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Full Discussion: Improve the performance of my C++ code
Top Forums Programming Improve the performance of my C++ code Post 302931794 by yifangt on Thursday 15th of January 2015 01:34:20 PM
Old 01-15-2015
Improve the performance of my C++ code
Hello,
Attached is my very simple C++ code to remove any substrings (DNA sequence) of each other, i.e. any redundant sequence is removed to get unique sequences. Similar to sort | uniq command except there is reverse-complementary for DNA sequence. The program runs well with small dataset, but when I increase the data size to ~1,000 entries (some maybe 100,000bp long), it took about 2 hours to finish.
My question is: How to improve the performance of my code?
It seems memory issue can be excluded as 256GB RAM is available.
1) What are the room for coding techniques based on my current algorithms, which is a simple "sorting---looping---comparing" with complexity n^2 ?
2) What are the better algorithms, for sure there are many?

Either of the two questions is too complicate for myself, but I am wondering if anybody can give me some help to increase the performance of the program. Thanks a lot!
rm_redundant_seqs_final.txt (3.7 KB) 
 

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LEARN ABOUT DEBIAN

ansi_code

term::ansi::code(3tcl)						 Terminal control					    term::ansi::code(3tcl)

__________________________________________________________________________________________________________________________________________________

NAME

       term::ansi::code - Helper for control sequences

SYNOPSIS

       package require Tcl  8.4

       package require term::ansi::code  ?0.1?

       ::term::ansi::code::esc str

       ::term::ansi::code::escb str

       ::term::ansi::code::define name escape code

       ::term::ansi::code::const name code

_________________________________________________________________

DESCRIPTION

       This package provides commands enabling the definition of control sequences in an easy manner.

       ::term::ansi::code::esc str
	      This command returns the argument string, prefixed with the ANSI escape character, "33."

       ::term::ansi::code::escb str
	      This command returns the argument string, prefixed with a common ANSI escape sequence, "33[".

       ::term::ansi::code::define name escape code
	      This  command defines a procedure name which returns the control sequence code, beginning with the specified escape sequence, either
	      esc, or escb.

       ::term::ansi::code::const name code
	      This command defines a procedure name which returns the control sequence code.

BUGS, IDEAS, FEEDBACK
       This document, and the package it describes, will undoubtedly contain bugs and other problems.  Please report such in the category term	of
       the  Tcllib  SF	Trackers [http://sourceforge.net/tracker/?group_id=12883].  Please also report any ideas for enhancements you may have for
       either package and/or documentation.

KEYWORDS

       control, declare, define, terminal

CATEGORY

       Terminal control

COPYRIGHT

       Copyright (c) 2006 Andreas Kupries <andreas_kupries@users.sourceforge.net>

term									0.1						    term::ansi::code(3tcl)
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