This directory contains the implementation of the core of the BLAST algorithm
(also known as the BLAST engine). In the future, NCBI may provide a simple
C API to access this implementation, in the meantime, working with these
sources directly is possible, but not recommended unless one is very familiar
with them.

NOTE: By following this approach some features supported by the NCBI C++ toolkit
such as BLAST database access, BLAST formatting, embedded logging, MT locking,
and configuration support will be absent or only partially supported. 

Getting the source code
-----------------------
Download the source distribution of BLAST+:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-VERSION+-src.tar.gz

Build instructions
------------------
Unpack the source archive in its installation directory and change working
directory to ncbi-blast-VERSION+-src/c++.

UNIX:
To build these source files into a library without the rest of the NCBI BLAST+
applications/libraries, one should use the following commands:

./configure --with-projects=scripts/projects/blast_core_lib.lst \
            --without-debug --with-mt --with-build-root=ReleaseMT
cd ReleaseMT/build
make all_p

This will configure and build an optimized library called blast, which can then
be referenced in makefiles as follows:

NCBI_HOME=<installation directory of the NCBI C++ toolkit>
-I$NCBI_HOME/c++/ReleaseMT/inc -I$NCBI_HOME/c++/include
-L $NCBI_HOME/c++/ReleaseMT/lib

Windows:
1) Open the ncbi_cpp.sln project/solution file 
   c++/compilers/msvc800_prj/static/build/ncbi_cpp.sln. 
2) Right click on the -CONFIGURE-DIALOG- project on the Solution Explorer and
   select "Build" from the context menu, which will bring up a window titled
   "Project Tree Builder". 
3) In the "Project Tree Builder" window's first text box, enter
   scripts\projects\blast_core_lib.lst, click OK, and on the subsequent window
   click "Reload". 
4) After the environment reloads, right click on blast.lib and select "Build".

The blast.lib library file will be found in
c++\compilers\msvc800_prj\static\lib\CONF\blast.lib, where CONF represents the
appropriate configuration (e.g.: debugdll, debugmt, releasedll, or releasemt),
and the headers will be found in c++\compilers\msvc800_prj\static\inc and
c++\include