Graphics

[ Program Manual | User's Guide | Data Files | Databases ]

Table of Contents

Overview

Connecting a Graphics Device to the Computer

Directing Graphics Output to a Port or Print Queue

Directing Graphic Output to the Terminal's Printer Port in Pass-Through Configuration

Directing Graphic Output to a Plotter in Eavesdrop Configuration

Directing Graphic Output from a Workstation

Configuring Graphics Languages and Devices

GIF* (Graphics Interchange Format)

Configuration

Considerations

Supported Formats

HPGL (Hewlett Packard Graphics Language)

Configuration

Considerations

Supported Devices

PNG (Portable Network Graphics)

Configuration

Considerations

PostScript

Configuration

Considerations

Supported Devices

Metafile Formats

ReGIS

Configuration

Considerations

Supported Devices

Sixel

Configuration

Considerations

Supported Devices

Tektronix

Configuration

Considerations

Supported Devices

X Windows

Configuration

Considerations

Supported Devices

X Server Software

Graphics Programs and Descriptions


Overview

[ Top | Next ]

You will find the following information in this appendix:


Connecting a Graphics Device to the Computer

[ Previous | Top | Next ]

For a computer to display output on a graphics device, there must be a connection between the computer and the device. Computers have ports, which are connections through which a separate device (such as a printer, plotter, or graphics terminal) can communicate with the computer. Every port has a name by which you refer to it to direct output its way.

Historically, ports were inside the computer. Now, however, there is often a network or phone line (via modem) which allows you to connect to ports on a terminal server or computer. In addition to the network ports available, you also may have ports available on your PC, Macintosh, or workstation.

In the configurations in this appendix, a port refers to a serial port to which the computer can direct output. You can connect a graphics terminal, printer, or plotter to a serial port.

This section describes four ways to connect graphics devices to the computer. After you have the graphic devices correctly connected, you can direct graphic output to them. You can

Directing Graphics Output to a Port or Print Queue

[ Previous | Top | Next ]

If unused ports are available, you can connect the printer, plotter, or graphics terminal to a port. In this configuration, the graphics device is independent of the terminal.

Example port name: /dev/ttyp16

Figure 1

Directing Graphic Output to the Terminal's Printer Port in Pass-Through Configuration

[ Previous | Top | Next ]

You can connect a supported graphics device to a computer through the terminal's printer port. This type of configuration is called "pass-through." When you configure any device (except Hewlett Packard plotters) directly to your terminal, the Wisconsin Package assumes you have it connected to the printer port. Each graphics program, then, automatically turns on the terminal's printer port whenever you send graphics output.

For HP plotters, where the Package does not automatically assume pass-through printing, use the -PASSthru command-line parameter when you run each graphics program to turn on your printer port.

To direct output to a graphics device connected to the terminal's printer port, define your graphics configuration for the appropriate graphics language and device (see "Defining Your Graphics Configuration" in Chapter 5, Using Graphics for more information). When you are prompted "To what port is your device connected:", type Term.

Note: If you are using a VT220, or a terminal emulator that supports pass-through printing, you can attach your graphics device to the terminal's pass-through port.

No output appears on your screen while a graphic is being printed or plotted. To stop a graphic from printing, plotting, or displaying, press <Ctrl>c.

Example port name: term


Figure 2

Directing Graphic Output to a Plotter in Eavesdrop Configuration

[ Previous | Top | Next ]

You can connect a supported Hewlett Packard graphics device to the Wisconsin Package in a configuration where the graphics device serves as an intermediate connection between the computer and the terminal. This type of configuration is called "eavesdrop." If you configure an HP7470, HP7475, or HP7550 plotter to your terminal, the Package will assume you have it connected in eavesdrop configuration.

Even if you are not going to draw graphics, you must turn on HP plotters connected in eavesdrop configuration for the terminal to communicate with the computer.

Example port name: term


Figure 3

Directing Graphic Output from a Workstation

[ Previous | Top | Next ]

You can use a workstation to connect to the Wisconsin Package and display graphics. In this configuration, the graphics devices may or may not be independent of the workstation. That is, on a workstation you may have access to supported graphics devices through network access or via a direct connection to your workstation's printer port (see dashed lines in figure below).

To direct output to your workstation (X Windows Graphics) or to a graphics device connected to the workstation's printer port, define your graphics configuration for the appropriate graphics language and device (see "Defining Your Graphics Configuration" in Chapter 5, Using Graphics for more information). If you are prompted "To what port is your device connected:", type the port name for the connected device.


Example port names:
/dev/ttyp10, /dev/ttyp11, term, /dev/tty01

Figure 4


Configuring Graphics Languages and Devices

[ Previous | Top | Next ]

You will find the following graphics languages and their Wisconsin Package supported devices described in this sectionchapter:

GIF* (Graphics Interchange Format)

[ Previous | Top | Next ]

* The Graphics Interchange Format(c) is the Copyright property of CompuServe Incorporated. GIFSM is a Service Mark property of CompuServe Incorporated. The GIF-LZW compression software is licensed under U.S. Patent 4,558,302 and foreign counterparts.

The GIF driver enables you to produce graphics files that a web browser can display. GIF is an optional graphics driver that is sold separately from the Wisconsin Package. For more details on purchasing this driver, contact Genetics Computer Group at (608) 231-5200.

Configuration

To initialize GIF as your graphics configuration, type % gif. The computer prompts you for specific setup information. For example

Figure 5

Considerations

Fonts

By default, characters are drawn with font 1 (see Appendix I of the Program Manual).

Color

The GIF driver supports the following colors:

White, Black, Forest Green,
Blue, Red, Magenta,
Cyan, Purple, Orange Red,
Light Green, Green, Light Blue,
Violet Red, Yellow, Navy Blue, and
Yellow Green

Note that some GIF viewers allow you to edit colors.

Interlaced GIF

The GIF driver is capable of generating interlaced GIF files. Interlaced GIF files allow the image to load in waves, which is sometimes described as the venetian blind effect. This effect lets the web browser load the image in waves instead of waiting until the entire image is downloaded before displaying it. You can turn this option on by setting the symbol GIFInterlace to the value TRUE.

% symbol -s GIFInterlace TRUE

Supported Formats

GIF87a
GIF89a GIF89a version files are written with a comment extension indicating the file creation date and time.

HPGL (Hewlett Packard Graphics Language)

[ Previous | Top | Next ]

Configuration

To initialize HPGL as your graphics configuration, type % hpgl. The computer prompts you for specific setup information. For example

Figure 6

Considerations

Pen Speed

Most HPGL devices allow you to reduce the pen speed to give better color saturation and precision. You can do this with the command-line parameter -SPEed=number, where number ranges from 1.0 (slowest) to 10.0 (fastest). The lower the number, the higher the pen quality. The default is 10.0.

Connecting a Graphics Device to the Computer

If your answer to the prompt "To what port is your device connected" is term:, the Wisconsin Package expects that your plotter is connected in "eavesdrop" configuration. However, if you connect a graphics device to the terminal's printer port, you have connected your graphics device in "pass-through" configuration. You then must add the parameter -PASSthru to the command line to print to the device. You must set the graphics device's internal switches to expect pass-through configuration.

(For more information, see "Directing Graphic Output to the Terminal's Printer Port in Pass-Through Configuration" earlier in this chapter.)

Supported Devices

ColorPro The ColorPro plotter does not support eavesdrop configuration.
HP7470 To use the HP7470 with the Wisconsin Package, do the following:

- Set the paper switch to either A3 for 11 x 17 inch or A4 for 8.5 x 11 inch paper.

- Set the USA/Metric switch to USA.

- Set the Eavesdrop-Direct (Y-D) switch to Y, even if the plotter is attached to its own port.
HP7475 See HP7470 above.
HP7550 To use the HP7550 with the Wisconsin Package, do the following:

- Set Monitor mode to Off.

- Set Handshake to XON/XOFF.

- Set Eavesdrop-Standalone to Eavesdrop, even if the plotter is standing alone on a port.

- Set Remote-Local-Standby to Remote.

- Set Bypass to On.

The HP7550 measures the page size automatically when the paper is loaded.
HP7580 See HP7550 above.
ColorPro
LaserJet III

PNG (Portable Network Graphics)

[ Previous | Top | Next ]

The PNG driver enables you to produce graphics files that a web browser can display.

Configuration

To initialize PNG as your graphics configuration, type % png. The computer prompts you for specific setup information. For example

Figure 7

Considerations

Fonts

By default, characters are drawn with font 1 (see Appendix I of the Program Manual).

Color

The PNG driver supports the following colors:

White, Black, Forest Green,
Blue, Red, Magenta,
Cyan, Purple, Orange Red,
Light Green, Green, Light Blue,
Violet Red, Yellow, Navy Blue, and
Yellow Green

Interlaced PNG

The PNG driver is capable of generating interlaced PNG files. Interlaced PNG files allow the image to load in waves, which is sometimes described as the venetian blind effect. This effect lets the web browser load the image in waves instead of waiting until the entire image is downloaded before displaying it. You can turn this option on by setting the symbol PNGInterlace to the value TRUE.

% symbol -s PNGInterlace TRUE

PostScript

[ Previous | Top | Next ]

Configuration

To initialize PostScript as your graphics configuration, type % postscript. The computer prompts you for specific setup information. For example

Figure 8

Considerations

Page Size

If the dimensions of the page are not exactly 8.5 x 11 inches, the plot may not be centered correctly.

Paper Loading

Laser printers always feed their paper automatically. Therefore, Wisconsin Package programs do not prompt you to press <Return> when your device is ready. Thus, with laser printers the -AUTOFeed command-line parameter is unnecessary.

Also, the -NOUNLoad command-line parameter does not work with PostScript.

Printer Memory Requirements

Hewlett Packard and PostScript printers have minimum memory requirements to print PostScript graphics. HP LaserJet III and HP LaserJet IV printers with PostScript cartridges require 4.5 megabytes of memory. PostScript printers require 2.5 megabytes of memory.

Supported Programs

% lprint. Prints text files on a PostScript printer connected to a port with the logical name LPrintPort.

% red. Lets you format text to create publication-quality documents on a PostScript laser printer.

Supported Devices

LaserWriter To use the LaserWriter with the Wisconsin Package, do the following:

- Connect to a port on a terminal or to a VT220 printer port.

- Set switch 2 in the Switch Bank down to direct input to the RS-232 port instead of the AppleTalk network.
Lzr1200 To use the Dataproducts LZR1200 with the Wisconsin Package, connect it to a port or to a VT220 printer port.
LN03-ScriptWriter
LPS20
ColorScript-100

Metafile Formats

EPS When the computer prompts you for the name of the port to which your device that supports Encapsulated PostScript (EPS) is connected, respond with the name of the file you want to contain the black and white EPS instructions.
CEPS See EPS above. Instead of black and white, color EPS instructions are written to a file. In the absence of a GIF driver at your site, this format might be the best to use when transporting a graphic file from the computer running the Wisconsin Package to the Macintosh or PC.

ReGIS

[ Previous | Top | Next ]

Configuration

To initialize ReGIS as your graphics configuration, type % regis. The computer prompts you for specific setup information. For example

Figure 9

Considerations

Fonts

By default, characters are drawn with font 1 (see Appendix I of the Program Manual).

Supported Devices

VT240 The black and white VT240 uses brightness to emulate color. To reset the terminal's ASCII mode to full brightness when the plot is done, you must reset the local terminal Setup to Color for the Wisconsin Package VT240 language driver.
VT241
VT330 See VT240 above.
VT340

Sixel

[ Previous | Top | Next ]

Configuration

To initialize Sixel as your graphics configuration, type % sixel. The computer prompts you for specific setup information. For example

Figure 10

Considerations

Fonts

By default, characters are drawn with font 1 (see Appendix I of the Program Manual).

Form Feeds

The Sixel language driver puts a form feed in front of and behind the graphic output to ensure that it draws the graphic on a clean page.

Supported Devices

The resolution and speed of the following dot-matrix printers are poor, but they provide a way to preview Wisconsin Package graphics on relatively inexpensive and widely available printers.

LA100 If you use 80-column paper (8.5 x 11 inches or A4) instead of 132-column paper (11 x 17 inches) in the LA100 or LA200 printer, define your device as LA50 within the Sixel command. Otherwise, the plot is too large for the paper. When you define the LA100 or LA200 as an LA50, the graphics may appear slightly distorted because of a difference in aspect between pixels.
LA200 See LA100 above.
LA75
LA50

Tektronix

[ Previous | Top | Next ]

Configuration

To initialize Tektronix as your graphics configuration, type % tektronix. The computer prompts you for specific setup information. For example

Figure 11

Considerations

Fonts

The Wisconsin Package normally uses a device's default font for text in graphic output. This is the font you see when you use -FONT=0. However, no high-quality firmware character set font (font 0) is available for Tektronix 4014 devices. Therefore, unless you specify otherwise, characters are drawn with font 1 (see Appendix I of the Program Manual).

Graphic Display

Tektronix 4100- and 4200-series terminals, which use picture segments, cannot be cleared from the terminal keyboard. That is, after displaying graphic output for the first time during a session, subsequent graphic displays are drawn on top of existing ones. Therefore, to clear the graphics from these terminal screens, type % clearplot. This command draws an empty plot to clear the screen.

Terminal Emulators

For those accessing the Wisconsin Package through terminal emulation software, you may need to toggle between your graphics window and text window manually. If you are using SmarTerm or VersaTerm Pro, GCG provides the "SmarTerm-Tek4014" and "VersaTerm-Tek4105" supported devices to automatically open and close the graphics window for you.

Supported Devices

Tek 4107 This configuration works on most 4100- and 4200-series terminals.
Tek 4014 This configuration does not have good firmware fonts and does not support color. Also, after Wisconsin Package graphics programs complete, they do not automatically switch from graphics to interactive mode. However, the graphics language is fast.
GraphOn-Tek4014 GraphOn makes a line of Tektronix-emulation terminals (235, 250, 407). They emulate a VT200 terminal when they are not in graphics mode. Most GraphOn terminals work well if you select the GraphOn-Tek4014 device in the Tektronix language menu. More recent versions like the GraphOn 407HR plot well with the Tek4107 protocol; however, they emulate a VT100 when they are not in graphics mode (rather than a VT220).
VT340-Tek4014 This configuration plots color graphs. The colors may map incorrectly.
SmarTerm-Tek4014 Terminal emulation software. Wisconsin Package graphics programs plot directly to the Tektronix 4014 window without requiring you to toggle this window by pressing <Alt>V.
LN03 PLUS Digital Equipment Corporation laser printer.
VersaTerm Pro-
Tek4105
Terminal emulation software. Wisconsin Package graphics programs plot directly to the Tektronix 4105 window without requiring you to open a window from the VersaTerm Pro menu.

X Windows

[ Previous | Top | Next ]

Configuration

To initialize X Windows as your graphics configuration, type % xwindows. The computer prompts you for specific setup information. For example

Figure 12

Considerations

Multiple Windows

By default, the X Windows driver creates only one graphics window per user on a workstation. You can create additional windows by using command-line control to specify a unique window name by typing % xwindows workstation_type window_name, where workstation_type refers to a color or monochrome display and window_name sets a unique name for the window, for example % xwindows color fred. This name (fred) appears in the banner at the top of the window.

If you have multiple X Windows open and you want to direct output to a specific window, initialize the window by typing the same % xwindows command you used to set it up. For example, if you created a window with the command % xwindows fred, type that command to switch to that window for graphic display. If you have a second window you created with the command % xwindows Window2, type that command to switch to the second window.

Color Configuration

X Windows can display with a background color you specify. For color terminals, you can use command-line control to specify the color as an optional third parameter to the % xwindows command, for example

% xwindows color window_name bgcolor=color_name. Use the parameter bgcolor=color_name

where color_name equals one of the following:

White, Black, Green,
Blue, Red, Magenta,
Cyan, Purple, Orange Red,
Light Green, Forest Green, Light Blue,
Violet Red, Yellow, Navy Blue, and
Yellow Green

Note: Enclose color names that have two words in double quotation marks, for example bgcolor="light blue".

Note: Not all terminals are able to display all colors. X servers have a limit to the number of simulations they can display. If X Windows is unable to display the color you request, a default background color is chosen.

Also, note that graphical web browsers, such as Netscape, use many of the available colors on your X terminal. By closing Netscape or starting it with the -install option, you will improve the chance that X Windows will be able to display all of the colors listed.

Monochrome Configuration

X Windows can display with a background color you specify. For monochrome terminals, the background window color can be either black or white. To switch your current monochrome background, type % xwindows mono window_name bgcolor.

To switch back to the original background color, type % xwindows mono.

Fonts

By default, characters are drawn with font 1 (see Appendix I of the Program Manual).

X Window Buttons

Use any mouse button to select a button on the bottom of the XWindows graphics screen. Click on the "Zoom" button to zoom and pan on the graphics in the window. Click the "Restore" button to return the graphic to normal window size. Click "Exit" to close and exit the graphics window.

Figure 13

Supported Devices

X Windows terminal or workstation

Microcomputer running X server software

X Server Software

Macintosh recommendations. TCP/IP capability must be available on both the Macintosh computer and UNIX computer to which you are connecting. You can use MacTCP to invoke TCP/IP capability on the Macintosh. We recommend that any Macintosh used as an X server should have a minimum of 8 MB RAM and a 14-inch color monitor.

The Macintosh X server product we recommend for use with SeqLab, the graphical user interface to the Wisconsin Package, is eXodus. MacX has also been tested and confirmed to work with minor difficulties.

IBM PC recommendations. TCP/IP capability must be available on both the IBM PC and or UNIX computer to which you are connecting. You can use PC/TCP to invoke TCP/IP capability on the IBM PC. Make sure you check with the X server vendor before buying to determine the amount of memory, type of ethernet card, and network protocol specifics required for your specific setup. We recommend a fast video card, a color monitor (at least 14 inches), and a three-button mouse if you're using SeqLab, the graphical user interface to the Wisconsin Package. (Cutting and pasting is often difficult or impossible with a one- or two-button mouse.)

For IBM PC X server, we have used X-Win32 and eXcursion. Some additional X servers that have been used successfully by our customers (but that have not been tested by GCG) are eXodus and Exceed. If you use and like an X server product that is not on our list, please let us know so that we can pass on that recommendation.

Note: Discounts are available for a number of the X server software packages listed below. See GCG's web page (http://www.gcg.com) for participating vendors.

Also, the web site and e-mail addresses were compiled in August 1998. If you find that any of this information is out-of-date, contact GCG's technical support.

Macintosh Addresses
MacTCP Apple Computer, Inc.
Tel: 408-996-1010
http://www.apple.com
eXodus White Pine Software
Tel: 603-886-9050 (USA)
33 (0) 4 93 59 43 43 (Europe)
E-mail: info@wpine.com
http://www.wpine.com
MacX Apple Computer, Inc.
Tel: 408-996-1010
http://www.apple.com
Pathworks Digital Equipment Corp.
Tel: 800-344-4825
http://www.openvms.digital.
com
PC Addresses
PC/TCP FTP Software, Inc.
Tel: 800-282-4387
E-mail: sales@ftp.com
http://www.ftp.com
X-Win32 Starnet Communications Corporation
Tel: 408-739-0881
E-mail: support@starnet.com or sales@starnet.com
http://www.starnet.com
eXcursion Digital Equipment Corporation
Tel: 800-344-4825
http://www.windowsnt.digital.com
eXodus White Pine Software
Tel: 603-886-9050 (USA)
33 (0) 4 93 59 43 43 (Europe)
E-mail: info@wpine.com
http://www.wpine.com
Exceed Hummingbird Communications Ltd.
In USA:
Tel: 416-496-2200
E-mail: sales@hummingbird.com or support@hummingbird.com
http://www.hcl.com

In Europe:
Tel: 41 (22) 733 18 58
E-mail: swissales@hummingbird.com
http://www.hummingbird.com

Graphics Programs and Descriptions

[ Previous | Top | Next ]

The table below alphabetically lists each Wisconsin Package program producing graphic output and its description. For more information about these programs, see the Program Manual or Command-Line Summary.

Program Description
CodonPreference Finds regions of each reading frame in a DNA sequence that show either strong codon preference or unusual compositional bias in the third position of each codon.

This program locates protein coding regions, determines their reading frames, estimates the level of expression of a gene, and locates DNA sequencing errors.
DotPlot Produces a dot-plot with the output file from Compare and StemLoop. Creating a dot-plot is the best way to see all of the structures in common between two sequences or to visualize all of the repeated or inverted repeated structures in one sequence.
Figure Creates figures by including both graphics and text.
Frames Marks the places where potential start and stop codons occur, indicating the open reading frames of a nucleic acid sequence.
FrameSearch /PLOt Plots a histogram showing the number of sequence comparisons with each different score. This plot can help you judge which of the sequences in the FrameSearch output are significant.
GapShow Plots the distribution of gaps and similarities in an alignment created with Gap or BestFit.
GrowTree Constructs a phylogenetic tree from a distance matrix created by Distances.
HelicalWheel Plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions.
Isoelectric Plots the total positive and negative charges and the net charge of a protein as a function of pH.
MapPlot Displays restriction sites in a DNA molecule.
Moment Makes a contour plot of the helical hydrophobic moment of a peptide sequence.
PepPlot Plots protein secondary structure and hydrophobicity on one coordinated plot.
PileUp Creates a multiple sequence alignment from a group of related sequences by using progressive, pairwise alignments. It can also plot a tree that shows the clustering relationship used to create the alignment.
PAUPDisplay Provides a GCG interface to tree manipulation, diagnosis, and display options in PAUP (Phylogenetic Analysis Using Parsimony). Starting with a trees file that contains a sequence alignment and one or more trees reconstructed from this alignment (such as the output from PAUPSearch), you can plot the tree(s); compute the score of the tree(s) according to the criteria of parsimony, distance, or maximum likelihood; or calculate a consensus tree (two or more input trees). PAUPDisplay can also plot the trees from a GrowTree trees file.
PlasmidMap Draws a circular plot of a plasmid construct. It can display restriction patterns, inserts, and known genetic elements.
PlotFold Plots circles, p-num plot, domes, energy dotplot, mountains, and squiggles from the output file from MFold.
PlotSimilarity Plots the running average of the similarity among the sequences in a multiple sequence alignment.
PlotStructure Plots the measures of protein secondary structure in the output file from PeptideStructure.
PlotTest Plots a test pattern to see if your plotter is configured properly.
PrettyBox Displays a multiple sequence alignment as shaded boxes indicating areas of conservation.
Prime Creates a plot that can help you rapidly review the primer binding sites for the primers selected by the program.
StatPlot Plots a set of parallel curves from a table of numbers created by the Window program. The statistics in each column of the table are associated with some position in the analyzed sequence.
TestCode Plots a measure of the non-randomness of the composition at every third base of a DNA sequence. Helps identify genes when you do not have specific knowledge of codon preference.
WordSearch -PLOt Plots a histogram of the number of diagonals that have the largest number of short perfect matches by using a Wilbur and Lipman-style search.

[ Program Manual | User's Guide | Data Files | Databases ]


Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com

Copyright (c) 1982-2001 Genetics Computer Group, Inc. A subsidiary of Pharmacopeia, Inc. All rights reserved.

Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.

All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.

Genetics Computer Group

www.gcg.com