ABIView 
 
V1.0  
 
Copyright 1996 David H. Klatte (dhk@cloud9.net) 
 
This program is freely distributable provided that this file accompanies 
ABIView.exe and that both files are left intact. 
 
ABIView displays the trace and basecall data of ABI automatic DNA 
sequencing files. At the present time, it only displays the unedited 
trace and basecalls. If you are not sure what this means, it's probably 
not important, but you can check my brief technical info document
(On the Web page). ABIView runs in either Windows 3.x or Windows95. 
 
I wrote this program so that we could review and edit our sequence data 
on the PCs in our lab. All the currently available programs for 
displaying traces seem to be for the Macintosh. Yuk. 
 
ABIView is not an editor itself, but it can be effectively used to edit 
sequence data in single ABI files with a separate text editor (like 
Notepad) using ABIView's clipboard functions. For more on this, see "How 
I Use ABIView" below. You will want to have a real sequence editor if 
you are doing a large project, but for the initial verification of your 
sequence data, ABIView + Notepad works great. And it's alot more 
convenient than borrowing someone else's macintosh. 
 
I've made every effort to make this program reliable and safe, but these 
days everyone seems to include a disclaimer, so here's mine. 
 
Disclaimer:  
 
I do not warrant the suitability of this program for any particular 
purpose. You should BACK UP YOUR DATA. I take no responsibilities 
whatsoever for any losses that this program might inadvertently cause.  
 
 
------------------------------------------------------------------------ 
Installation:  
 
Unzip the ABIVIEW1.ZIP file into a temporary directory (e.g. C:\TEMP) or 
onto a floppy disk. Make a directory on your hard drive where you want 
to keep ABIView (e.g. C:\ABIVIEW) and copy ABIView.exe and ABIView.txt 
into that directory (C:\ABIVIEW).  
 
Then copy the files CMDIALOG.VBX and VBRUN300.DLL into C:\WINDOWS\SYSTEM 
(or wherever your windows\system directory is located). If VBRUN300.DLL 
and CMDIALOG.VBX already exist in your system directory, you can skip 
this step. You can then delete all four files in your temporary 
directory (C:\TEMP). 
 
Then add an icon in Program Manager (in Windows 3.x). The default 
initial directory can be stipulated via the Properties setting in the 
Program Manager. In Windows95, just make a shortcut to either your 
desktop or start menu. 
 
 
------------------------------------------------------------------------ 
Features:  
 
 
Main window controls. 
 
The "Jump:" box allows you to jump to any base number. Type in a number 
and hit ENTER and that base will define the left side of the display. In 
version 1.0 and later it also keeps track of the current base position 
in the left side of the window. 
 
The "File:" box displays the current file name. The sequence name as it 
is encoded in the ABI file, which may be different from the filename, is 
displayed in the window caption.  
 
The "|<< and ">>|" buttons take you to the beginning or end of the trace 
data respectively.  
 
The "<" and ">" buttons take you backward or forward one screen.  
 
The "<1/2" and "1/2>" buttons take you backward or forward one-half 
screen.  
 
The "Automatic Scaling" checkbox controls whether the scale is 
automatically adjusted when the window is resized. Automatic scaling 
always attempts to keep the proportionality the same, so that the trace 
is easy to read. If you want to change the proportionality (e.g. make 
the peaks taller, but not wider) you have to use manual scaling. You can 
also switch this by typing Alt-A. 
 
The "Scale" button, when Automatic Scaling is off, pops up a window that 
allows you to set the scaling in both the X and Y dimensions in 
multiples of two (relative to the default X=1, Y=1, which is the scale 
that was used when you first started the program, regardless of the 
current size of the window). You can also type Alt-S. 
 
The ReDraw button forces the window to re-draw if it gets messed up. You 
can also type Alt-R, or use the menu item. 
 
The File menu.  
 
"Open" opens a Windows open file dialog box. By default it looks for 
files with a *.abi extension, but you can name your files whatever you 
want. If you name your files with a different extension, choose *.* as 
the filter. 
 
"Exit" quits the program.  
 
 
The Options menu. 
 
"ReDraw" redraws the display area.  
 
"Auto Redraw ON/OFF" switches the autoredraw property of the main 
window. The default is autoredraw turned off because it seems to me that 
the program runs faster that way. Autoredraw is the property that allows 
you to put window A in front of window B without disturbing window B's 
contents. If you typically work with lots of open windows that you 
frequently switch between, you might want to turn Auto Redraw on. 
 
"Export sequence to clipboard (plain)" takes the encoded (unedited) 
sequence and places it into the Windows clipboard, with a trailing 
carriage return. 
 
"Export formatted sequence to clipboard" adds formatting to make editing 
easier. It is best viewed with a non-proportional font, or in a plain 
text editor like notepad. It's difficult to describe exactly what this 
does. Try this: load an ABI file, select this menu item, then open 
notepad and select "Paste" from the edit menu. 
 
"Unformat sequence in clipboard" allows you to modify sequence data that 
you have placed on the Windows clipboard so that you can remove unwanted 
formatting for input to a sequence editor. I added this function so that 
I could edit a sequence with base numbers to guide me and then strip out 
the numbers afterwards. The characters listed on the right of the menu 
will be kept, all other characters will be removed. This feature is 
potentially very useful - use your imagination. It will work on ANYTHING 
in the clipboard, whether you are editing an ABI file, or not. 
 
"As Plain" keeps only (ACGTN and agctn).  
 
"As Staden" keeps only (ACGT123345678RYDVBHKLMN and acgtrydvbhklmn)  
 
"As IUB/GCG" keeps only (AGCTMRWSYKVHDBXN and agctmrwsykvhdbxn)  
 
 
The Help menu. 
 
"About" displays information about the current version. To get back to 
your sequence, click "ReDraw". 
 
 
How I use ABIView:  
 
1.I open the ABIView program and position it near the top of the screen. 

2.I then open Notepad and position it underneath ABIView. 

3.I open the sequence I want to edit in ABIView and choose 
"Options/Export Formatted Seq to Clipboard". 

4.Then in Notepad I choose "Edit/Paste". 

5.In Notepad I delete all obviously bad bases at the beginning and the end. 

6.Then I step through the trace data, updating the sequence in 
Notepad whenever I find an error. 

7.When I am done, I select the entire sequence that I want to save 
(in Notepad), then choose "Edit/Copy". 

8.Then in ABIView I choose "Options/Unformat Sequence in Clipboard/Plain". 

9.Then I place the cursor at the end of the Notepad file and choose 
"Edit/Paste". 

10.I verify that it's what I intended, delete all of the unnecessary 
information from the Notepad window and save the edited sequence (I use 
a *.seq extension). 

11.The edited sequence is now ready to be imported into your favorite 
analysis software.  
 
 
Known limitations and bugs:  
 
- This version is 16-bit code, so it can't handle Windows95 long file 
names.  
 
- Only the first 16300 data points (not bases, but laser scans) will be 
displayed. Most traces that I have seen are shorter than this and I 
haven't seen any with useful data beyond this. I'm sure that I could fix 
this, but I haven't seen any real reason to. If this causes you a 
problem, let me know and I'll do something about it. 
 
- When the window is re-sized, it won't redraw automatically. Dynamic 
redrawing is WAY too slow in Visual Basic. My workaround is that any 
mouse movement in the window will force a redraw if the window has been 
resized, so usually you won't even notice, I hope. 
 
- If you have a sequence loaded and you start to load another in the 
"Open File" dialog box, then you hit cancel, your sequence display will 
be reset to the beginning of the current trace. 
 
 
Possible Future Improvements:  
 
ABIView fulfills my needs now, so improvements will be dependent upon 
how much free time I have. 
 
- Allow printing?? Or graphics export?? 
 
- Display all the encoded information about the sequence (time/date, 
lane#, conditions, etc.) Does anyone actually care about this stuff? 
 
- Allow custom colors.  
 
- A 32-bit version. If I do this, I'll probably port it to Delphi 
(object pascal). I expect the execution would be at least 10-20 times 
faster, but it would no longer run under Windows 3.x. Or maybe I'll do 
16 and 32 bit versions in Delphi - it shouldn't be too hard. 
 

