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: