Many programs in GCG have graphic output, such as restriction maps or RNA secondary structure predictions. You have several choices as to how to handle the graphic output:

1) Display it on your screen.
2) Print it directly to the printer attached to your PC or Mac terminal.
3) Save the output to a file and then print it later.

For printing PostScript or HPGL files through the network directly to the printer attached to your PC, you will need to use a terminal program capable of printing in "transparent mode", so that the files are sent directly to the printer without processing by your PC. The shareware QVT/Net Terminal program is a good choice for these purposes. Note that you can use these methods for printing any files, not just files created by GCG.

If you do not have a PostScript-capable printer available, you can use the freeware programs GhostScript and GhostView for viewing and printing PostScript files on your PC.

These instructions assume you are using the Genetics UNIX Biocomputing Workstation.

Before you run a program with graphics output, use the GCG setplot program to tell GCG how you want to display, print, or save your graphics output. In HYGCGmenu, go into and execute setplot from the Display / Graphics menu. From the genetics% prompt, type setplot and press enter. This program presents you with a menu of choices:

|colorX     Color X Windows Graphics Window                         |
|monoX      Monochrome X Windows Graphics Window                    |
|psfile     PostScript output saved as file graphics-time.ps        |
|hpfile     HPGL output saved as file plot-time.hp                  |
|lw         PostScript output on your LaserWriter                   |
|laser      HPGL output on your LaserJet                            |
|tek        Tektronix output on your telnet screen                  |
|pngfile    PNG output saved as file program-time.png               |


Make your selection with the up or down arrow keys and press return.  

XWINDOWS

The colorX or monoX choices will display the graphic in a window on your screen. It works very nicely if you have an XWindows server program on your PC or Mac, or if you are using a UNIX workstation with XWindows built in. For this to work, you must first startup your XWindows program, and then tell GCG where your Mac or PC is by typing from the genetics% UNIX prompt:

setenv DISPLAY my.ip.address:0 

PSFILE AND HPFILE

These choices save the graphic to either a PostScript or HPGL file, respectively, that you can print later on any PostScript (e.g. Apple LaserWriter or HP LaserJet 4M) or HPGL printer (e.g. HP LaserJet 4M or Lexmark Optra). The "-time" in the file name indicates that it will automatically put a date/time stamp in the name of the file. To print the file later, download it to your PC or Mac and send it to your printer. During downloading and copying to the printer, remember that PostScript files are simple ASCII text files, whereas HPGL files are binary files. Printing instructions are included later in this discussion.

LW

With this option, the graphic is sent directly to a PostScript printer attached to your PC or Mac. It can be any PostScript printer, not just a LaserWriter. Make sure you set your terminal to print in transparent mode, and you may have to set up page protection from the printer's control panel to get it to print the entire graphic on one page.

LASER

With this option, the graphic is sent directly to a HPGL printer attached to your PC or Mac. It can be any HPGL printer, not just a LaserJet. Make sure you set your terminal to print in transparent mode, and you may have to set up page protection from the printer's control panel to get it to print the entire graphic on one page.

TEK

Some telnet programs, such as NCSA telnet, have built-in Tektronix emulation. With this choice, the graphic is displayed in a Tek window on your screen, similar to the XWindows example above. However, you don't need to set the DISPLAY variable with this choice.

PNGFILE

With this option the graphic is saved as a .png graphics file that can be displayed in a Web browser or imported into various graphics software. The "-time" in the file name indicates that it will automatically put a date/time stamp in the name of the file. To print the file later, first download it to your PC or Mac. .png files are binary or image files.

ADDITIONAL GRAPHICS COMMANDS

Other GCG graphics commands that are not included in the setplot menu customized for Genetics give you additional flexibility and a greater range of graphics output devices. These commands include: hpgl, postscript, tektronix, xwindows, regis, and sixel. Please read Chapter 5 of the GCG User's Guide for information about these additional commands.

GCG USER'S GUIDE

After using setplot to make your graphics choice, you can list your graphics setup with the showplot program. You can test your graphics setup with the plottest program, which plots a GCG test pattern. In HYGCGmenu, go into and execute plottest from the Display / Graphics menu. From the genetics% prompt, type plottest and press enter (if saving the plot to disk, use the -plot=filename option). Follow the instructions on the screen.

Most GCG results files are plain text that you can print on any printer. Some of the programs store graphics output in HPGL or PostScript files. Here are some examples that illustrate some of your options for printing these files. This is not an exhaustive list, and details will depend on what kind of computer you are using for a terminal, what kind of printer you have, what operating system is running on your computer, and what terminal software you are using, i.e. the number of combinations is astronomical.

Note also that you can use these methods for printing any files, not just files created by GCG.

1. Printing a simple text file from Genetics directly to your printer.

Use the GCG listfile command to print any text file on Genetics, e.g. this file, to the printer attached to your PC or Mac. Example:

genetics% listfile -noheading filename.txt

2. Printing a simple text file from Genetics directly to a PostScript printer attached to your PC or Mac.

Use the GCG lprint command to print any text file in your directory on Genetics to a PostScript printer attached to your PC or Mac. Be sure to set your terminal to print in transparent mode before printing. Example:

genetics% lprint -noheading filename.txt

First, download the file to your machine with FTP or Zmodem. Use ASCII text mode to transfer a PostScript file. Then, on a PC, go to a DOS prompt and copy the file to your printer attached to the appropriate printer port, such as:

C:\ copy graphics.ps lpt1

CREATING AND PRINTING POSTSCRIPT PROGRAM MANUAL FILES

You may wish to print sections of the GCG Program Manual for your own use. The following example shows how to use the GCG red command to create a PostScript file for the section of the Program Manual about the pileup multiple sequence alignment program. The red command creates PostScript output that is identical to the printed versions of the GCG manuals that you can read in our libraries or purchase from the GCG company.

Activate gcg by typing gcg from the genetics% prompt. Next, activate the gcg support environment by typing gcgsupport. Then, from the genetics% prompt, type:

red Program_Manual:pileup.red -out=pileup.ps

Another option is to print out whole sections of the GCG manual at once. To print out the whole section that includes all programs that begin with the letter P (which would include pileup among them), type:

red GenDocDriver:p.driver -out=p.ps

PRINTING ASCII TEXT VERSIONS OF THE MANUALS

If you do not have a PostScript printer, or if you prefer plain text, you may use red to prepare files in ASCII text format instead of PostScript. For the above example, the command line would be:

red Program_Manual:pileup.red  -ascii=pileup.txt -lml=4 -rml=75

PRINTING THE ONLINE DOCUMENTATION