Main contents
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Main Contents
Vised help contents

Select an item from the list below to see the contents for that section.

Vised Basicis	Starting and exiting Vised, accessing menu commands, getting help, and definitions
Workplace	Fonts, keyboard, toolbar, status bar, scrolling, Vised windows, and menu
Editor	Working with documents, entering and editing data, working with sequences
Sequence analysis	Vised sequence analysis functions
Dialog boxes	Vised dialog box help
Information	Registration, distrubution, credits, about Vised (version info etc)


Definitions

Clipboard

Current sequence

Current position

Cursor

Editor window

Insert mode

Insertion point

Landscape

Menu

Overtype mode

Non-scrolling position line

Path

Scroll bar

Sequence block

Sequence name

Sequence number

Sequence type

Status bar

Title bar

Toolbar


Insert mode

An option for inserting typed characters into a sequence by moving existing characters down stream. You can select the insertion mode by pressing the INS key. When you select the Insert option, the letters "INS" appear in the status bar at the bottom of the Vised window.


Sequence name

The Sequence name appears to the left of each line of sequence data.  When you import a sequence from a disk file, the file name is used as a sequence name.


Sequence number

The sequence number appears to the left of the sequence name, and indicates the position of the sequence in the editor.


Sequence type

One letter code to the left ot the sequence name indicating the sequence type.  Sequence types may be 'N' for nucleic acids, 'P' for proteins, 'A' for alignment or 'U' for unassigned.


Caret

The caret is the flashing vertical line that indicates the current insertion point.


Cursor

The cursor is the mouse pointer.  Its shape depends on where on the screen the pointer is located.  For example, in the menu bar, the cursor is an arrow [image].  In the document window the cursor is an I-beam


Current sequence

The sequence that is currently active is the sequence that contains the caret.  All Vised commands that apply to individual sequences are applied to the current sequence.  The number of the current sequence is indicated on the Status bar after "Seq".


Current position

The current position is the position in the current sequence where the caret is located, and is the position where data is inserted.  Many Vised commands that apply to individual sequences are applied at the current position.  The current position number is indicated on the Status bar after "Pos".


Document window
Editor window

The window containing open sequences in an editor document.  Note that you cannot close the editor window.


Insertion point

Vertical blinking bar on the Vised screen that shows your current location and where data are inserted. The insertion point also determines where Vised will begin an action, such as translation or removing spaces.


Landscape

A term used to refer to horizontal page orientation; opposite of "portrait," or vertical, orientation.

Landscape

Portrait


Non-scrolling position line

The Non-scrolling position line is a position line displayed at the bottom of the screen.  It is primarily used to indicate what positions are on screen when there are too many sequences open to fit on the screen.


Overtype
Overtype mode

An option for replacing existing characters one by one as you type. You can select overtype by pressing the INS key. When you select the Overtype option, the letters "OVR" appear in the status bar at the bottom of the Vised window.


Path

Drive, directory, and filename. For example, the complete path for Vised might be C:\VISED\VISED.EXE.


Scroll bar

A graphical device for moving vertically and horizontally through a document with a mouse. Scroll bars are located at the right and bottom edges of the document window. You can display or hide scroll bars with the Horizontal Scroll Bar and Vertical Scroll Bar check boxes in the Options dialog box (Settings menu).


Sequence block

A veritical group of sequence lines.


Title bar

The horizontal bar at the top of a window that shows the name of the document or application that appears in that window.


Toolbar

A bar containing buttons that perform some of the most common commands in Vised, such as opening, saving, and printing files.  To display the Toolbar, select the Toolbar check box from options dialog box (Settings menu). You may need to enlarge the Vised window to the full width of the screen to see the entire Toolbar.


Statusbar

A line at the bottom of the Vised window that displays information about the current status of the document.


Menu

A list of commands that drops down from the menu bar. The menu bar is displayed across the top of the Vised window and lists the menu names, such as File and Edit.


Clipboard

A temporary storage area for cut or copied text or graphics. You can paste the contents of the Clipboard into any Vised sequence or into a file of another application, such as a word processor. The Clipboard holds the information until you cut or copy another piece of text.


Vised Basicis

Starting Vised

Exiting Vised

Accessing menu commands

Getting help

Definitions


Getting help

To view the Vised Help File from the editor, select 'Contents' from the Help Menu.  To search help topics, select 'Index' from the Help Menu.  To learn how to use Help, select 'Help on Help' from the Help Menu.

To get help within dialog boxes, click on the Help button.

Shortcut:

 Press the 'Help' icon on the tool bar.

 Press F1.


Accessing menu commands

Menu commands can be accessed with the mouse or with the keyboard.

 Mouse:

To access the menu with a mouse, position the pointer on the desired menu item and click the left mouse button once.  Items from drop down menus are selected in the same way.

 Keyboard:

To access the menu using the keyboard, press ALT and the underlined letter in the menu item name.  For example, to access the File menu, press ALT-F.  To select an item in a drop down menu, press the letter that is underlined in the item name, or use the arrow keys to select the desired item and then press ENTER.

Many menu commands have keyboard shortcuts.  When this is the case, the keystrokes are indicated beside the menu item in the dropdown menu.

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Related topics:

Menu

Keyboard


Exiting Vised

When you exit Vised, you will be prompted to save any changes you have made to Vised documents

To exit:

You can exit Vised through the Vised menu or the system menu, or by using a keyboard shortcut.

To exit Vised through the menu:

  1.  Select the File menu with the mouse or by typing ALT-F

  2.  Select exit from the File Menu with the mouse, or by typing X

To exit through the system menu:  Double click on the system menu box at the upper left hand corner of the main Vised Window.

To exit using the keyboard shortcut:,  Type ALT-F4


Starting Vised

You can start Vised from either Windows or the command prompt:

From the program manager:

To start Vised from the Windows Program Manager

  1.  Switch to the Program Manager window.

  2.  Open the group window that contains the Vised icon.

  3.  Do one of the following:

Double-click the Vised icon.

Use the arrow keys to select the Vised icon, and then press ENTER.

From the windows file menu

To start Vised from the Windows File menu

  1.  From the Program Manager File menu, choose Run.

  2.  Do one of the following:

If Vised is in your path, type Vised

If Vised is not in your path, type the path for Vised -- for example:

c:\Vised\Vised.exe

  3.  Choose the OK button.

From the DOS Command prompt

To start Vised from the command prompt

  1.  At the command prompt, type win Vised

  2.  Press ENTER.

Note: If a message appears stating that the command failed, the directory

containing Vised is not on your path. Change to the directory containing

VISED.EXE and try again.


Workplace

Menu

Editor toolbar

Pretty display  tool bar

Moving the insertion point

Scrolling through the editor

Status bar

Vised windows

Keyboard

Selecting fonts


Menu

The menu bar is located below the aplication title bar, along the top of the main window.  All Vised commands can be acessed through the menu bar.

To view all the commands in a menu, do one of the following:

 Click the menu name.

 Press ALT+n, where n is the underlined letter in the menu name. For example, press ALT+F to open the File menu.

Menu bar items:

File menu

Edit menu

Sequence menu

Options menu

Window menu

Help menu

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Accessing menu commands


File menu

Commands For Manipulating Files: Create, Open, Print And Save Files, And Exit.

New Document

Creates An New Vised Document.  All All Sequences In The Editor Window Are Discarded.  You Will Be Prompted To Save Changes, If Any.

Open Document

Opens An Vised Document That Has Already Been Saved To A Disk File.  Calls The Open File Dialog Box.

Save Document

Saves The Active Vised Document To A Disk.  Calls The Save As Dialog Box.  To Save The File Under Its Original Name, Just Press Enter.  If You Want To Save The File Under A New Name, Enter The Name In The File Name Edit Box Before You Press Enter.

Print Document

Prints the Editor Window.  Calls The Print Dialogbox.

Print Pretty Display

Prints The Contents of the Pretty display Window.

Exit

Exits Vised.  You Will Be Prompted To Save Documents That Have Been Changed Before Exiting.

Recent File List

A List Of The Last Four Files Saved Is Displayed At The Bottom Of The File Menu.  Selecting Any One Of These Files Causes That File To Be Opened.


Edit menu

Commands for editing: undo, cut, copy, paste, convert to upper or lower case, insert or remove spaces, and search.

Undo

Undoes the last change made in the editor.

Cut

Deletes selected (highlighted) sequence data from the current sequence and copies it to the clipboard.

Copy

Copies selected (highlighted) sequence data from the current sequence from the edit window, or a selection from the pretty display window, to the clipboard.

Paste

Copies information from the clipboard into the current sequence.  If sequence data is selected, Paste overwrites the selection with the data in the clipboard.  Otherwise, the data is inserted at the current position.

Remove spaces

Removes spaces deletes blanks from a sequence.  If sequence data is selected, spaces are removed from the selection only.  Otherwise, spaces are removed from the current position to the end of the sequence.

Insert spaces

Inserts a specified number of spaces at a given interval.  Calls the Insert Spaces dialog box.  If sequence data is selected, spaces are inserted into the selection only.  Otherwise, spaces are inserted from the current position to the end of the sequence.

Delete to end of seq

Deletes the sequence from the current position to the end of the sequence.

Upper case

Convert data to upper case characters

Lower case

Convert data to lower case characters

Find

Searches the current sequence for the next occurance of a text string.  Calls the Find dialog box.

Seacrh again

Repeats the last find operation.


Sequence menu

The Sequence menu contains commands that apply to both nucleotide (type N) and protein (Type P) sequences.

Create

Generates an empty sequence.  If too many sequences are already open, or if there is insufficient memory to create the sequence, an error message is displayed.

Import

Opens formated sequence file that has already been saved to a disk.  Calls the Import dialog box.  See Importing a sequence for supported formats.

Export

Saves the current sequence to a disk file.  Calls the Export dialog box.

Delete

Deletes the current sequence.  You will be prompted to save the sequence and given an opportunity to cancel the command.

Reverse

Causes a sequence to be written out the reverse orientation.  This command does not create a new sequence.

Complement

Creates a new sequence that is the complement of the current sequence.

Translate in frame

Creates a new sequence that is the translation product of the current sequence.

Translate all

Translate the sequence in all six frames.

Match

Identifies identical posistions in a sequence with the sequence above.  If sequence data is selected, the match is applied to the selected portion of the sequence only.  Otherwise, the match is applied from the current position to the end of the sequence.  Note that the sequences must have be the same type.

Pretty display

Displays all open sequences for formatted output.

Pattern search

Search the current sequence for a pattern using the prosite data base pattern syntax.


Options menu

Commands to set options for analysis functions, editor, individual sequences, and fonts.

Editor options

Set editor options.

Pretty display opitons

Set options used for Pretty display.

Sequence options

Sets the sequence name, type and position, and Display mode numbering options for the current sequence.  Calls the Sequence Info dialog box.

Title font

Set the font used in pretty display title.

Font

Set the font used in the editor and pretty display windows.


Window menu

Commands for manipulating Vised windows: tile, cascade, set active window.

Cascade

Arranges document windows in a cascaded format.

Tile

Arranges document windows in a tiled format.

Edit window

Brings the editor window to the foreground and makes it active.

Pretty display window

Brings the prettyt display window to the foreground and makes it active.


Help menu

Commands for displaying the help index, the help search dialog box, and the Vised About dialog box.

Contents

Displays the Vised Help File contents.

Search

Displays the Vised Help File Search dialog box.

Help on help

How to use help.

About Vised

Displays a copyright notice and information about Vised.


Toolbar
Editor toolbar

The tool bar is a collection of buttons displayed under the menu bar that you can use to accomplish common tasks quickly.  To use the tool bar, position the mouse cursor over the desired button and click the left mouse button.

Vised displays two tool bars, an editor tool bar that is displayed when the editor window is active, and a graph/data tool bar that is displayed when the graph or data window is active:

Editor tool bar

This tool bar is displayed when the editor window is active

Create file

Creates a new Vised file by clearing all currently open sequences.

Open file

Open an Vised file from a disk.

Save file

Save an Vised file to a disk.

Print file

Print the contents of the Editor window

Create sequence

Create a new blank sequence.

Import sequence

Import a sequence from a disk file.

Export sequence

Export a sequence to a disk file.

Delete sequence

Delete the current sequence.

Cut

Delete highlighted data from the current sequence and copy the data to the clipboard.

Copy

Copy highlighted data to the clipboard.

Paste

Insert data from the clipboard into the current position.

Undo

Undo the most recent edit.

Top of 1st sequence

Move the insertion point to position one of the first sequence.

Top of the current sequence

Move the insertion point to postion one of the current sequence.

End of the current sequence

Move the insertion point to the last position of the current sequence.

End of the largest sequence

Move the insertion point to the last position of the largest sequence.

Help

Veiw the help file contents.


Pretty display tool bar

This tool bar is displayed when the pretty display window is active.

Print

Print the contents of the active window.

Save

Save table or graph/map as picture

Options

Set analysis function options.

Font

Set the font for the current window.

Help

View the help file contents.


Moving the insertion point

To change the current position or current sequence, you must move the insertion point, which is shown by the caret.  You can move the caret using the keyboard or the mouse.  You can also scroll through the editor window without moving the current position.

To set the current position:

 With the mouse:

1.  Scroll to the desired location

2.  Position the cursor over the desired sequence position

3.  Click the left mouse button once.  The caret will move to the new position.

 With the keyboard:

To move:	Press:
One position down stream
One position up stream
Up one sequence
Down one sequence
Start of the current line	HOME
End of the current line	END
Start of the current sequence	CONTROL + HOME
End of the current sequence	CONTROL + END
Start of the 1st sequence	CONTROL + PAGEDOWN
End of the largest sequence	CONTROL + PAGEUP
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Related topics:

Scrolling through the editor


Scrolling through the editor

You can scroll through the editor window without changing the current positon using either the mouse or the keyboard.

To scroll through the editor

With the mouse:

Use the horizontal and vertical scroll bars, as illustrated below:

  With the keyboard:

To scroll:	Press:
up by one screen	PAGE UP
down by one screen	PAGE DOWN

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Related topics:

Moving the insertion point


Status bar

The Status bar is located at the bottom of the Vised window.  When the menu is active, the status bar displays a message descibing what the selected menu command does.  Otherwise, the contents of the status bar depend on what window is active.

Editor status bar

When the editor window is active, the status bar displays:

Current sequence

Indicates which of the sequences in the editor currently has the carret (the caret is the flashing vertical bar that indicates the inserion point).

Current position

Indicates the position of the caret in the current sequence.

Insertion mode

Indicates whether keystrokes will be inserted at the current position or will be typed over the existing data.

CAPS

Indicates the status of the caps lock key.  If the caps lock key is on, CAPS will be displayed.  Otherwise, this section will be blank.

Current genetic code

Indicates what genetic code is in use.  This may be either the standard genetic code or a user defined genetic code.


Vised windows

Vised displays either one or two windows at any given time:  the Editor window, and the pretty display window.  The Editor window is always open.  The pretty display window is shown when you select the pretty display function from the sequence menu..

Editor window

The editor window displays your sequence data  You will use the editor window to enter and edit data.  You will also use the editor as a launch pad for sequence analysis functions.  The editor window displays up to twenty sequences simultaneously, and also displays the sequence number, type and name.

Pretty display window

The pretty display window displays all of your sequences in user defined formats.  You cannot edit the data in the pretty display window.


Keyboard

Many commands can be executed more quickly using keyboard short cuts.  These are the key combinations you can press to execute menu commands.

Control Key combinations:

Press:	To:
Ctrl+N	Create a new document
Ctrl+O	Open an existing document from a disk file
Ctrl+S	Save the active document
Ctlr+P	Print the active document
Ctrl+X	Cut the selected data
Ctrl+C	Copy the selected data to the clipbord
Ctrl+V	Paste data from the clipboard to the current position
Ctrl+A	Create a new sequence
Ctrl+M	Import a sequence from a disk file
Ctrl+E	Export the current sequence to a disk file
Ctrl+D	Delete the current sequence
Ctrl + Home	Move to start of current sequence
Ctrl + End	Move to end of current sequence
Ctrl + Pageup	Move to start of first sequence
Ctrl + Pagedown	Move to end of largest sequence
Alt+BackSpace	Undo
Function Keys:

Key:	Command:
F1	Help contents
Shift+F1	Help search
F2	Remove spaces
Shift+F2	Insert spaces
Ctrl+F3	Delete to end of sequence
F3	Find
Shift+F3	Find again
Alt+F4	Exit Vised
F5	Match
Ctrl+F5	Pattern search
Alt+F5	Pretty display
F7	Translate in frame
Shift+F7	Translate all
Alt+F7	Reverse
Ctrl+F7	Complement
F10	Pretty display options
Shift+F10	Sequence options
Alt+F10	Editor options
F11	Editor font
Ctrl+F11	Title font


Selecting fonts

To set the font used in the editor and pretty display windows, select 'Font' from the options menu.  To set the font used in the pretty display title, select 'Title font' from  the options menu.  Both of these commands call the font dialog box.

Note:  The editor and pretty display windows use fixed pitch fonts only.


Editor

Documents

Creating a document

Opening an existing document

Saving a document

Printing documents

Editor options

Editing

Undo

Entering data

Editing data

Selecting data

Cutting sequence data

Copying sequence data

Pasting sequence data

Deleting to the end of a sequence

Removing spaces from a sequence

Inserting spaces into a sequence

Finding text

Sequences

Creating a sequence

Importing a sequence

Exporting a sequence

Moving a sequence

Sequence options: name,  type, and number


Creating a document

To Create a new document:

Select "New document" from the file menu.

Shortcut:

 Press the 'New document' icon on the tool bar.

Notes:

 If you have made changes to the current document, you will be prompted to save your work.

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Related topics:

Opening an existing document

Saving a document


Opening an existing document

To open an existing document, do the following:

 select 'Open' from the file menu.  This will open the File open dialog box

.

 In the File Name box, type or select the document you want to open.

 If the document you want to open is not listed in the File Name box, do one or more of the following:

--In the Drives box, select a new drive.

--In the Directories box, select a new directory.

--In the List Files Of Type box, select the type of document you want to open with its 3-character extension.

 Choose the OK button.

Shortcuts:

 Press the 'Open' icon on the tool bar.

 If the document was recently saved, you can open it by selecting the file name from the recent file list in the file menu.

Notes:

Vised will automatically recognize and import Macaw files.

You can see a list of all the files with a specific extension in a drive or directory with a specific extension. In the File Name box, type an asterisk (*), before a period (.) and the extension. For example, to see all the files with a .DAT extension in a directory, type *.DAT in the File Name box. To see all the files in a directory, type *.*

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Related topics:

Creating a document

Saving a document

File open dialog box


Saving a document

To Save a document, do the following:

 select 'Save' from the file menu.  This will open the File save dialog box.

 In the File Name box, type or select the document you want to Save.

 If the document you want to Save is not listed in the File Name box, do one or more of the following:

--In the Drives box, select a new drive.

--In the Directories box, select a new directory.

--In the List Files Of Type box, select the type of document you want to Save with its 3-character extension.

 Choose the OK button.

Shortcut:

 Press the 'Save' icon on the tool bar.

Notes:

You can see a list of all the files with a specific extension in a drive or directory with a specific extension. In the File Name box, type an asterisk (*), before a period (.) and the extension. For example, to see all the files with a .DAT extension in a directory, type *.DAT in the File Name box. To see all the files in a directory, type *.*

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Related topics:

Creating a document

Opening an existing document

File save dialog box


files
Printing documents

You can print the contents of the Editor and Pretty display windows.  The commands used to print are:

Window	Menu	Command
Editor window	File menu	Print document
Pretty display window	File menu	Print pretty display

To print a file:

1. Select the appropriate print command from the File menu as listed in the above table.  This will call the Print dialog box.

2. Select the desired numer of copies and print quality.

3. Press the Setup button if you wish to change the printer in use, or to set the paper size, source and orientation.  This will call the Print setup dialog box, shown below:

4. Press the OK button.

Cancelling a print job:

Printing takes place in two stages.  First the out put is sent to a print spooler, such as the Print manager that comes with MS Windows.  Then the print spooler sends the output to the printer.

While Vised is sending its output to the spooler, the "printing file" message box is displayed .  You can cancel the job by pressing Cancel in the message box,.

Once the file acutally starts to print, you must use the print manager to cancel the job.


Document options
Editor options

You can set editor options to change the appearance of the editor, or to determine what genetic code is used in the translation of nucleic acid sequences.

The editor options are:

Line length:  Sets the number of characters displayed on each line.  The line length must be an even mutlple of 10, and may not be greater than 250.

Name field width:  Sets the number of characters displayed of the name of each sequence.  The name field width may be any number bewteen 0 and 16.  If the name field width is less than the number of characters in the name of a sequence, the name is truncated.

Genetic code:  You may choose to use the standard genetic code, or a user defined genetic code to translate your Nucleic acid sequences.  You can edit the user defined genetic code by pressing the button labeled "Edit user defined code".

To set the editor options:

1. Select Editor options from the options menu.

2. Enter the desired options.

3. Press the OK button.

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Related topics:

Selecting fonts

Editor options dialog box


Creating a sequence

To Create a new sequence:

 select "Create" from the sequence menu.

Shortcut:

 Press the 'Create sequence' icon on the tool bar.

Notes:

 The newly created sequence is type "U" (Unassigned).

 If there are too many sequences open, an error message is displayed (the maximum number of sequences is 30).

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Related topics:

Sequence options: name,  type, and number

Importing a sequence


Importing a sequence

Vised automatically detects and reads sequences in a variety of formats.  If the format is not recoginzed, Vised reads in the whole file, including information that may not be part of the sequence.  If this happens, you can remove the extraneous information using the editor.

Currently, Vised recognizes sequence data in the following formats:

DNAStrider	NBRF
EMBL	Olsen
Fitch	Pearson/Fasta
GCG	PIR/CODATA
GenBank/GB	Plain/Raw
IG/Stanford	Zuker

To import an existing sequence:

 select 'Import' from the sequence menu.  This will open the Import Ascii File dialog box.

 In the File Name box, type or select the sequence you want to import.

 If the sequence you want to import is not listed in the File Name box, do one or more of the following:

--In the Drives box, select a new drive.

--In the Directories box, select a new directory.

--In the List Files Of Type box, select the type of file you want to open with its 3-character extension.

 Choose the OK button.

Shortcut:

 Press the 'Import' icon on the tool bar.

Notes:

You can see a list of all the files with a specific extension in a drive or directory with a specific extension. In the File Name box, type an asterisk (*), before a period (.) and the extension. For example, to see all the files with a .DAT extension in a directory, type *.DAT in the File Name box. To see all the files in a directory, type *.*

If the file name specifies a library (a file that contains more than one sequence), the Select sequence dialog box will be called.  This dialog box alows you to select which sequence you wish to import from the library.  Note that this alows you to import individual sequences from Vised files, as well as sequences from libraries in any of the formats listed above.

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Related topics:

Creating a sequence

File open dialog box

Select sequence dialog box.


Exporting a sequence

To Export a sequence:

 select 'Export' from the sequence menu.  This will open the Export Ascii File dialog box.

 In the File Name box, type or select the sequence you want to Export.

 If the sequence you want to Export is not listed in the File Name box, do one or more of the following:

--In the Drives box, select a new drive.

--In the Directories box, select a new directory.

--In the File format box, select the sequence format you want.

  Supported formats are:

DNAStrider	NBRF
EMBL	IG/Stanford
Fitch	Pearson/Fasta
GCG	PIR/CODATA
GenBank/GB	Plain/Raw
 Choose the OK button.

Shortcut:

 Press the 'Export' icon on the tool bar.

Notes:

You can see a list of all the files with a specific extension in a drive or directory with a specific extension. In the File Name box, type an asterisk (*), before a period (.) and the extension. For example, to see all the files with a .DAT extension in a directory, type *.DAT in the File Name box. To see all the files in a directory, type *.*

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Related topics:

File save dialog box


Moving a sequence

The sequence postion is indicated by a number to the right of the sequence name in Edit Mode.

To change the sequence order:

 Open the Sequence Info dialog box by selecting 'Sequence Options' from the sequence menu or by double clicking on the name field of the sequence you wish to move.

 Enter a new position for the sequence in the Number edit box to the left of the sequence name.

Shortcut:

 Use the mouse to click on the name field of the sequence you wish to move and drag it to the new position.  A black box will appear around the sequence that is being moved, as shown below:

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Related topics:

Sequence options: name,  type, and number

Sequence options dialog box


Sequence options: name, type, and number

Options for each sequence are:

Name:  The sequence name can be any combination of characters, up to 16 characters total.  When you import a sequence from a disk file, the file name is automatically used as the seqence name.

Type:  Sequences may be type 'N' for nucleic acids, 'P' for protein, 'A' for alignment, or 'U' for unclassified.  The sequence analysis fuctions available for a given sequence depend on the sequence type.

Number:  This option specifies the position of the sequence in the editor.  For example, entering a 3 in this edit field will cause the sequence to be moved to the third position.  Note that the number you enter must not be greater than the total number of sequences open.

To set the options for a given sequence:

1. Position the caret in the sequence whose option you wish to change

2. Select Sequence options from the options menu

3. Enter the desired options in the sequence options dialog box.

4. Press the OK button.

Short cut:  Position the cursor over the sequence name or number and Double click the mouse left button to call the sequence options dialog box.


Undoing mistakes
Undo

You can undo an error in the editor using the Undo command in the edit menu.  This command reverses the most recent edit.

To undo the most recent edit:

Select undo from the edit menu

shortcuts:

   Press Alt+Backspace.

Press the undo button on the toolbar


Entering data

When you start Vised, a single type 'N' sequence is created, and the insertion point, or caret, is positioned at position 1, ready to receive your typed data.

To enter sequence data from the key board, position the caret within the desired sequence.  Data can be entered from the keyboard in either insert mode or typeover mode:

Insert mode:  Keystrokes are inserted into the sequence at the current position, and the characters downstream from the current position are moved to the right to make room for the insertion.

Typeover mode:  Typed characters displace the characters already present.

Notes:

If any data is highligted, typing replaces the highlighted data regardless of insertion mode.

You cannot enter data after the end of sequence marker.  If you attempt to do so, an error message will be displayed.

______________

Related topics:

Editing data

Selecting data


Selecting data

Selected (highlighted) data appears as white characters on a black background.  You can select data using the mouse or the keyboard.

 With the mouse:

To select part of the sequence:

1. Place the cursor over the desired selection start point.

2. Click the left mouse button and hold it down.

3. Drag the cursor to the desired end point.

Note: If you drag the mouse outside of the editor window, the window will be scrolled.

To select all of a sequence:

1. Place the cursor over the desired sequence.

2. Double click the left button.

 With the keyboard:

1. Position the caret at the point where you wish the selection to begin.

2. Hold down the shift key, and press the arrow keys to extend the selection in the desired direction.


Editing data

Data may be cut, copied, pasted or deleted, just as text is in a word processor.  You can also use the commands in the edit menu to remove or insert spaces in the sequence, convert the sequence to upper or lower case, or delete to the end of the sequence.  If you make an error when editing your data, immediately select undo from the edit menu, or press the undo icon on the toolbar.

Note:  You cannot edit beyond the end of sequence marker.  If you try to do so, an error message will be displayed.

For step by step instructions on specific editing tasks, view the help topics listed below:

Undo

Entering data

Selecting data

Cutting sequence data

Copying sequence data

Pasting sequence data

Deleting to the end of a sequence

Removing spaces from a sequence

Inserting spaces into a sequence


Cutting sequence data

To cut data from the current sequence use the mouse to select the data that you wish to cut.  Then select 'Cut' from the edit menu.

Shortcut:

 Press the 'Cut' icon on the tool bar.

Note:

 If no data is selected, the 'Cut' command in the edit menu is disabled (grayed)

______________

Related topics:

Selecting data

Copying sequence data

Pasting sequence data


Copying sequence data

To copy data to the clipboard:

1. Use the mouse to select the data that you wish to copy.

2. Then select 'Copy' from the edit menu.

Shortcut:

 Press the 'Copy' icon on the tool bar.

Note:

 If no data is selected, the 'Copy' command in the edit menu is disabled (grayed)

______________

Related topics:

Selecting data

Cutting sequence data

Pasting sequence data


Pasting sequence data

To paste data from the clipboard into a sequence:

1. Position the caret at the point in the sequence where you would like to insert the data.

2. Select 'Paste' from the edit menu

Shortcut:

 Press the 'Paste' icon on the toolbar.

Notes:

 If no data in the target sequence is selected (highlighted), pasting will cause the data in the clipboard to be inserted into the sequence at the current position.

 If data in the target sequence is selected, pasting will cause the data in the clipboard to replace the highlighted data.

 If the clipboard is empty, the 'Paste' comand in the edit menu is disabled (grayed).

______________

Related topics:

Selecting data

Cutting sequence data

Copying sequence data


Deleting to the end of a sequence

To delete to the end of a sequence:

1. Position the caret at the point you wish to delete from.

2. Select 'Delete to end of seq' from the edit menu.

Note:

 If the caret is positioned beyond the end of the sequence, an error message is displayed.


Removing spaces from a sequence

To remove spaces from a sequence:

1. Position the caret at the point in the sequence where you want the removal of spaces to start.

2. Select 'Remove spaces' from the edit menu.

Notes:

 If no data is selected (highlighted), spaces will be removed from the current position to the end of the sequence.  Spaces located at positions upstream from the current position will not be removed.

 If data is selected, spaces will be removed from the highlighted portion of the sequence.  Spaces will not be removed from the unhighlighted portions of the sequence.

______________

Related topics:

Selecting data


Inserting spaces into a sequence

To insert spaces into a sequence:

1. Position the caret at the point in the sequence where you want the insertion of spaces to start.

2. Select 'Insert spaces' from the edit menu.

3. Enter the frequency of insertion and the number of spaces to insert in the Insert spaces dialog box.

4. Press the OK button.

Notes:

 If no data is selected (highlighted), spaces will be inserted from the current position to the end of the sequence.  Spaces will not be inserted at positions upstream from the current position.

 If data is selected, spaces will be inserted into the highlighted portion of the sequence only.  Spaces will not be inserted into the unhighlighted portions of the sequence.

______________

Related topics:

Selecting data

Insert spaces dialog box.


Finding text

You can search your sequence data for short substrings as follows:

1. Position the caret at the point where you wish to search from.

2. Select Find from the edit menu.  This will call the Find dialog box.

3. Enter the desired string in the 'Find what' field.

4. Select the 'Match case' and 'Search up' or 'Search down' options as desired.

4. Press the OK button.

Notes

If the string is found in the data, the editor will scroll to the position of the string, and the string will be selected.

To repeat a search without using the Find dialog box, select Search again from the edit menu, or press Shift+F3


Sequence analysis

Reverse

Complement

Translate in frame

Translate all

Match

Pretty display

Pattern Search


Reversing a sequence
Reverse

Reversing causes a sequence to be written out backwards.

To reverse a sequence:

1. Position the caret in the sequence you wish to reverse.

2. Select 'Reverse' from the sequence menu.

Note:

 Only nucleotide sequences (type 'N') can be reversed.  Reversing other sequence types causes an error message to be displayed.

______________

Related topics:

Sequence options: name, type, and number


Complementing a sequence
Complement

Creates a new sequence that is the complement of the current sequence.

To complement a sequence:

1. Position the caret in the sequence you wish to complement.

2. Select 'Complement' from the sequence menu.

Notes:

 Only nucleotide sequences (type 'N') can be reversed.  Complementing other sequence types causes an error message to be displayed.

 Only the nucleotides A, G, T, C, U, R and Y are complemented.  All other characters are copied into the new sequence without change.

 If no data in the current sequence is selected, complementation begins at the current position and continues to the end of the sequence.

 If data in the current sequence is selected, complementation extends along the length of the selection only.

 If there are too many sequences open to create the new sequence, an error message is displayed.


Translate in frame

Translate in frame predicts an amino acid sequence in the reading frame starting at the current position, or at the begining of the current selection.  The function creates a new protein sequence, containing the translation product shown below the translated sequence.

To translate in frame:

1. Position the caret in the sequence you wish to translate.

2. Select 'Translate in frame' from the sequence menu.

Setting the genetic code:

You may choose to use the universal genetic code or a user defined genetic code that you can edit.  To set genetic code options, select Editor options from the Options menu, then choose from the following:

Universal: Use the standard genetic code

User defined: Use the user defined genetic code.

Edit user defined code:  Calls the edit genetic code dialog box.

Notes:

This function applies to type 'N' (nucleic acid) sequences  only.  If you attempt to apply this fuction to other sequence types, an error message will be displayed.

 If no data in the current sequence is selected, translation begins at the current position and continues to the end of the sequence.

 If data in the current sequence is selected, translation extends along the length of the selection only.

______________

Related topics:

Translate all

Selecting data


Translate all six frames
Translate all

This function creates six new protein sequences, one for each reading frame.  The forward translation products are shown above the translated sequence, and are give names starting with a plus sign.  The reverse translation products are shown below the translated sequence, and are give names starting with a minus sign.

To translate all six frames:

1. Posistion the caret in the sequence you wish to translate.

2. Select 'Translate all' from the sequence menu..

Setting the genetic code:

You may choose to use the universal genetic code or a user defined genetic code that you can edit.  To set genetic code options, select Editor options from the Options menu, then choose from the following:

Universal: Use the standard genetic code

User defined: Use the user defined genetic code.

Edit user defined code:  Calls the edit genetic code dialog box.

Notes:

This function applies to type 'N' (nucleic acid) sequences  only.  If you attempt to apply this fuction to other sequence types, an error message will be displayed.

This function is applied to the whole sequence regardless of data selection.

______________

Related topics:

Translate in frame


Pretty display

Pretty display is intended to provide you with a flexible way of displaying the sequences in the editor.  When you select Pretty display, all of the sequences in the editor are included.  So if you want to display just one sequence, you will have to delete all the other open sequences before you select pretty display.

How to:  To display your sequences with pretty display:

1. Make sure that only the sequences you want to display are open in the editor.

2. Select Pretty display from the sequence menu

To set display options:

1. Select Pretty display options from the options menu.  This calls the Pretty display options dialog box.

2. Choose from the following options:

Line length:  The number of characters to display on each line.

Name field:  The number of characters from the sequence names to display. For example, if the Name field is set to 8, only the first 8 characters of each sequences name is displayed.

Vert. spaces:  The number of veritical spaces to place between groups of lines.

Space every:  Displays the sequence in groups of n characters.  For example, if Space every is set to 10, a space in inserted after every 10th charater.

Box identities:  Draws boxes around each sequence character that is identical to the character in the same position in the first sequence.  Note that this option only applies to the display of more than one sequence.  The Space every option is ignored when Box identities is selected

Numbers:  Determines the placement of sequence numbering.  The options are:

None:  No numbers are displayed.

Left:  Numbers are displayed to the left of the sequence.  Note: The sequence names are not displayed when this option is choosen.

Right:  Numbers are displayed to the right of the sequence.

Top:  Numbers are displayed above the sequence.

Bottom:  Numbers are displayed below the sequence.

4. Press the OK button

Notes:

This function is applied to all sequences currently open in the editor.

 The start and end point values are not used for this function.

You can copy from the pretty display window.  Position the mouse at the point you want to start at.  Click the left mouse button and hold it down while you move the mouse.  This will draw a box.  Release the left button and select copy from the edit menu.  You can then paste the selection into your drawing program or word processor.


Pattern Search

Pattern Search alows you to search both nucleotide and amino acid sequences for patterns using the prosite data base syntax.  The results of the search are displayed as a map in the graph window and as a table in the data window.  In addition, the sites are highlighted on the sequence in the editor.

To search for a pattern:

1. Position the caret in the sequence you wish to search.

2. Select Pattern search from the Edit menu.

3. Enter a pattern in the Pattern search dialog box.

4. Press the OK button.

Pattern syntax:

Pattern search uses the prosite data base pattern syntax as specified in the prosite database (Bairoch A., Bucher P., PROSITE: recent developments. Nucleic Acids Res. 22:3583-3589(1994)).

The patterns are described using the following conventions:

The standard IUPAC one-letter codes for the amino acids are used.

The symbol `x' is used for a position where any amino acid is accepted.

Ambiguities are  indicated by  listing the acceptable amino acids for a given position,  between square  parentheses `[  ]'. For example: [ALT] stands for Ala or Leu or Thr.

Ambiguities are  also indicated  by listing between a pair of curly brackets `{  }' the  amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.

Each element in a pattern is separated from its neighbor by a `-'.

Repetition of  an element  of the pattern can be indicated by following that element  with a  numerical value  or  a  numerical  range  between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.

When a  pattern is  restricted to  either the  N- or  C-terminal  of  a sequence, that  pattern either starts with a `<' symbol or respectively ends with a `>' symbol.

Examples:

[AC]-x-V-x(4)-{ED}.

This pattern  is translated  as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}

<A-x-[ST](2)-x(0,1)-V.

This pattern,  which must  be in  the N-terminal of the sequence (`<'), is translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val


Matching two sequences

Matching is used to identify data points in a sequence that are identical to the same data points at the same position in the sequence imediately above it.  Identical elements are connected by a vertical line.

For example, matching the sequence ATGACGA with the sequence ATGGATA results in a match that looks like this:

To match data from the current sequence with the sequence above, select 'Match' from the sequence menu.

Shortcuts:

 Press the 'Match' icon on the tool bar.

 Type the keys <CTRL>-M

Notes:

 If no data in the current sequence is selected, the match extends from the current position to the end of the current sequence or the end of the sequence above, whichever is smaller.

 If data in the current sequence is selected, the match extends along the length of the selection only.

 If there is no sequence above the current sequence, or if there are too many sequences open, an error message is displayed.

______________

Related topics:

Selecting data


Dialog boxes

Edit genetic code

Editor options

File open

File save

Find

Fonts

Insert spaces

Pretty display options dialog box

Pattern search

Print setup

Print

Sequence options

Select sequence


Edit genetic code
Edit genetic code dialog box

This dialog box is used to edit the user defined genetic code:

Enter code:

Codon:  Displays the current codon.

Three letter code:  Enter the three letter code for the residue you wish to associate with the current codon.

One letter code:  Enter the one letter code for the residue  you wish to associate with the current codon.

Scroll bar: Sets the current codon.  Use the scroll bar to scroll through the availble codons.

Codes:

Lists the standard three and one letter codes for reference purposes.

______________

Related topics:

Editor options

Translate in frame

Translate all


Editor options
Editor options dialog box

Use this dialog box to set editor options to change the appearance of the editor, or to determine what genetic code is used in the translation of nucleic acid sequences.  The editor options are:

Lines:

Line length:  Sets the number of characters displayed on each line.  The line length must be an even mutlple of 10, and may not be greater than 250.

Name field width:  Sets the number of characters displayed of the name of each sequence.  The name field width may be any number bewteen 0 and 16.  If the name field width is less than the number of characters in the name of a sequence, the name is truncated.

Non-scrolling position line:

Always on:  Non-scrolling position line  displayed at all times.

Always off:  Non-scrolling position line of at all times.

On when screen full:  Non-scrolling position line  line displayed only when there are too many sequences to fit on the screen.

Genetic code:

Universal:  Use the universal genetic code for translation of DNA sequences.

User defined:  Use the user defined genetic code for translation of DNA sequences.

Edit user defined code:  Calls the edit genetic code dialog box.  Alows you to edit the genetic code used when the user defined option is selected.

______________

Related topics:

Editor options


File open
File open dialog box

This dialog box alows you to specify the name and path of a file to open.

File Name

Type or select the filename you want to open.

Files list

This box lists files with the extension you select in the List Files Of Type box.  Click once on a file name in this box to place the file in the file name box.  Click twice to open the file.

Note: To see a list of files with a particular extension, type an asterisk (*), a period, and the three-character extension in the File name box. For example, if you want to see all files with a .TXT extension in a directory, type *.txt.

List Files Of Type

Select the type of file you want to open.

Drives

Select the drive that has the file that you want to open.

Directories

Select the directory that has the file that you want to open.

OK button:  Opens the file in the file name box.  If the file name in the name box is not complete, the OK button is ignored.

Cancel button:  Closes the dialog box without opening the file.

______________

Related topics:

Opening an existing document

Importing a sequence


Pretty display options dialog box

Title:

Sets the title displayed at the top of the pretty display window.

Line length:

The number of characters to display on each line.

Name field:

The number of characters from the sequence names to display. For example, if the Name field is set to 8, only the first 8 characters of each sequences name is displayed.

Vert. spaces:

The number of veritical spaces to place between groups of lines.

Space every:

Displays the sequence in groups of n characters.  For example, if Space every is set to 10, a space in inserted after every 10th charater.

Box identities:

Draws boxes around each sequence character that is identical to the character in the same position in the first sequence.  Note that this option only applies to the display of more than one sequence.  The Space every option is ignored when Box identities is selected

Numbers:

Determines the placement of sequence numbering.  The options are:

None:  No numbers are displayed.

Left:  Numbers are displayed to the left of the sequence.  Note: The sequence names are not displayed when this option is choosen.

Right:  Numbers are displayed to the right of the sequence.

Top:  Numbers are displayed above the sequence.

Bottom:  Numbers are displayed below the sequence.


File save
File save dialog box

This dialog box alows you to specify the name and path of a file to save.

File Name

Type or select the filename you want to save.

Files list

This box lists files with the extension you select in the List Files Of Type box.  Click once on a file name in this box to place the file in the file name box.  Click twice to save the file.

Note: To see a list of files with a particular extension, type an asterisk (*), a period, and the three-character extension in the File name box. For example, if you want to see all files with a .TXT extension in a directory, type *.txt.

List Files Of Type

Select the format that you want the file to be saved under.

Drives

Select the drive that you want the file to be saved to.

Directories

Select the directory that you want the file to be saved to.

OK button

Saves the file in the file name box.  If the file name in the name box is not complete, the OK button is ignored.

Cancel button

Closes the dialog box without opening the file.

______________

Related topics:

Exporting a sequence

Saving a document


Fonts
Fonts dialog box

This dialog box alows you to set a font for a given window or for the title displayed in the graph window.

Font

The name of the font.  You can type the name in the font edit box, or you can select a font from the font list box by clicking on it with the left mouse button.

Font Style

The style of the font.  You can type the style in the font style edit box, or you can select a style from the style list box by clicking on it with the left mouse button.

Size

The size of the font.  You can type the size in the font size edit box, or you can select a size from the font size list box by clicking on it with the left mouse button.

Sample

Displays a sample of what your selected font will look like.

______________

Related topics:

Selecting fonts


Pattern search dialog box

This dialog box alows you to enter the pattern you wish to search the current sequence with.

Pattern:  Enter the search pattern using the prosite data base syntax (see Pattern search).  To choose a  recently used pattern, press the down arrow, select the desired pattern with the mouse and press OK.

______________

Related topics:

Pattern search.


Select sequence dialog box

This dialog box alows you to select a sequence to be imported from a library.

Sequence information:

Lib:  Name of the library file.

Format:  Format of the library file.

Number of sequences:  Number of sequences in the file.

Selected seq:  The currently selected sequence.

Sequence list:

Lists the sequences in the library.  To select a sequence to import, scroll the list until the desired sequence name is visible, click on the sequence name with the mouse and press OK.

______________

Related topics:

Importing sequences.


Print
Print dialog box

This dialog sets basic printer options.

Printer

Displays the currently selected printer.

Print Range

All: Print the whole document, table or graph.

Selection:  Print the selected parts of the document only.

Pages:  Print the specified pages only.

Print Quality

Sets the printer resolution.

Copies

Sets the number of copies to print.

Collate copies

Sort copies.

Setup

Calls the Print setup dialog box.  Selects the printer and sets printer options.

______________

Related topics:

Printing

Print setup dialog box.


Print setup

Use this dialog box to specify printer settings for your printer.

Printer

Default Printer:  Use the printer that you defined as the default printer from the windows control panel.

Specific Printer:  Select a printer other than the default.  Note: you must install printers from the windows control panel before you can select them with this dialog box.

Orientation

Portrait:  Print using the portrait orientation (height is greater than width).

Landscape:  Print using the landscape orientation (height is greater than width).

Paper

Size:  Select the size of the paper used.

Source: Select the source of the paper for printers that use more than one source.

Options

Specify other, printer specific options.

______________

Related topics:

Print dialog box

Printing


Sequence options

This dialog box alows you to change options that apply to the current sequence only.

Name

Displays the sequence name.  You can enter a name of up to 15 characters.  Note that the name may be truncated on the screen if the name field width is set to less than 15.

Number

Displays the sequence postion on the screen.  Entering a new postion will cause the sequence postion to change.

Sequence type

To set the sequence type, click on the option you want.

______________

Related topics:

Sequence options: name,  type, and number


Insert spaces

This dialog box alows you to insert spaces into a sequence in a regular pattern.  Any existing spaces are first removed from the sequence before the new spacing is applied.

Insertion interval

Displays how often spaces are to be inserted.

Number of spaces:

Displays how many spaces are to be inserted.

Example:   If you enter an insertion interval of three, and Number of spaces of two, two spaces will be inserted between every third character.

______________

Related topics:

Inserting spaces into a sequence

Removing spaces from a sequence


Find

Use this command to search for specified text in the current sequence.

Find What

Type the text you want to find, or paste it from the Clipboard (CTRL+V).

Match Case

Select this option to find only those occurrences with the combination of uppercase and lowercase letters specified in the Find What box.

Direction

Up:  Searches from the insertion point or the end of the selection to the beginning of sequence.

Down:  Searches from the insertion point or the beginning of the selection to the end of the sequence.


Information

Registration

Software Distribution and Licensing Information

Credits

About Vised


Registration

Vised is ShareWare

Vised is "ShareWare".  This entitles you, the customer, to try out the software for up to 30 days without obligation to pay for it.

Shareware (non-registered) Vised is a "full" version.  This means that the same capabilities available in the registered software are present in the non-registered software.  In fact, the non-registered software includes a bonus feature - the shareware nag box

If you use Vised beyond the 30 days, you should register it.  Registration entitles you to free upgrades to the software, which is nice.

How Much Does It Cost To Register?

Registering Vised costs you only $30.00 US.  If you are part of an organization and wish to use several copies, greatly reduced site licensing rates are also available.

How To Register

To register, please print out a registration form and send it to:

Ken Peters

487, Aquila Place

Parksville, BC

Canada.

V9P 1C1

Before you register, please take a look at the Licensing section of this help file.

Unlocking the Software

You will receive a notification of registration  which contains your personal registration name and number.

First, bring up the Reigistration Dialog by first invoking About dialog box, then clicking on the Register button.

Enter your name in the registration dialog.  Be sure to type your name exactly as it appears in your notification, as capitalization, spaces and punctuation are all taken into account when computing your registration number.

Now enter your personal registration number, and select Register  If all is well, Vised will respond with a message thanking you for your registration.  Otherwise Vised will complain that your name and number don't match, and you will have to correct the information.


Software Distribution and Licensing Information

Distribution

This shareware software may be freely distributed, provided that:

(1)	Such distribution includes only the original archive.  You may not alter, delete or add any files in the distribution archive.

(2)	The distrubution does not include a registration number.  In particular, you may not distrubute a registered version of Vised.

(3)	 No money is charged to the person receiving the software, beyond reasonable cost of packaging and other overhead.

License

By receiving and/or using Vised, you accept the following Evaluation and Registered User Agreement.  This agreement is a binding legal agreement.  If you do not intend to honor this agreement, remove Vised from your computer now.

Evaluation (Unregistered) and Registered User Agreement

You may evaluate the Shareware program for maximum of thirty calendar days, after which you must register the program, or remove the software from your computer.

All parts of Vised are copyright protected.  No program, code, part, image, video clip, audio sample, text or computer generated sequence of images may be copied or used in any way by the user except as intended within the bounds of the single user program.

The evaluator/user/buyer/owner of Vised will indemnify, hold harmless, and defend the author of Vised against lawsuits, claims, costs associated with defense or accusations that result from the use of Vised software.

The author of  Vised is not responsible for any damages whatsoever, including loss of information, interruption of business, personal injury and/or any damage or consequential damage without limitation, incurred before, during or after the use of our products.  Our entire liability, without exception, is limited to the customers' reimbursement of the purchase price of the software.

Each registered copy of Vised may be used in only one single location.  Use of the software means that you have loaded the program and run it or have installed the program onto a computer.  If you install registered copies of the software onto a multi-user platform or network, each and every individual user of the software must be registered separately.

You may make one copy of the registered software for backup purposes, providing you only have one copy installed on one computer.

The sale of and or distribution of registered copies of this software is strictly forbidden.  It is a violation of this agreement to loan, rent, lease, borrow, or transfer the use of registered copies Vised.


Credits

Vised uses sequence import and export functions from Readseq (c) 1990 by Don Gilbert.  Thank you, Don for making those functions public!

The multi-sequence editor format used by Vised was inspired by the DOS program, esee, by Eric Cabot.


About Vised

About the author:

I have a Ph.D. in genetics from the University of British Columbia.  About Three years ago, I decided to stay home with my kids.  In order to keep myself from going crazy, I taught myself how to program and wrote this and several other pieces of software.  I am open to job offers...

How to contact the author:

e-mail:  kpeters@qb.island.net

Version history:

Version 1.0 - May 1996.

-Initial release.

Version 1.0a - July 1996.

-Fixed file open bug that caused vised to crash when the file contained too many sequences.

-Increased number of sequences from 20 to 30.

Version 1.1 - September, 1996

-Fixed resource leak in pretty display.

-Fixed bug that caused loss of pretty display title on setting window focus.

-Increased number of sequences to 200.

-Changed scrolling from block-by-block to line-by-line so that more sequences than would fit on the screen at one time could be displayed.

-Added a non-scrolling position line to aid in navigation when more than a screen full of sequences are open.

-Added navigation buttons and keyboard shortcuts.

Upcoming:

Version 2.0 will add the following features:

- User-definable color display of bases.

- Support for standard codon tables.

- Option to turn off line-wrap so that sequences can be displayed on one long line.

- Support for third party applications.


Registration form

Please print this form, fill it out and send it to:

         Vised

         487 Aquila Place

         Parksville, BC

         Canada

         V9P 1C1

Name___________________________________________ Date_______________

Company________________________________________ Phone______________

Street_________________________________________ FAX________________

City__________________ Country_________ ZIP/Postal code____________

Email___________________________________________________________	___

                ALL AMOUNTS ARE UNITED STATES DOLLARS

SINGLE USER LICENSE:    @ $30.00                          = _______

SITE LICENSE:   Must supply a proper business name.

   3 to  9 computers    @ $21.00 each X ____units         = _______

  10 to 29 computers ...@ $19.00 each X ____units         = _______

  30 to 99 computers    @ $15.00 each X ____units         = _______

 100 &  up computers    @ $11.00 each X ____units         = _______

        Total (US funds only)                               _______

Method of payment:  Cheque__           Money order__

                    Purchase order__   Credit card__

Purchase order number: (universities only)_________________________

Credit card:

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Name exactly as on credit card ___________________________________

Card Number________________________________  Exp.Date_____________

Signature_________________________________________________________