Copyright: HelpBuilder ® 1993 - 1998 G.Plowman


Introduction

Plasmid Processor Pro is an advanced tool for plasmid presentation for scientific and educational purposes. Plasmid Processor Pro comes from the same authors as the famous and popular Plasmid Processor software. (Plasmid Processor software is freeware and available from http://www.hytti.uku.fi/~oikari/plasmid.html)

Plasmid Processor Pro features both circular and linear DNA, user defined restriction sites, genes and multiple cloning site. Plasmid Processor Pro includes advanced methods and tools for plasmid  manipulation by inserting and deleting fragments. Plasmid Processor Pro includes also advanced graphics and presentation properties.

Plasmid Processor Pro alpha version is freeware, so you can use and distribute it freely.

Plasmid Processor Pro alpha version is a development and testing version of Plasmid Processor Pro complete release. Possible bugs will be corrected and limited capabilites of Plasmid Processor Pro alpha version will be converted to fully working capabilities in Plasmid Processor Pro complete release. Plasmid Processor Pro complete release is under development and will be available soon.

Copyright © Tapio Kivirauma, Pekka Oikari ja Janne Saarela

All rights reserved.

This software is subject to the legal notes set forth in Legal Notes.

Please read and agree to all terms before using this software.

Report any problems through the plasmid@uku.fi mailing list. You can get the latest information and the latest version of the program from http://www.hytti.uku.fi/~oikari/plaspro.html

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Legal Notice
Plasmid Processor Pro alpha version Legal Notes

Copyright © Tapio Kivirauma, Pekka Oikari ja Janne Saarela

All rights reserved.

Please read and agree to all terms before using this software.

BY USING THIS PLASMID PROCESSOR PRO ALPHA VERSION YOU ARE CONSENTING TO BE BOUND BY THESE LEGAL NOTES. IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THESE LEGAL NOTES YOU MAY NOT CONTINUE USING PLASMID PROCESSOR PRO ALPHA VERSION SOFTWARE AND YOU ARE ASKED TO DELETE YOUR COPY OF THE SOFTWARE.

DISCLAIMER OF WARRANTY

Free of charge Software is provided on an "AS IS" basis, without warranty of any kind, including without limitation the warranties of merchantability, fitness for a particular purpose and non-infringement. The entire risk as to the quality and performance of the Software is borne by you.  Should the Software prove defective, you and not the authors assume the entire cost of any service and repair.

You may use the Software on as many computers and as many copies simultaneously as you like. You may also distribute this Software freely as long as you do not motify the Sofware by any means.

You may not modify, translate, reverse engineer, decompile, disassemble or create derivative works based on the Software;

TITLE.

Title, ownership rights, and intellectual property rights in the Software shall remain in the authors of the software. The Software is protected by the copyright laws and treaties. Title and related rights in the content accessed through the Software is the property of the applicable content owner and may be protected by applicable law.

LIMITATION OF LIABILITY. UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, TORT, CONTRACT, OR OTHERWISE, SHALL THE AUTHORS OF THE SOFTWARE BE LIABLE TO YOU OR ANY OTHER PERSON FOR ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES. IN NO EVENT WILL THE AUTHORS OF THE SOFTWARE BE LIABLE FOR ANY DAMAGES, EVEN IF THE AUTHORS SHALL HAVE BEEN INFORMED OF THE POSSIBILITY OF SUCH DAMAGES, OR FOR ANY CLAIM BY ANY OTHER PARTY.

HIGH RISK ACTIVITIES.

The Software is not fault-tolerant and is not designed, manufactured or intended for use in hazardous environments requiring fail-safe performance, in which the failure of the Software could lead directly to death, personal injury, or severe physical or environmental damage ("High Risk Activities"). The authors of the software specifically disclaim any express or implied warranty of fitness for High Risk Activities.

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Object inspector
Using the Program: The Object Inspector

Overview

Main function of Object inspector is to substitute multiple separate dialogs thus representing them as single entity. This kind of presentation of dialogs is common on typical MS-Windows RAD development tools (ie. Inprise (Borland) Delphi or Microsoft Visual Basic). Main idea of Object inspector is to provide instant access to objects parameters, which in this program are genes, RST-sites, MCS-sites etc.

Layout of Object inspector

Object inspector is standard windows tab-dialog type window. Two tabs visible are Objects and Data. Objects tab represents plasmids and Data tab represents currently active plasmid object (Gene,RST,MCS) data. Dropbox of Objects tab is reserved for future use, and is inactive. Dropbox of Data tab can be used for fast selection of plasmid object category using mouse or left/right arrows when selected as active control.

Basic usage of Object Inspector

When you create new plasmid object (Gene,RST,MCS) on plasmid window and click its nameplate using mouse, then object inspector automatically switch its data to represent selected object. You can now alter these parameters as like by selecting object inspector's parameter window using mouse. Currently editable parameter is highlighted by white and cursor is visible if parameter (ie. Position (Pos) of RST) is editable. Alternatively there could be simple dropbox visible (ie. ShowPosition (ShowPos) of RST) for selecting appropriate action for parameter (true, false etc).

You can select wanted parameter using mouse, and when Object inspector is active window with selected parameter, you can move up and down on parameters using up/down cursor movement keys on keyboard. Divisor bar between Name-of-the-parameter (left) window and value-of-the-parameter (right) window can be used to adjust size of them if needed. Whole window is also resizable and minimizable by doubleclicking windows titlebar.

Some items are autoupdate type, meaning that when you type something to parameters editbox, it is automatically updated to object it is representing (ie. Name of the RST). Others need enter key to be pressed before changes are made to object (ie. Pos of the RST). Reason for this is that you don't want to see RST's position to jump manically all the time when you alter value on editbox.

Plasmid object categories (Data tab dropbox)

Plasmid

Name	: Represents plasmid name and is autoupdate type (Auto).

Lenght 	: Currently unused (should set plasmid lenght, now fixed to 10k)

OldPos 	: Old position of plasmid cursor. Changes when selection of area starts on plasmid window.

CurPos	: Current position of cursor. Changes when cursor is moved around on plasmid window.

SelLen	: Selected area lenght on plasmid window.

+Font	: Unused currently.

+Info	: Unused currently.

Linear	: True/False dropbox for linear or circular presentation of plasmid.

(Restriction) Site

Name	: Represents RST-sites name and is autoupdate type (Auto).

Pos	: Position of RST-site, changes are confirmed by pressing enter key (Enter).

+Font	: Font of RST-site. Opens font selection dialog for choosing of appropriate font.

Use Enter key to open dialog.

ShowPos : True/false dropbox for presentation of RST-sites postion on plasmid window next to name.

Gene

Name	: Name of the gene (Auto).

Start	: Starting position of the gene (Enter).

End 	: Ending position of the gene (Enter).

+Font	: Font selection dialog of the gene (Enter).

Level	: Dropbox of the gene representation level proportional to plasmid circle.

Pattern : Representation pattern of the gene (DropBox).

Thick 	: Thickness of the gene (DropBox).

Sharp	: Selects representation of the gene end for sharp or blunt type (DropBox).

Clockwise : Representation of the gene is clock- or anticlockwise (Dropbox).

ShowPos : Unused currently.

MCS

Name	: Name of the MCS (Auto).

Start	: Starting position of the MCS (Enter).

End 	: Ending position of the MCS (Enter).

Width	: Width of MCS box (Enter).

Height	: Height of MCS box (Enter).

Rows	: Reserved for future use currently.

ShowPos : T/F dropbox for position presentation next to MCS name.

Border	: T/F dropbox for MCS box border presentation.

WordWrap: T/F dropbox for wordwrapping of text in MCS editbox.

Type	: Unused currently.

Outlook : Outlook of MCS box (unusable for copy-paste operations of plasmid).

Operation

Unusable currently.

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Plasmid Processor Pro
Welcome to the Plasmid Processor Pro alpha 1 help!

Introduction

Using the Program

Tips and Tricks

Plasmid Processor Pro: the complete version

Legal Notes

last modified: 01/11/1999


Plasmid Processor Pro: the complete version
The complete version

Plasmid Processor Pro complete version will have the following features (and more):

- insert/delete fragments

- save/load functionality

- printing from within the program

- additional drawing objects

No promises regarding the release schedule can be given. Check out our home page

for more information.


Plasmid viewer
Using the Program:  Plasmid viewer

Overview

Plasmids are drawn onto Plasmid viewer windows. Multiple Plasmid viewer windows can be open at the same time. The size of the windows can be changed, the size of the plasmid changing accordingly.

Main features of the Plasmid viewer window

Cursor

This little cursor follows the circumference or the line of the plasmid. The cursor is moved by holding left mouse button down while moving the mouse. Area can be selected by pushing also the right mouse button down and moving the mouse. To stop making the selection release both buttons. Open the quick menu by clicking the right mouse button and select desired action eg. create gene.

Quick menu

Click right mouse button to open the quick menu, which currently includes the following items:

1. Create Gene - by selecting area and choosing this item you can create a gene.

2. Create Rst - by choosing this item you can create a gene at the current location of the cursor.

3. Locked (on/off) - when manually relocating labels you may lock them in place

4. Proportional (on/off) - when manually relocating labels you may lock them in place relative to the plasmid size.

5. Invalidate - redraws the drawing surface. Only in the alpha version, may help in solving some bugs.

"File" menu

At the top of each plasmid viewer window there are couple of items:

Plasmid - not available yet.

Genes, Sites and MCS - opens a small utility window, which displays all objects of the given type. Selecting an object will display it's properties in the MainInspector-window.

Copy  - copy the current plasmid to clipboard. (Click this, open eg. a word processor and select Paste from the word processor).

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THE MAIN MENU AND TOOLBAR
Using the Program: The main menu and toolbar

Overview

The main window contains currently only a toolbar with these seven buttons:

1. Create empty plasmid template

2. Create new gene

3. Create new Rst-site

4. Create new Mcs

5/6. Back/Forward-buttons scroll currently selected plasmid object in the Maininspector Window

7. Open Plasmid Processor Pro help

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Tips and Tricks

Plasmid size is currently fixed at 10 000 base pairs, so there's not so much that you can do with the program.

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Using the Program

Plasmid Processor pro consists of 3 windows:

1. The main menu and toolbar

2. Object Inspector

3. Plasmid viewer(s)

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