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dna2abc: Scanners: Rules
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The Rules sub-page of the Scanners page contains controls for
editing the rule table for the selected scanner.  It also
contains controls for the scanner's frame length and step size.
The rest of the controls do not affect the operation of the
scanner, they are aids in writing regular expressions.

The selected scanner's rules, frame, and step slots are edited
by the table and the two number fields to its upper right.
The large text fields (with colored backgrounds) at the top
contain the test buffers, their values are stored in slots 
bufferA, bufferB, bufferC, and bufferD.  The horizontal slider
marks the current position in the test buffers, its value is
stored in the index slot.
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Rule Table
==========

Each rule consists of a Tcl regular expression (regexp)
and a Tcl script.  The table starts out empty, insert
a new rule with the "Insert above" button.  Two text
editing boxes appear.  Each of them colorizes the text
you type to highlight the syntax of what you're typing
(i.e., the left box highlights regexp syntax, while the
right box highlights Tcl).  

You can select a rule by clicking in either its regexp
or script box.  The number in the leftmost column will
light up to indicate that the rule is selected, and the
buttons below the table will be enabled for moving
the rule, inserting and deleting rules.  There is no 
undo, so save early and often!

(Note: the order of the rules matters, since more than
one rule may fire per step, and they fire in the order
listed in the table.  If a script returns with a break,
subsequent rules won't fire that step.)

You can drag the borders of the table to resize the
rows and columns.  You can also expand each row
to be big enough to make all its text visible
using the "Beautify Rule Table" item in the Run
menu.

============
Test Buffers
============

When the scanner reads a DNA sequence, it chops it into
"frame"-sized pieces and advances "step" bases each time.
The four colored text boxes at the top of the Rules page
can be used to test the regexps in your rule table.  Fill
one or more with a test sequence (perhaps cut and paste 
a line from your input DNA file into each box).  A sequence
"frame" bases long will be highlighted in white in each
box, you can advance this "step" bases at a time using
the slider beneath the test buffers.

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Matching
========

Each time you move the slider, change the frame or step
values, or type in a test buffer or regexp box, dna2abc
matches all of the regexps in the table against the 
highlighted portions of the four test buffers.  To the
right of each test buffer is an indicator, an X will
appear if one or more regexps match that test sequence.
To the left of each regexp is a cluster of four indicators
corresponding to the which of the four test buffers are
matched by the regexp.  

If you have a long, complicated rule table, you might
want to shut off the "Compute match on each keypress"
option.  Matches will still be computed when you move
the slider or change the frame or step, and also when
the "Compute Matches" item on the Run menu is chosen.