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Name |
|
Date |
Size |
#Lines |
LOC |
| .. | | 03-May-2022 | - |
| Makefile.blast.lib.unix | H A D | 03-Aug-2021 | 1.6 KiB | 36 | 32 |
| Makefile.in | H A D | 08-Aug-2003 | 194 | 10 | 3 |
| README | H A D | 04-Apr-2013 | 2.2 KiB | 53 | 43 |
| aa_ungapped.c | H A D | 04-May-2016 | 46.5 KiB | 1,159 | 730 |
| blast_aalookup.c | H A D | 04-May-2016 | 51 KiB | 1,376 | 868 |
| blast_aascan.c | H A D | 04-May-2016 | 21.8 KiB | 578 | 358 |
| blast_diagnostics.c | H A D | 04-May-2016 | 5.4 KiB | 161 | 111 |
| blast_dynarray.c | H A D | 04-May-2016 | 10.6 KiB | 406 | 292 |
| blast_dynarray.h | H A D | 04-May-2007 | 7.4 KiB | 201 | 64 |
| blast_encoding.c | H A D | 04-May-2016 | 4.1 KiB | 122 | 78 |
| blast_engine.c | H A D | 13-Sep-2021 | 69.1 KiB | 1,798 | 1,234 |
| blast_extend.c | H A D | 04-May-2016 | 11.6 KiB | 376 | 255 |
| blast_filter.c | H A D | 17-Apr-2017 | 44.8 KiB | 1,407 | 1,066 |
| blast_gapalign.c | H A D | 04-Mar-2019 | 160.8 KiB | 4,525 | 3,254 |
| blast_gapalign_priv.h | H A D | 28-Nov-2012 | 6.3 KiB | 148 | 37 |
| blast_hits.c | H A D | 09-Oct-2019 | 124.9 KiB | 3,884 | 2,850 |
| blast_hits_priv.h | H A D | 04-May-2007 | 2.9 KiB | 76 | 17 |
| blast_hspstream.c | H A D | 09-Oct-2019 | 27.2 KiB | 867 | 600 |
| blast_hspstream_mt_utils.c | H A D | 04-May-2016 | 5.9 KiB | 172 | 111 |
| blast_hspstream_mt_utils.h | H A D | 18-Mar-2016 | 3.2 KiB | 85 | 24 |
| blast_itree.c | H A D | 04-Jun-2019 | 44.4 KiB | 1,260 | 735 |
| blast_itree.h | H A D | 09-Feb-2011 | 7.6 KiB | 180 | 59 |
| blast_kappa.c | H A D | 26-Aug-2020 | 147.3 KiB | 3,905 | 2,773 |
| blast_lookup.c | H A D | 04-Jan-2017 | 9.8 KiB | 302 | 188 |
| blast_message.c | H A D | 04-May-2016 | 7.8 KiB | 257 | 174 |
| blast_nalookup.c | H A D | 23-Oct-2018 | 71.1 KiB | 2,312 | 1,614 |
| blast_nascan.c | H A D | 27-Jun-2016 | 104.1 KiB | 3,008 | 2,055 |
| blast_options.c | H A D | 19-Jul-2018 | 60.2 KiB | 1,986 | 1,527 |
| blast_parameters.c | H A D | 23-Oct-2018 | 40.7 KiB | 1,137 | 761 |
| blast_posit.c | H A D | 04-May-2016 | 14 KiB | 414 | 311 |
| blast_posit.h | H A D | 04-May-2007 | 6.1 KiB | 156 | 52 |
| blast_program.c | H A D | 20-Jun-2016 | 3.9 KiB | 109 | 53 |
| blast_psi.c | H A D | 29-Jan-2019 | 25.5 KiB | 766 | 564 |
| blast_psi_priv.c | H A D | 04-May-2016 | 105.8 KiB | 3,177 | 2,233 |
| blast_psi_priv.h | H A D | 16-Dec-2011 | 31.2 KiB | 758 | 259 |
| blast_query_info.c | H A D | 17-Oct-2016 | 12.3 KiB | 388 | 257 |
| blast_seg.c | H A D | 09-Aug-2016 | 164.5 KiB | 2,338 | 1,923 |
| blast_seqsrc.c | H A D | 02-Apr-2020 | 16.9 KiB | 582 | 430 |
| blast_setup.c | H A D | 20-Jun-2016 | 40.5 KiB | 1,112 | 821 |
| blast_stat.c | H A D | 26-Jun-2018 | 173.9 KiB | 5,253 | 3,512 |
| blast_sw.c | H A D | 20-Jun-2016 | 26.3 KiB | 731 | 468 |
| blast_traceback.c | H A D | 02-Apr-2020 | 72.2 KiB | 1,839 | 1,271 |
| blast_traceback_mt_priv.c | H A D | 31-Oct-2018 | 8.4 KiB | 242 | 182 |
| blast_traceback_mt_priv.h | H A D | 22-Nov-2013 | 6.5 KiB | 164 | 58 |
| blast_tune.c | H A D | 04-May-2016 | 15.6 KiB | 461 | 243 |
| blast_util.c | H A D | 13-Sep-2021 | 41.2 KiB | 1,414 | 1,116 |
| boost_erf.c | H A D | 14-Apr-2016 | 10.4 KiB | 257 | 149 |
| boost_erf.h | H A D | 14-Apr-2016 | 1.6 KiB | 49 | 11 |
| gapinfo.c | H A D | 04-May-2016 | 6.2 KiB | 233 | 152 |
| gencode_singleton.c | H A D | 04-May-2016 | 2.2 KiB | 71 | 31 |
| greedy_align.c | H A D | 04-Mar-2019 | 44.2 KiB | 1,252 | 677 |
| hspfilter_besthit.c | H A D | 09-Oct-2019 | 20.8 KiB | 636 | 449 |
| hspfilter_collector.c | H A D | 09-Oct-2019 | 12.2 KiB | 360 | 208 |
| hspfilter_culling.c | H A D | 12-Jul-2018 | 25.4 KiB | 831 | 581 |
| hspfilter_mapper.c | H A D | 04-Jun-2019 | 153.6 KiB | 4,859 | 3,374 |
| index_ungapped.c | H A D | 19-Nov-2018 | 4.1 KiB | 154 | 89 |
| index_ungapped.h | H A D | 04-May-2007 | 4.5 KiB | 131 | 37 |
| jumper.c | H A D | 02-Dec-2019 | 140.6 KiB | 4,577 | 3,454 |
| jumper.h | H A D | 04-Jan-2019 | 11.5 KiB | 316 | 150 |
| link_hsps.c | H A D | 10-Nov-2020 | 65.9 KiB | 1,815 | 1,182 |
| lookup_util.c | H A D | 20-Jun-2016 | 4.9 KiB | 205 | 110 |
| lookup_wrap.c | H A D | 23-Aug-2017 | 10.4 KiB | 290 | 216 |
| masksubj.inl | H A D | 25-Jul-2011 | 2.5 KiB | 60 | 58 |
| matrix_freq_ratios.c | H A D | 04-May-2016 | 107.6 KiB | 1,754 | 1,684 |
| matrix_freq_ratios.h | H A D | 02-Jul-2014 | 2.6 KiB | 84 | 18 |
| na_ungapped.c | H A D | 30-Aug-2017 | 90.1 KiB | 2,324 | 1,637 |
| ncbi_erf.c | H A D | 01-Feb-2012 | 16.1 KiB | 473 | 258 |
| ncbi_math.c | H A D | 04-May-2016 | 12.7 KiB | 495 | 362 |
| ncbi_std.c | H A D | 04-May-2016 | 4.8 KiB | 182 | 84 |
| pattern.c | H A D | 04-May-2016 | 22.6 KiB | 598 | 409 |
| pattern_priv.h | H A D | 04-May-2007 | 4 KiB | 110 | 23 |
| phi_extend.c | H A D | 04-May-2016 | 3.2 KiB | 87 | 36 |
| phi_gapalign.c | H A D | 30-Jun-2016 | 35.3 KiB | 906 | 642 |
| phi_lookup.c | H A D | 30-Jun-2016 | 31.8 KiB | 758 | 543 |
| spliced_hits.c | H A D | 05-Apr-2017 | 4.5 KiB | 189 | 125 |
| split_query.c | H A D | 04-May-2016 | 10.3 KiB | 339 | 263 |
README
1This 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
3C API to access this implementation, in the meantime, working with these
4sources directly is possible, but not recommended unless one is very familiar
5with them.
6
7NOTE: By following this approach some features supported by the NCBI C++ toolkit
8such as BLAST database access, BLAST formatting, embedded logging, MT locking,
9and configuration support will be absent or only partially supported.
10
11Getting the source code
12-----------------------
13Download the source distribution of BLAST+:
14ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-VERSION+-src.tar.gz
15
16Build instructions
17------------------
18Unpack the source archive in its installation directory and change working
19directory to ncbi-blast-VERSION+-src/c++.
20
21UNIX:
22To build these source files into a library without the rest of the NCBI BLAST+
23applications/libraries, one should use the following commands:
24
25./configure --with-projects=scripts/projects/blast_core_lib.lst \
26 --without-debug --with-mt --with-build-root=ReleaseMT
27cd ReleaseMT/build
28make all_p
29
30This will configure and build an optimized library called blast, which can then
31be referenced in makefiles as follows:
32
33NCBI_HOME=<installation directory of the NCBI C++ toolkit>
34-I$NCBI_HOME/c++/ReleaseMT/inc -I$NCBI_HOME/c++/include
35-L $NCBI_HOME/c++/ReleaseMT/lib
36
37Windows:
381) Open the ncbi_cpp.sln project/solution file
39 c++/compilers/msvc800_prj/static/build/ncbi_cpp.sln.
402) Right click on the -CONFIGURE-DIALOG- project on the Solution Explorer and
41 select "Build" from the context menu, which will bring up a window titled
42 "Project Tree Builder".
433) In the "Project Tree Builder" window's first text box, enter
44 scripts\projects\blast_core_lib.lst, click OK, and on the subsequent window
45 click "Reload".
464) After the environment reloads, right click on blast.lib and select "Build".
47
48The blast.lib library file will be found in
49c++\compilers\msvc800_prj\static\lib\CONF\blast.lib, where CONF represents the
50appropriate configuration (e.g.: debugdll, debugmt, releasedll, or releasemt),
51and the headers will be found in c++\compilers\msvc800_prj\static\inc and
52c++\include
53