CPS 100, Spring 2004, DNA Snarfing/Files
You are given the classes/files below, also
accessible by snarfing with Eclipse or on the acpub system in
/afs/acpub/project/cps/courses/cps100/dna from
which you can copy them as follows.
cd ~
cd cps100
mkdir dna
cd dna
cp /afs/acpub/project/cps/courses/cps100/dna/* .
(don't forget the trailing dot)
- dna.h an abstract base class
for any DNA molecule/strand/enzyme.
- strand.h an abstract base class
(subclass of DNA).
- stringstrand.h a concrete
subclass of Strand implemented using strings.
- stringstrand.cpp the
implementation of StringStrand.
- testcut.cpp a program to test
the implementation of a Strand subclass implementation
of the cutWith function and other member functions.
- restrictor.h header file
for the Restrictor class representing a restriction enzyme
(subclass of DNA).
- restrictor.cpp implementation
of Restrictor class.
- strandbench.h a class
for simulating an enzyme repeatedly cutting a DNA strand.
- strandbench.cpp implementation
of StrandBench.
- dnasimulate.cpp the main program
for driving the simulation.
- Makefile (site specific)
If you snarf the assignment you'll get all the data files, but on Unix
you can link to them insrted of copying them.
You should link three data files to your directory, use links instead
of copying because these files are large. When testing
your code use a data file you create, not the data files here. When
you're confident your code works, you can run on these files. Only
the file ecoli.dat should take a really long time for
StringStrand.
ln -s /afs/acpub/project/cps/courses/cps100/data/ecoli.dat
ln -s /afs/acpub/project/cps/courses/cps100/data/ecolimed.dat
Owen L. Astrachan
Last modified: Wed Jan 28 12:25:48 EST 2004