Appendix B. Preferences Manager

Table of Contents

Display Pages with
White Background

Generate Multiple
Sequence Alignments
in Color

Specify Graphics Size
for Results

Save Files Locally

Change Password

This appendix discusses the SeqWeb user preferences settings and explains how to use the Preferences Manager to change them.

About Preferences

Preferences are the settings that define your user environment when you are using SeqWeb. Each of the settings is explained below.

To verify or change your user preferences:

Click the Managers button in the top left SeqWeb frame.

The icons for the SeqWeb Managers display in the lower left frame.
Click the Preferences icon in the lower left frame.

The Preferences Manager window displays.

Display Pages with White Background

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Most web browsers allow you to specify a background color. However, the color you choose may affect the readability of SeqWeb pages. For this reason, SeqWeb sets the default backgound color to white, overriding your web browser's settings.

Note Results are always displayed with a white background.

To change the display page background setting:

Deselect the Display Pages with White Background checkbox.

SeqWeb will use your web browser's background color setting.
Click Update.

Color changes will take effect when pages are reloaded.

To reset the display page background setting to its SeqWeb default:

Select the Display Pages with White Background checkbox.
Click Update.

Color changes will take effect when pages are reloaded.

Generate Multiple Sequence Alignments in Color

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PileUp, GrowTree, and ProfileSearch create multiple sequence alignments where the bases or residues are represented by different colors. This display is useful for noting columns of aligned data that share the same color. For this reason, the SeqWeb default is to display multiple sequence alignments in color.

To change this setting:

Deselect the Generate Multiple Sequence Alignments in Color checkbox.
Click Update.

SeqWeb will display all residues and bases as black in sequence alignments.

To reset this setting to its SeqWeb default:

Select the Generate Multiple Sequence Alignments in Color checkbox.
Click Update.

SeqWeb will display residues and bases as different colors in sequence alignments.

See Interpreting Color in Results in the Results Manager chapter for more information about the use of color in SeqWeb results.

Note Sequence alignment color applies to results generated after the setting was changed.

Specify Graphics Size for Results

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For the programs that produce graphic results, you can specify the size of the graphics so they fit better within the display area of your monitor. The SeqWeb default is the medium graphics size.

To specify the size of the graphics in your results:

Choose one of the following under In Results, Display:
- Select Small Graphics if you have a low-resolution monitor (such as 640 x 480 display area).
- Select Medium Graphics if you have a medium-resolution monitor (such as 800 x 600 display area).
- Select Large Graphics if you have a high-resolution monitor (such as 1024 x 768 display area or higher).
  Graphics generated at this size will fill an 8.5" x 11" page when printed at 300 dpi in landscape mode.
Click Update.

A change to this setting takes effect immediately for newly generated results. Previously generated results will display according to the setting when they were generated.

Save Files Locally

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You can access SeqWeb via a web browser running on PC, Macintosh, and UNIX computers. Each of these platforms requires that you save files in a specific format that dictates how line breaks occur within the file. Files saved in one platform's format are often not usable on another platform.

To specify the appropriate format for saving files locally on your type of computer:

Choose one of the following under Save Files Locally:
- PC Format
- Mac Format
- UNIX Format
Click OK.

A change to this setting takes effect immediately.

Change Password

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SeqWeb logins require a password, which you may need or want to change periodically. (However, this option may be disabled by your SeqWeb Administrator.)

To change your password:

Select the checkbox next to Change Password.
Type a password in the New password text box.

To keep your password private, asterisks (*) appear in place of the letters or numbers you type.
Type your new password again in the New password (verify) text box to verify the spelling.
Click Update.

SeqWeb verifies the two passwords you specified. If there is a problem, SeqWeb displays a message at the top of the window to inform you. If there is not a problem, SeqWeb updates your password.

Your new password goes into effect immediately. As soon as you load another SeqWeb page, you'll be prompted to log in to SeqWeb again.