Weeder 1.4.2 Patched

Description

This is a refactored version of Weeder 1.4.2

Find the original version here:

http://159.149.160.51/modtools/downloads/weeder.html

Compiling and Installation

see INSTALL for compilation instructions

This will build the executables

weederlauncher weederTFBS adviser locator

Remarks

The directory python contains re-implementations of adviser and weederlauncher in Python. weederlauncher.py provides an way to define the location of the FreqFiles directory through it --ffdir option

Modifications

Refactored weeder:

Cleanup of code

• generalized redundant code into functions
• generalized linked list mergesort
• renamed variables
• removed unused code and variables
• replaced magic numbers with symbolic constants
• translated most variables to english
• code now compiles with significantly stricter settings and ISO C90

Optimizations

• all base-4 power computations are replaced with a symbolic constant or a specialized base 4 power 4 function
• replaced majority of malloc() based allocations with stack-based allocations, results in up to 100% improvement on the 12mer computation

Bug fixes

• hamming distance

Enhancements/Customizations

• Build with autotools
• MAX_SEQ and executable names can be changed in one central place in the makefile
• Location of FreqFiles can be specified for weederTFBS

Open Questions

• hamming distance