hongqin / t-coffee

Tools for multiple alignments of DNA, RNA, and Proteins.

Overview

This is a modification of the last stable release of TCOFFEE that allows it to build and run natively on Windows with MSVC.

Modifications

• Use threads instead of process forking, because there is no equivalent on Windows.
• Renamed some constants and variables that conflicted with macro names defined deep in Windows headers, such as DELETE, IN, OUT, OPTIONAL, UNALIGNED, min, max.
• Unportable functions were renamed or re-implemented to use a Windows equivalent, such as directory creation or traversal, file existance.
• Temp names were altered to use process AND thread ids, because unforkable code needs more info than just process id.
• Custom makefile to use MSVC compiler and linker.
• Complex function pointer declarations had to be typedef-ed to compile.
• Variable Length Arrays (VLA) are not supported, so arrays were allocated or made reasonable static sizes.
• Some functions returned nothing, but declared non-void return type.
• Uninitialized variables were give reasonable defaults.
• Indentation was adjusted and to use only spaces.
• A large else-if block was split to make it compilable by MSVC.
• Process memory ownership assumptions had to be refactored due to threading.
• Clock utilities were replaced with std::chrono.
• Get core count was enhanced to support Windows.
• Use Windows environment variables where necessary.
• Disabled embedded perl script due to exceeding MSVC compiler limits. This needs to be revisited to re-activate.
• Removed some unused variables, functions and function args, but some might still remain.
• Allow input and executable filenames to have spaces.
• Build and run without crashing 64-bit executable on Windows built natively with MSVC.

Building

You'll need a c++11 compliant compiler.

Mac/Linux

cd t_coffee_source
make -j

Windows

You have to use GNU Make to support some convenient make extensions. Get it from either Chocolatey, GnuWin32 or a Git package.

cd t_coffee_source
gmake -j -f makefile.win

Debugging

QtCreator can be used to debug the executable. First create a project file:

cd t_coffee_source
qmake -project

Then open the new t_coffee_source.pro file in QtCreator and disable qmake in QtCreator > Projects > Build > Build Steps, otherwise qmake will overwrite our makefile.

Only on Windows, use an extra required flag when building due to how the MSVC compiler works:

gmake -f makefile.win DEBUG_ENABLED=1

Set args in QtCreator > Projects > Run:

-infile C:\tmp\input.fasta -type=dna -outfile C:\tmp\output.txt