`	Last Saturation, 0.0 to 1.0.
`-nVal1`	`value`	`1.0`	First Value (Brightness), 0.0 to 1.0.
`-nVal2`	`value`	`1.0`	Last Value (Brightness), 0.0 to 1.0.

Color Management:

`-XOR`	`Always`	XOR Drawing Keyword: Always Sometimes Never
`-labMode`	`Normal`	Label Drawing Keyword: Normal XOR Overlay
`-svri`	`No`	Server Image Color Palette.
`-virt`	`Never`	Virtual Colormap Keyword: Always Sometimes Never
`-virtOff`	`64`	Virtual Color Index Offset.
`-static`		Use Static Color Table.

Program Colors:

`-colors`	`clrList`	`Below`	Color Name List.
`-color0`	`zeroClr`	`lightGray`	Zero Line Color.
`-color1`	`1dClr`	`yellow`	Active 1D Plot Color.
`-colorC`	`cClr`	`magenta`	Cursor Bar Color.
`-colorG`	`gridClr`	`dimGray`	Grid Line Color.
`-colorX`	`xClr`	`cyan`	X-Axis 1D Plot Color.
`-colorY`	`yClr`	`red`	Y-Axis 1D Plot Color.
`-colorZ`	`zClr`	`green`	Z-Axis 1D Plot Color.
`-colorA`	`aClr`	`orange`	A-Axis 1D Plot Color.
`-colorL`	`lClr`	`white`	Axis Label Color.
`-colorP1`	`p1Clr`	`white`	Peak Label Color 1D.
`-colorP2`	`p2Clr`	`white`	Peak Label Color 2D.
`-colorE`	`eClr`	`black`	Background Color.

Generic Window Arguments (See also, Output of: nmrDraw -help):

`-size`	`x y`	Initial NMRDraw Window Width and Height, Pixels.
`-position`	`x y`	Initial NMRDraw Window Positions, Pixels.
`-geometry`	`geom`	Initial NMRDraw Window Geometry, X11 style.

Default Color Names:

 black        red          orange       yellow      
 green        blue         violet       cyan        
 magenta      lightGray    dimGray      gray30      
 gray20       white

Frank Delaglio, Ph.D.