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C++/src/algo/blast/core/

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  Name Size Date (GMT) Description
Back   Parent directory   2009-12-10 01:53:52
File   Makefile.blast.lib 1111  2009-12-10 01:49:23
File   Makefile.in 194  2009-12-10 01:49:23
File   README 1980  2009-12-10 01:49:23
C file   aa_ungapped.c 47057  2009-12-10 01:49:23
C file   blast_aalookup.c 52299  2009-12-10 01:49:23
C file   blast_aascan.c 23001  2009-12-10 01:49:23
C file   blast_diagnostics.c 4837  2009-12-10 01:49:23
C file   blast_dynarray.c 11045  2009-12-10 01:49:23
C file   blast_dynarray.h 7532  2009-12-10 01:49:23
C file   blast_encoding.c 4388  2009-12-10 01:49:23
C file   blast_engine.c 56665  2009-12-10 01:49:23
C file   blast_extend.c 12088  2009-12-10 01:49:23
C file   blast_filter.c 44297  2009-12-10 01:49:23
C file   blast_gapalign.c 146374  2009-12-10 01:49:23
C file   blast_gapalign_priv.h 7286  2009-12-10 01:49:23
C file   blast_hits.c 103036  2009-12-10 01:49:23
C file   blast_hits_priv.h 2950  2009-12-10 01:49:23
C file   blast_hspstream.c 27249  2009-12-10 01:49:23
C file   blast_itree.c 37169  2009-12-10 01:49:23
C file   blast_itree.h 7206  2009-12-10 01:49:23
C file   blast_kappa.c 95369  2009-12-10 01:49:23
C file   blast_lookup.c 5095  2009-12-10 01:49:23
C file   blast_message.c 6853  2009-12-10 01:49:23
C file   blast_nalookup.c 35328  2009-12-10 01:49:23
C file   blast_nascan.c 95814  2009-12-10 01:49:23
C file   blast_options.c 55171  2009-12-10 01:49:23
C file   blast_parameters.c 37987  2009-12-10 01:49:23
C file   blast_posit.c 14516  2009-12-10 01:49:23
C file   blast_posit.h 6218  2009-12-10 01:49:23
C file   blast_program.c 3657  2009-12-10 01:49:23
C file   blast_psi.c 21942  2009-12-10 01:49:23
C file   blast_psi_priv.c 95801  2009-12-10 01:49:23
C file   blast_psi_priv.h 29272  2009-12-10 01:49:23
C file   blast_query_info.c 12120  2009-12-10 01:49:23
C file   blast_seg.c 169578  2009-12-10 01:49:23
C file   blast_seqsrc.c 14040  2009-12-10 01:49:23
C file   blast_setup.c 32823  2009-12-10 01:49:23
C file   blast_stat.c 157739  2009-12-10 01:49:23
C file   blast_sw.c 27078  2009-12-10 01:49:23
C file   blast_traceback.c 55447  2009-12-10 01:49:23
C file   blast_tune.c 16186  2009-12-10 01:49:23
C file   blast_util.c 41148  2009-12-10 01:49:23
C file   gapinfo.c 6552  2009-12-10 01:49:23
C file   gencode_singleton.c 2441  2009-12-10 01:49:23
C file   greedy_align.c 45093  2009-12-10 01:49:23
C file   hspfilter_besthit.c 14877  2009-12-10 01:49:23
C file   hspfilter_collector.c 13738  2009-12-10 01:49:23
C file   hspfilter_culling.c 25509  2009-12-10 01:49:23
C file   index_ungapped.c 4123  2009-12-10 01:49:23
C file   index_ungapped.h 4632  2009-12-10 01:49:23
C file   link_hsps.c 67471  2009-12-10 01:49:23
C file   lookup_util.c 5183  2009-12-10 01:49:23
C file   lookup_wrap.c 9313  2009-12-10 01:49:23
File   masksubj.inl 2962  2009-12-10 01:49:23
C file   matrix_freq_ratios.c 110283  2009-12-10 01:49:23
C file   matrix_freq_ratios.h 2674  2009-12-10 01:49:23
C file   na_ungapped.c 63941  2009-12-10 01:49:23
C file   ncbi_math.c 12855  2009-12-10 01:49:23
C file   ncbi_std.c 5121  2009-12-10 01:49:23
C file   pattern.c 23318  2009-12-10 01:49:23
C file   pattern_priv.h 4104  2009-12-10 01:49:23
C file   phi_extend.c 3466  2009-12-10 01:49:23
C file   phi_gapalign.c 36345  2009-12-10 01:49:23
C file   phi_lookup.c 32770  2009-12-10 01:49:23
C file   split_query.c 10485  2009-12-10 01:49:23 
  1 This directory contains the implementation of the core of the BLAST algorithm
  2 (also known as the BLAST engine). In the future, NCBI may provide a simple
  3 C API to access this implementation, in the meantime, working with these
  4 sources directly is possible, but not recommended unless one is very familiar
  5 with them.
  6 
  7 Build instructions
  8 ------------------
  9 
 10 NOTE: By following this approach some features supported by the NCBI C++ toolkit
 11 such as BLAST database access, BLAST formatting, embedded logging, MT locking,
 12 and configuration support will be absent or only partially supported.
 13 
 14 UNIX:
 15 To build these source files into a library without the rest of the NCBI C++
 16 toolkit, one should use the following commands:
 17 
 18 ./configure --with-projects=scripts/projects/blast_core_lib.lst \
 19             --without-debug --with-mt --with-build-root=ReleaseMT
 20 cd c++/ReleaseMT/build
 21 make all_p
 22 
 23 This will configure and build an optimized library called blast, which can then
 24 be referenced in makefiles as follows:
 25 
 26 NCBI_HOME=<installation directory of the NCBI C++ toolkit>
 27 -I$NCBI_HOME/c++/ReleaseMT/inc -I$NCBI_HOME/c++/include
 28 -L $NCBI_HOME/c++/ReleaseMT/lib
 29 
 30 Windows:
 31 1) Open the ncbi_cpp.sln project/solution file 
 32    c++/compilers/msvc800_prj/static/build/ncbi_cpp.sln. 
 33 2) Right click on the -CONFIGURE-DIALOG- project on the Solution Explorer and
 34    select "Build" from the context menu, which will bring up a window titled
 35    "Project Tree Builder". 
 36 3) In the "Project Tree Builder" window's first text box, enter
 37    scripts\projects\blast_core_lib.lst, click OK, and on the subsequent window
 38    click "Reload". 
 39 4) After the environment reloads, right click on blast.lib and select "Build".
 40 
 41 The blast.lib library file will be found in
 42 c++\compilers\msvc800_prj\static\lib\CONF\blast.lib, where CONF represents the
 43 appropriate configuration (e.g.: debugdll, debugmt, releasedll, or releasemt),
 44 and the headers will be found in c++\compilers\msvc800_prj\static\inc and
 45 c++\include
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