+++ /dev/null
-
- $Name: fa_34_26_5 $ - $Id: readme.v34t0,v 1.167 2007/04/26 18:42:43 wrp Exp $
-
->>April 26, 2007
-
-Modify scaleswn.c to prevent mle_cen() from hanging when it fails to
-converge. Also, free() more arrays in work_thr.c; initialize
-m_msg.hist.entries=0 in comp_lib.c, and various clean-ups for a_res
-encoded alignments.
-
->>March 22, 2007
-
-Update faatran.c genetic codes (and documentation on -t option). Update
-ncbl2_mlib.c to parse non-NCBI format 12 databases better.
-
->>March 21, 2007 fasta-34_26_2
-
-Fix conflict between "-S" "-s matrix.file".
-
->>February 26, 2007 fasta-34_26_2
-
-Fix problem with dropfs2.c (curv.start = lpos before initialized).
-
->>January 12, 2007
-
-Fix a problem with pssm_asn_subs.c reading strings (sequences) longer
-than 1024 bytes.
-
-Remove searchfa.cgi, searchnn.cgi, cgi-lib.pl, my-cgi.pl - this code
-was used for an ancient FASTA WWW implementation and has been replaced
-by the FASTA_WWW package.
-
-FASTA Version numbers are being modified to make releases easier to
-track, thus fa34t26b5 has become fasta-34_26_1. I would prefer to use
-decimal versions, but CVS does not allow '.' in tags.
-
->>January 4, 2007 fasta-34_26_1
-
-Include scripts for building Mac OS X Universal binaries on a PPC
-machine. Programs are compiled first with Makefile.os_x (gcc-3.3 for
-PPC) and then installed into ./ppc/. Programs are next compiled with
-Makefile.os_x86 for i386, and the resulting executables installed into
-./i386/. Finally, the "make_osx_univ.sh" script is run to build the
-universal binaries from the two executables using "lipo".
-
->>December 12, 2006
-
-Fix some problems with p2_workcomp.c: (1) no longer initialize pad
-characters for non-existant sequences. (2) deal with small libraries
-consistently with the serial versions.
-
->>November 17, 2006 fa34t26b5
-
-Fixed a problem reading ASN.1 format 2 PSSM's. It is now possible to
-download a PSI-BLAST PSSM RID and search properly. Next, the query
-sequence from the PSSM should be used instead of the provided query
-sequence, so that the query sequence is ignored.
-
->>October 19, 2006 fa34t26b4
-
-Fixed problem with SSE2 code when PSSM's are used.
-
->>October 6, 2006 fa34t26b3
-
-A new set of WIN32 programs is now available that use the Intel C++
-9.1 compiler, rather than the much older Borland Turbo-C compiler. All
-of the unthreaded programs that are part of the Unix and MacOSX FASTA
-distributions are now available. Threaded (multiprocessor) versions
-of the program as available as well, as are sse2 accelerated versions
-of ssearch34 (ssearch34sse2.exe, ssearch34sse2_t.exe).
-
-Th new WIN32 code also uses Microsoft's "nmake" program to build the
-programs, which allows much greater consistency between the Unix and
-Windows versions.
-
-
->>September 18, 2006
-
-Static global alignment variables removed from dropnfa.c, dropfx.c,
-dropfz2.c. dropnfa.c, dropfx.c and dropfz2.c should be thread safe.
-Together with the earlier changes, all the FASTA functions should now
-be thread safe during the alignment process.
-
->>August 17, 2006
-
-Begin removal of static variables from Smith-Waterman alignment
-functions. These variables kept the functions from being thread-safe.
-Now dropgsw.c and dropnsw.c are thread-safe.
-
->>August 15, 2006 fa34t26b2
-
-Fixed a problem with pv34compfx/mp34compfx (and fy) producing
-improperly labeled alignments and de-allocating memory for the reverse
-complement.
-
->>July 18, 2006
-
-The library file name parsing programs now provide the option for
-environment variable substitions. For example, SLIB2=/slib2 as an
-environment variable (e.g. export SLIB2=/slib2 for ksh and bash), then
-
- fasta34 -q query.aa '${SLIB2}/swissprot.fa' expands as expected.
-
-While this is not important for command lines, where the Unix shell
-would expand things anyway, it is very helpful for various
-configuration files, such as files of file names, where:
-
- <${SLIB2}/blast
- swissprot.fa
-
-now expands properly, and in FASTLIBS files the line:
-
- NCBI/Blast Swissprot$0S${SLIB2}/blast/swissprot.fa
-
-expands properly. Currently, Environment variable expansion only
-takes place for library file names, and the <directory in a file of
-file names.
-
->>July 14, 2006 fa34t26b1
-
-Updated Farrar smith_waterman_sse2.c code to address possible bug
-(code from Michael Farrar). Include <sunmedia_intrin.h> for
-compilation with Sun compiler with Makefile.sun_x86.
-
->>July 2, 2006 fa34t26b0
-
-This release provides an extremely efficient SSE2 implementation of
-the Smith-Waterman algorithm for the SSE2 vector instructions written
-by Michael Farrar (farrar.michael@gmail.com). The SSE code speeds up
-Smith-Waterman 8 - 10-fold in my tests, making it comparable to Eric
-Lindahl's Altivec code for the Apple/IBM G4/G5 architecture.
-
-The Farrar code is largely confined to smith_waterman_sse2.c and
-smith_waterman_sse2.h, which are copyright (2006) by Michael Farrar,
-and cannot be redistributed without his permission. Mr. Farrar has
-agreed to provide his code under the same policy used by FASTA -
-e.g. the code can be used without permission, but not redistributed.
-
-The Farrar code uses GCC version 4.0 SSE2 intrinsic functions to avoid
-assembly language code. Unfortunately, in my hands, "gcc -O3" causes
-"out of memory" errors, and other problems, so "gcc -O" is used instead.
-
->>June 23, 2006 fa34t25d10
-
-Modifications to comp_lib.c, compacc.c, and other files to ensure that
-function-specific MAXTOT values are used properly. MAXTOT is now
-available as m_msg.max_tot, which is set in initfa.c (m_msg.max_tot =
-MAXTOT) to ensure that functions that need very large MAXTOT values
-(e.g. TFASTX) can get them. tfastx can now search successfully with
-titin, a 27,000 residue protein.
-
-Other changes have been made to accomodate long query sequences.
-
-A serious bug was found in fastx34(_t) that caused alignment
-coordinates to be calculated improperly when the DNA sequence was much
-longer than the protein sequence.
-
->>May 31, 2006 fa34t25d9
-
-Fixed some problems with fasts/fastf alignments when -m 9 options were
-used. Unlike the other algorithms, the a_res structure does not
-capture all the information to re-produce an alignment, so do_walign
-now sets bptr->have_ares to indicate whether the a_res structure is
-valid.
-
-Various problems with bad library names, and short query titles were
-also fixed.
-
-Updated version number/date on all drop*.c functions.
-
->>May 24, 2006 fa34t25d8
-
-Revised code for NCBI *.pal/*.nal databases has been tested on all
-architectures, including Windows.
-
-In addition, support for ASN.1 PSSM:2 files provided by the NCBI
-PSI-BLAST WWW site is included. This code will not work with
-iteration 0 PSSM's (which have no PSSM information). For ASN.1
-PSSM's, which provide the matrix name (and in some cases the gap
-penalties), the scoring matrix and gap penalties are set appropriately
-if they were not specified on the command line. ASN.1 PSSM's are type 2:
- ssearch34 -P "pssm.asn1 2" .....
-
->>May 18, 2006
-
-Support for NCBI Blast formatdb databases has been expanded. The
-FASTA programs can now read some NCBI *.pal and *.nal files, which are
-used to specify subsets of databases. Specifically, the
-swissprot.00.pal and pdbaa.00.pal files are supported. FASTA supports
-files that refer to *.msk files (i.e. swissprot.00.pal refers to
-swissprot.00.msk); it does not currently support .pal files that
-simply list other .pal or database files (e.g. FASTA does not support
-nr.pal or swissprot.pal).
-
-In the process of providing this support, the routines used to read
-ASN.1 binary formatdb files were substantially improved. It is now
-possible to see multiple description lines for a single sequence.
-
-IS_BIG_ENDIAN has been removed from all of the Makefiles. The code
-now looks for the definition of __BIG_ENDIAN__ or _BIG_ENDIAN to
-decide whether the architecture IS_BIG_ENDIAN. If, for some reason,
-one of these macros is not defined on a BIG_ENDIAN architecture, then
--DIS_BIG_ENDIAN is required.
-
->>May 12, 2006 CVS fa34t25d7
-
-Corrected serious problem with coordinate display calculation for
-fasta34 and ssearch34 - in some cases the coordinates and alignment
-symbols were off by the length of the context (typically 30 residues).
-
-Added capability to read ASN.1 binary PSSM information. This
-information is provided (in an encoded form) from the NCBI PSI-BLAST
-WWW site. (What is actually provided from the WWW site is a bzip2-ed
-binary file that is converted to ASCII HEX. The ASCII HEX file must
-be converted to binary, and then bunzip'ed. This bunzip-ed file is
-binary ASN.1.) These files can also be generated by
-
- blastpgp -J T -C pssm.asn1_bin -u 2
-
-I am parsing the ASN.1 binary manually, not using the NCBI toolkit, so
-there may be some files that are not parsed properly - if so, let me
-know.
-
-(May 12, 2006 - The NCBI changed the format of the psi-blast ASN.1
-PSSM - and has not yet provided documentation of the new structure, so
-this code does not work. It does work with blastpgp v 2.2.13, but not
-with the web site version 2.2.14. A fix was provided 24-May-2006)
-
->>April 18, 2006
-
-Small modification in mshowbest.c to provide more consistent display
-widths with -m 9i in list of best hits.
-
->>April 11, 2006 CVS fa34t25d6
-
-Corrected a problem introduced with the new, more efficient method for
-displaying alignments. For the tfast* programs, which must translate
-the library sequence, translations were not done when alignments were
-re-displayed.
-
-Corrected an older problem with tfastx34 against very long sequence
-databases - the code to more efficiently do the display alignment did
-not use the correct sequence coordinates.
-
-Modifications to dropfs2.c to ensure that exact peptide matches are
-captured more frequently.
-
->>March 16, 2006 CVS fa34t25d5
-
-Change to initfa.c to allow lower case DNA libraries using the
--DDNALIB_LC compile time option.
-
-Modify p2_complib.c, p2_worklib.c (and doinit.c, msg.h) to allow the
--V annotation option for the parallel programs. Also modify to allow
-specification of the query range (but only for the first query, like
-fasta34) for the parallel programs.
-
-Modification of p2_workcomp.c to correct some problems presenting
-percent similarity. Also correct unreleased bugs in the alignment
-routines that allow more efficient alignment re-calculation.
-
->>Nov 20, 2005
-
-Changes to support asymmetric matrices - a scoring matrix read in from
-a file can be asymmetric. Default matrices are all symmetric.
-
->>Oct 24, 2005
-
-Modifications extended to p2_complib.c/p2_workcomp.c. Incorporation
-of drop_func.h into p2_workcomp.c greatly simplifies things. No
-changes in communication - struct a_res_str is internal to
-p2_workcomp.c.
-
-Additional changes to do_walign() so that aln_func_vals() must be
-called to set llfact, qlfact, etc in a_struct aln before or after
-do_walign is called. do_walign produces a_res_str a_res, which has
-all the information necessary to produce a calcons() or calc_code()
-alignment.
-
->>Oct 19, 2005 CVS fa34t26b0
-
-Modifications to drop*.c and c_dispn.c to separate (and simplify) some
-of the alignment coordinate calculations. Before, the "a_struct" had
-the coordinates of the alignment used in the display (seqc0, seqc1)
-AND in the original sequences (aa0, aa1), as well as other information
-used to calculate alignment coordinates. In the new version, astruct
-coordinates always refer to seqc0,1, while a new structure, a_res_str,
-has coordinates for aa0, aa1 as well as the alignment encoding in res[nres].
-Eventually, this should make it possible to display multiple local
-alignments from the same two sequences.
-
-In addition, the file "drop_func.h" has been added to the project, and
-is included by many of the files (all the drop*.c functions,
-mshowbest.c, mshowalign.c) to ensure that the various functions are
-declared and used consistently.
-
->>Sept 19, 2005 CVS fa34t25d4
-
-Changes to support Mac OS 10.4 - Tiger (include sys/types.h in more
-files). Documentation update for prss34/prfx34. Modifications to
-comp_lib.c to support prss34_t/prfx34_t. Shuffle numbers for
-prss/prfx can now be specified by "-k #".
-
->>Sept 2, 2005
-
-The prss34 program has been modified to use the same display routines
-as the other search programs. To be more consistent with the other
-programs, the old "-w shuffle-window-size" is now "-v window-size".
-
-prss34/prfx34 will also show the optimal alignment for which the
-significance is calculated by using the "-A" option.
-
-Since the new program reports results exactly like other
-fasta/ssearch/fastxy34 programs, parsing for statistical significance
-is considerably different. The old format program can be make using
-"make prss34o".
-
->>Aug 26, 2005
-
-Modifications to save_best() in comp_lib.c to support prss34_t. It
-did not work before.
-
->>July 25, 2005
-
-Modify mshowbest.c to suppress gi|12345 in HTML mode.
-
->>July 18, 2005 CVS fa34t25d3
-
-Modifications to Makefile.tc to support NCBI formatdb formats under
-Windows.
-
->>May 19, 2005 CVS fa34t25d2
-
-Modifications to dropfs2.c to fix an obscure bug that occurred when
-correctly ordered peptides aligned one residue apart.
-
->>May 5, 2005 CVS fa34t25d1
-
-Modification to the -x option, so that both an "X:X" match score and
-an "X:not-X" mismatch score can be specified. (This score is also used
-
-give a positive score to a "*:*" match - the end of a reading frame,
-while giving a negative score to "*:not-*".
-
->>March 14, 2005 CVS fa34t25b4
-
-Fixed some problems caused by padding characters required for
-Smith-Waterman ALTIVEC in the parallel (p2_complib.c, p2_workcomp.c)
-versions.
-
->>Feb 24, 2005 CVS fa34t25b3
-
-Changes to comp_lib.c (and Makefile.pcom) to support prss34_t.
-
->>Feb 12, 2005
-
-Modify dropfs.c to dynamically allocate space for alignments, so that
-queries with a large number of fragments can still place all the
-fragments on the alignment. Also fix a problem produced by removing
--DBIGMEM from most of the Makefile's, but not fixing defs.h to use
-BIGMEM sizes by default.
-
->>Jan 24, 2005
-
-Include a new program, "print_pssm", which reads a blastpgp binary
-checkpoint file and writes out the frequency values as text. These
-values can be used with a new option with ssearch34(_t) and prss34,
-which provides the ability to read a text PSSM file. To specify a
-text PSSM, use the option -P "query.ckpt 1" where the "1" indicates a
-text, rather than a binary checkpoint file. "initfa.c" has also been
-modified to work with PSSM files with zero's in the in the frequency
-table. Presumably these positions (at the ends) do not provide
-information. (Jan 26, 2005) blastpgp actually uses BLOSUM62 values
-when zero frequencies are provided, so read_pssm() has been modified
-to use scoring matrix values for zero frequencies as well.
-
->>Jan 13, 2005
-
-Change to initfa.c to have fasts34 do a protein comparison by default,
-rather than an unknown sequence type. Automatic checking for fasts34
-does not work reliably, because queries can be very short. Likewise
-for fastm34. [Jan 26, 2004] Undo this change, which broke DNA
-comparison when "-n" was specified.
-
->>Jan 7, 2005
-
-Changes to tatstats.h, dropfs2.c to allow larger numbers of peptides
-to match when fasts is used to show coverage on a proteomics
-experiment. Previously fasts could match no more than 30 peptides,
-that has been increased to 50. In addition, ktup=2 can be used
-to increase the likelihood that short exact matchs trump longer
-mismatched regions.
-
->>Nov 11, 2004 CVS fa34t25
-
-Finished merge of earlier fa34t24 branch with HEAD. Correct
-labeling of TFASTM.
-
->>Nov 4-8, 2004
-
-Incorporation of Erik Lindahl "anti-diagonal" Altivec code for
-Smith-Waterman, only. Altivec SSEARCH is now faster than FASTA for
-query sequences < 250 amino acids.
-
-Small modifications to output score display to ensure that the correct
-scores are shown, and that they are correctly labeled.
-
->>Aug 25,26, 2004 CVS fa34t24b3
-
-Small change in output format for p34comp* programs in
-">>>query_file#1 string" line before alignments. This line is not present
-in the non-parallel versions - it would be better for them to be consistent.
-
-Change in last_stats.c to properly label fasts statistics with -z != 1.
-
-Change in dropfs2.c to ensure that tatprobs are not precalculated with -z 4.
-
-Modify -m 9i output option to show in HTML output.
-
-Add "#ifdef NOOVERHANG" to dropfs2.c that causes overlapping
-alignments to score a 0, rather than the partial overlap score.
-Useful for SAGE alignments, because "fasts" requires global alignments
-(except for for overhangs, unless NOOVERHANG is defined).
-
->>Aug 23, 2004
-
-Fix problem with very long definition lines with formatdb version4
-ASN databases. Fix mshowalign.c to re-enable "-L" option.
-
->>July 28, 2004
-
-Fix to re-enable -w window shuffle for PRSS. Modify comp_lib.c
-for PRSS to ensure that the unshuffled score and probability
-are shown, even for very high probabililty alignments.
-
->>July 21, 2004
-
-Modifications to support PostgreSQL databases with the same commands
-as MySQL databases. MySQL database libraries are type 16, PostgreSQL
-are type 17. Makefile.linux_sql and Makefile.pvm4_sql support both
-database types simultaneously.
-
->>June 23, 2004 CVS fa34t24b2
-
-Additional fixes to enable -n or -p with fasts34 and
-fastm34. Makefile.pcom was fixed for fastm34_t. A new file,
-mgstm1.nts, of DNA fragments from mgstm1.seq, is included for testing
-fasts34 and fastm34.
-
->>May 4, 2004
-
-Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM. This change
-introduced a bug that broke FASTS completely, but was fixed June 18,
-2004 (and retagged fa34t24b2).
-
->>April 23, 2004 CVS fa34t24b1
-
-Fix bug in initfa.c that caused tfasts/tfastf not to examine all six
-frames.
-
->>May 4, 2004
-
-Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM.
-
->>March 19, 2004 CVS fa34t24b0
-
-Modify all the drop*.c files, plus mshowbest.c and mshowalign.c, to
-display percent similarity, rather than percent ungapped. An
-alignment is counted as similar if the score is greater than or equal
-to zero (the same criterion used for placing ".". To disable this
-change, remove -DSHOWSIM from the appropriate Makefile.*.
-
->>March 18, 2004 CVS fa34t23b8
-
-Fix bug in initfa.c tables that caused prss to generally compare
-proteins.
-
->>March 15, 2004
-
-Fix bug in calls to revcomp(); make revcomp() guarantee NULL termination.
-
->>March 2, 2004 CVS fa34t23b7
-
-Fix a very embarrassing and surprising bug that caused insertions
-in fasta alignments to appear in the wrong sequence.
-
->>Feb 7, 2004 CVS fa34t23b6
-
-Change initfa.c to allow "-i" (reverse complement) and "-i -3" with
-"fastx34" and "prfx34". In addition, "prfx34" now examines both query
-DNA strands in calculated the shuffled statistical significance.
-
->>Feb 5, 2004
-
-Reverse assignments for G:U baseparing in initfa.c.
-
-Fix memory allocation error caused by doubling DNA alignment width.
-
->>Jan 7, 2004 CVS fa34t23b5
-
-Change in do_walign() in dropnfa.c to make final DNA alignments use a
-band that is 2X as large as the search band width.
-
->>Dec 22, 2003 CVS fa34t23b4
-
-Fix typo in p2_complib.c that prevented compilation. Fix problem
-with karlin.c for assymetrical matrices, such as used with -U.
-
->>Dec 10, 2003 CVS fa34t23b3
-
-Fix problem in resetp()/initfa.c that disabled banded Smith-Waterman
-DNA alignments.
-
-Allow spam() to do extended alignments for DNA if one of the sequences
-is < 50 nt.
-
-Cause default ktup to drop for short sequences. For protein < 50, ktup=1;
-for DNA < 20, 50, 100 ktup = 1, 2, 3, respectively.
-
->>Dec 7, 2003
-
-A new option, "-U" is available for RNA sequence comparison. "-U"
-functions like "-n", indicating that the query is an RNA sequence. In
-addition, to account for "G:U" base pairs, "-U" modifies the scoring
-matrices so that a "G:A" match has the same score as a "G:G" match,
-and "T:C" match has the same score as a "T:T" match. The asymmetric
-matrix required changes in dropnfa.c that were similar to the changes
-in dropgsw.c required for profiles. In addition, m_msg.qdnaseq and pst.dnaseq
- can now be SEQT_DNA, SEQT_RNA, SEQT_PROT, SEQT_UNK, or SEQT_OTHER.
-m_msg.ldnaseq does not use SEQT_RNA, only SEQT_DNA. A new member of
-struct pstruct: int nt_align, is used to indicate nucleotide
-alignments.
-
->>Nov 19, 2003
-
-Changes to Makefile's to distinguish between tatstats_fs.o and
-tatstats_ff.o.
-
->>Nov 2, 2003
-
-Substantial changes to comp_lib.c, p2_complib.c, mshowbest.c, and
-mshowalign.c to support more sophisticated display options.
-Previously, one could have only on "-m #" option, even though several
-of the options were orthogonal (-m 9c is independent of -m 1 and -m2,
-which is independent of -m 6 (HTML)). The programs now use a bitmask
-that allows independent options to be combined. In particular -m 9c
-can be combined with -m 6, which can be very helpful for runs that
-need HTML output but can also exploit the encoding provided by -m 9c.
-
-The "-m 9" option now also allows "-m 9i", which shows the standard
-best score information, plus percent identity and alignment length.
-
->>Oct 26, 2003 CVS fa34t23b1
-
-Additional fixes to Makefiles to enable tfastf34(_t). Changes to
-support ossearch34 (a non-Phil Green optimized Smith-Waterman).
-
->>Oct 8, 2003 CVS fa34t23b0
-
-Fixes to get DNA queries working in both directions, and to fix PCOMPLIB
-programs for "-V" option. Currently, the parallel programs cannot use
-the "-V" option.
-
->>Sept 25, 2003
-
-A new option is available for annotating alignments. -V '@#?!'
-can be used to annotate sites in a sequence, e.g:
- >GTM1_HUMAN ...
- PMILGYWDIRGLAHAIRLLLEYTDS@S?YEEKKYT@MG
- DAPDYDRS@QWLNEKFKLGLDFPNLPYLIDGAHKIT
-might mark known and expected (S,T) phosphorylation sites. These
-symbols are then displayed on the query coordinate line:
-
- 10 20 @? 30 @ 40 @ 50 60
-GTM1_H PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-gtm1_h PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
- 10 20 30 40 50 60
-
-This annotation is mostly designed to display post-translational
-modifications detected by MassSpec with FASTS, but is also available
-with FASTA and SSEARCH.
-
->>Sept 22, 2003 CVS fa34t22b5
-
-The Altivec Smith-Waterman code has been removed.
-
->>Sept 17, 2003 CVS fa34t22b4
-
-A variety of different bugs have been fixed. (1) All the functions in
-the old initsw.c are now in initfa.c; initsw.c will be removed.
-Specifically, the Profile/PSSM code is now in initfa.c. initfa.c is
-now fully table driven. (2) various problems with prss34 and prfx34
-have been fixed in initfa.c. (3) An additional ncbl2_mlib.c buffer
-overrun has been fixed. (4) fastf34 is now available in this package.
-Its performance is very similar to, but not identical to, fastf33. I
-am tracking down the differences. In general, the raw scores
-calculated by both programs are the same, but the statistical analysis
-seems to be slightly different.
-
->>July 30, 2003 CVS fa34t22b3
-
-Fix bug in ncbl2_mlib.c that caused buffer overrun with blast/formatdb
-v3 description lines.
-
->>July 28, 2003
-
-The initfa.c file has been substantially re-structured to use a
-table-driven approach to parameter setting, rather than the previous
-confusing combinations of #ifdef's. Two tables of parameters are
-used, pgm_def_arr[] and msg_def_arr[], which specify values like the
-program name, reference, scoring matrix, default gap penalties, etc.
-msg_def_arr[] has the sequence types for the query, library, and
-algorithm, as well as other parameters (qframe, nframe, nrelv, etc),
-which greatly simplifies the sequence recognition logic. ppst->pgm_id
-can be used to identify the program that is running. Eventually,
-almost all of the program specific #ifdef's will be removed from
-initfa.c. initfa.c now provides initsw.c functionality, so that
-initsw.c is no longer needed.
-
->>July 25, 2003
-
-A new file is included - fasta.defaults - that lists the scoring
-matrix, gap penalty, and other defaults for all of the fasta34
-programs. This file will be used soon to simplify parameter setting
-for the FASTA programs, and should also be used by Javascript WWW
-interfaces to the FASTA programs.
-
->>July 22, 2003 CVS fa34t22b2
-
-Fixes to dropfs2.c, tatprobs.c to ensure that negative probabilities
-cannot occur. Negative probabilities were never seen with standard
-matrices, but did occur with BL50. Another optimization in dropfs.c
-considerably improves fasts34 performance in some cases.
-
-Fix a problem with formatdb v4 ASN.1 format files.
-
->>July 12, 2003
-
-Fix a bug that prevented "-L" (long sequence descriptions) from
-working.
-
->>July 9, 2003
-
-Fix reverse complement (M:K) error. Fix off-by-one error for FASTA
-DNA alignments that caused the first aligned residue pair to be
-missed.
-
->>July 4 - 8, 2003
-
-Incorporate blast-def-line ASN.1 parsing so that NCBI formatdb version
-4 files can be read.
-
->>June 26, 2003
-
-The strategy for displaying the match/mismatch line (" .:" for -m 0)
-has been changed dramatically to acommodate more sophisticated
-strategies for indicating conservative replacements, e.g. because of
-PSSM's. In addition to seqc0 and seqc1, which hold the aligned
-sequences for display, there is also seqca, which holds the alignment
-symbol. calcons(), do_show(), and discons() have all changed to
-include seqca. calcons() is somewhat more complex; discons() is much
-simpler. (June 29, 2003 - dropgsw.c calcons() now displays profile
-similarity accurately - it is very very illuminating.)
-
->>June 16, 2003 version: fasta34t22
-
-ssearch34 now supports PSI-BLAST PSSM/profiles. Currently, it only
-supports the "checkpoint" file produced by blastall, and only on
-certain architectures where byte-reordering is unnecessary. It has not
-been tested extensively with the -S option.
-
- ssearch34 -P blast.ckpt -f -11 -g -1 -s BL62 query.aa library
-
-Will use the frequency information in the blast.chkpt file to do a
-position specific scoring matrix (PSSM) search using the
-Smith-Waterman algorithm. Because ssearch34 calculates scores for
-each of the sequences in the database, we anticipate that PSSM
-ssearch34 statistics will be more reliable than PSI-Blast statistics.
-
-The Blast checkpoint file is mostly double precision frequency
-numbers, which are represented in a machine specific way. Thus, you
-must generate the checkpoint file on the same machine that you run
-ssearch34 or prss34 -P query.ckpt. To generate a checkpoint file,
-run:
-
-blastpgp -j 2 -h 1e-6 -i query.fa -d swissprot -C query.ckpt -o /dev/null
-
-(This searches swissprot for 2 iterations ("-j 2" using a E()
-threshold 1e-6 saving the resulting position specific frequencies in
-query.ckpt. Note that the original query.fa and query.ckpt must
-match.)
-
->>June 5, 2003
-
-Fix to mshowbest.c to get -m 9 coordinates correct on reverse strand
-with pv34comp*. Some additional fixes for prfx34.
-
->>May 22, 2003
-
-Changes to llgetaa.c, getseq.c, comp_lib.c to provide a different
-library residue lookup table (sascii) for queries and libraries. This
-allows one to make a prfx34 (like prss34, but using the fastx
-algorithm). prfx34 is now available.
-
->>May 13,14 2003
-
-Fixes to most of the drop*.c files, and mshowbest.c, to ensure that
-coordinates displayed with -m 9(c) and the final alignment are
-consistent. They were consistent for fasta34/ssearch34/fasts34, but
-not for fastx34/fasty34. The alignment coordinate system has been
-been revised for consistency in allthe drop*.c programs (coordinates
-used to be off-by-one for some, but not other functions).
-
-Fixes to -m 9c for fasty34/pv34compfy. In addition, a problem was
-fixed with fastx34/fasty34 that appeared with a protein sequence was
-considerably longer than the DNA query, e.g. an EST vs titin (26K
-residues). This problem only appeared on pv34compfx/fy on Xserve's
-under OS_X; but it should improve fastx34/fasty34 performance with
-very long protein sequences on all platforms.
-
->>May 7,8 2003
-
-Changes to p2_workcomp.c, compacc.c, and p_mw.h to fix persistent
-bugs in the -m 9c display. Previous pv34comp* programs would not
-return the correct coded alignment if more than 100 alignments came
-from the same node, or if an encoding was longer than 127 chars.
-
-Also, fixes to p2_complib.c, comp_lib.c, to allow long query sequences
-to be segmented. Previously, only the first 20,000 residues were
-used. The segmented queries are not overlapped; segmented library
-sequences are.
-
->>May 5, 2003
-
-Changes to last_tat.c, scaleswt.c to ensure that all fasts alignments
-that are likely to have significant scores are displayed. In previous
-implementations, if the query had more than 10 fragments, only the 100
-best scores were shown. Now, we rescore up to 2500 alignments. The
-new approach allows large mixtures to be used for searches, where some
-of the fragments from the mixture match too many proteins
-(e.g. actins). Some differences between the fasts34 and pv34compfs
-implementations have been fixed. The two programs typically will not
-give exactly the same results, because of small differences in the
-sampling procedures, but the results are essentially equivalent.
-
->>Apr 11, 2003 CVS fa34t21b3
-
-Fixes for "-E" and "-F" with ssearch34, which was inadvertantly disabled.
-
-A new option, "-t t", is available to specify that all the protein
-sequences have implicit termination codons "*" at the end. Thus, all
-protein sequences are one residue longer, and full length matches are
-extended one extra residue and get a higher score. For
-fastx34/tfastx34, this helps extend alignments to the very end in
-cases where there may be a mismatch at the C-terminal residues.
-
--m 9c has also been modified to indicate locations of termination
-codons ( *1).
-
->>Mar 17, 2003 CVS fa34t21b2
-
-A new option on scoring matrices "-MS" (e.g. "BL50-MS") can be used to
-turn the I/L, K/Q identities on or off. Thus, to make "fastm34" use
-the isobaric identities, use "-s M20-MS". To turn them off for "fasts34",
-use "-s M20".
-
-More fixes for correct alignment coordinates. There was a conflict between
--m 9 and -m 9c and subsequent alignment displays.
-
->>Mar 13, 2003
-
-Various fixes to produce correct fastm34 alignments. Changes to all
-functions to correct potential problem with -m 9 alignment coordinates
-when both -m 9 and actual alignments are shown.
-
->>Feb 25,27, 2003
-
-Modifications to re-activate showsum.c, which included corrections to
-the showbest() call in p2_complib.c.
-
->>Feb 13, 2003 CVS fa34t21b1
-
-Modifications to dropfx.c to dramatically improve alignment speed for
-cases where the DNA sequence is considerably longer than the protein
-sequence. Previously, a 200 aa vs 5000 nt comparison would do a full
-200 x 5000 Smith-Waterman alignment; with this modification, no more
-than a 200 x 1200 (2x3x200) alignment is done. This optimization has
-not (yet) been applied to dropfz2.c (fasty/tfasty).
-
->>Feb 11, 2003
-
-Small modifications to comp_lib.c, p2_complib.c, and nmgetlib.c to
-pass openlib() a possibly old lmf_str. This allows openlib() to
-re-use memory mapped files. closelib() no longer releases memory
-mapped file buffers. Under Linux, memory mapped file buffers were not
-really released, so when comparing a set of sequences against nr, the
-program could not mmap() the database after several searches. This
-will also speed up memory mapped multiple sequence searches.
-
->>Jan 28-31, 2003 CVS fa34t21b0
-
-Fix another bug (all of v34t20) involved with overlapping long
-sequences. And another bug that occurred when using sampled
-statistics, but appeared only on the SGI platform - thanks to Dmitri
-Mikhailov. Several other issues have been addressed based on more
-instrumented runtime testing.
-
-Fix an old (all v34) bug that caused problems with -z 11-16 (shuffled
-sequence array was not allocated properly). Fixed another bug with -z
-6/16 when using threaded (_t) searches in fasta34_t.
-
-Restructure statistical analysis functions (scaleswn.c, scaleswt.c) to
-return the "final" statistical estimation routine done in pst.zsflag_f.
-This allows the program to cope with searches against a single sequence
-correctly.
-
-Corrected an error for DNA sequences needing Altschul-Gish statistics.
-
->>Jan 25, 2003
-
-Add option "-J start:stop" to pv34comp*/mp34comp*. "-J x" used to
-allow one to start at query sequence "x"; now both start and stop can
-be specified.
-
->>Jan 14, 2003
-
-Changes to apam.c to provide an error message on stderr when a scoring
-matrix cannot be found.
-
-Changes to dropfs2.c, initsw.c, initfa.c to provide -m9c information
-for fasts34 searches. Modify the alignment algorithm to use
-probabilistic scores properly.
-
->>Dec 22, 2002
-
-Change to compacc.c (sortbeste()) to do a second sort on zscore when
-several sequences have E() == 0.
-
->>Nov 27, 2002
-
-Change FSEEK_T to fseek_t to keep Borland BCC5 happy.
-
->>Nov 14-22, 2002 CVS fa34t20b6
-
-Include compile-time define (-DPGM_DOC) that causes all the fasta
-programs to provide the same command line echo that is provided by the
-PVM and MPI parallel programs. Thus, if you run the program:
-
- fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12
-
-the first lines of output from FASTA will be:
-
- # fasta34_t -q gtt1_drome.aa /slib/swissprot
- FASTA searches a protein or DNA sequence data bank
- version 3.4t20 Nov 10, 2002
- Please cite:
- W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
-
-This has been turned on by default in most FASTA Makefiles.
-
-Fix p2_complib.c so that qstats[] is always allocated before it is used.
-
-Fix serious bug in non-threaded comp_lib.c that caused some high
-scoring sequences to be missed by fasts34. New tests are included in
-test.sh to detect this problem in the future.
-
-The shell sort algorithm in sortbeste(), sortbestz(), and sortbesto()
-has been modified to use an improved algorithm that will not go
-quadratic in pathological cases.
-
-nmgetlib.c and mmgetaa.c have been modified to remove "^A" in libstr
-when used with p2_complib.c.
-
-Fix problem with MAXSEG in tatstats.h with IBM/AIX.
-
-Changes to most Makefiles to use -DSAMP_STATS; fixes to p2_complib.c
-for SAMP_STATS.
-
->>Oct 22, Nov 3, Nov 9, 2002 CVS tag fa34t20b5
-
-Fix problem in comp_lib.c that caused the query sequence length to be
-counted twice.
-
-Fixed problem with prss34 (updated find_zp in showrss.c).
-
-Correct shuffling function in several places.
-
-Add jitter back to addhistz() - improves appearance with prss34.
-
-Changes to fix problems with aln_code using -m 9c.
-
-Fix to serious bug in scaleswt.c (fasts34, etc) that caused sorts on
-the high scores to take much to long. The program is now 10X faster,
-and scales well on PVM/MPI.
-
-Fix to llgetaa.c to work with new getseq() API with automatic alphabet
-recognition.
-
->>Oct 12, 2002 CVS tag fa34t20b4
-
-Several very obscure (and sometimes old) bugs that appeared in certain
-MPI environments have been fixed. This occurred because the pst.sq[]
-array did not always have a '\0' at the end. In addition,
-mshowalign.c/p2_workcomp.c sometimes failed to put the '\0' at the end
-of seqc0/seqc1. Correct bug introduced in fa34t20b3 for fasts34(_t).
-
->>Oct 9, 2002 CVS tag fa34t20b3
-
-Fix to apam.c build_xascii() to not zero-out qascii[0]. Fix
-Makefile.pvm4. Mix problem with -m 9c with compacc.c.
-
->>Sept 28, 2002
-
-Additional fixes to -m 9c in p2_complib.c/compacc.c/mshowbest.c.
-Remove restriction in fasts34(_t) to less than 30 peptides (though no
-more than 30 peptides can be aligned currently).
-
->>Sept 24, 2002
-
-Fix p2_workcomp.c so that e_scores are delivered correctly when
-last_calc flag is set, and -m 9c provides alignments when only one
-best hit is present.
-
-Fix comp_lib.c to use different maxn and overlap for each different
-query sequence. fasta34 and fasta34_t now have identical results when
-a long sequence is searched.
-
-Add '@C:101' support to memory mapped FASTA format files.
-
-Fix mshowalign.c so that coordinates returned by cal_coord() use
-loffset+l_off.
-
->>Sept 14, 2002 CVS tag fa34t20b2
-
-Changes to p2_complib.c, compacc.c to fix statistics problems with
-pv34compfs on query sequences with more than 10 fragments.
-
->>Aug 27, 2002
-
-Modifications to mshowbest.c and drop*.c (and p2_workcomp.c,
-compacc.c, doinit.c, etc.) to provide more information about the
-alignment with the -m 9 option. There is now a "-m 9c" option, which
-displays an encoded alignment after the -m 9 alignment information.
-The encoding is a string of the form: "=#mat+#ins=#mat-#del=#mat".
-Thus, an alignment over 218 amino acids with no gaps (not necessarily
-100% identical) would be =218. The alignment:
-
- 10 20 30 40 50 60 70
-GT8.7 NVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQ
- :.:: . :: :: . .::: : .: ::.: .: : ..:.. ::: :..:
-XURTG NARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQ
- 20 30 40 50 60
-
-would be encoded: "=23+9=13-2=10-1=3+1=5". The alignment encoding is
-with respect to the beginning of the alignment, not the beginning of
-either sequence. The beginning of the alignment in either sequence is
-given by the an0/an1 values. This capability is particularly useful
-for [t]fast[xy], where it can be used to indicate frameshift positions
-"/#\#" compactly. If "-m 9c" is used, the "The best scores" title
-line includes "aln_code".
-
->>Aug 14, 2002 CVS tag fa34t20
-
-Changes to nmgetlib.c to allow multiple query searches coming from
-STDIN, either through pipes or input redirection. Thus, the command
-
- cat prot_test.lseg | fasta34 -q -S @ /seqlib/swissprot
-
-produces 11 searches. If you use the multiple query functions, the
-query subset applies only to the first sequence.
-
-Unfortunately, it is not possible to search against a STDIN library,
-because the FASTA programs do not keep the entire library in memory
-and need to be able to re-read high-scoring library sequences. Since
-it is not possible to fseek() against STDIN, searching against a STDIN
-library is not possible.
-
->>Aug 5, 2002
-
-fasts34(_t) and fastm34(_t) have been modified to allow searches with
-DNA sequences. This gives a new capability to search for DNA motifs,
-or to search for ordered or unordered DNA sequences spaced at
-arbitrary distances.
-
->>Aug 4, 2002
-
-comp_lib.c has been modified to provide comp_mlib.c function.
-comp_mlib.c is no longer used. comp_lib.c with the "mlib" function
-can now recognize protein or DNA sequences automatically, and reads
-from stdin can now detect DNA/protein sequence types automatically.
-Changes to compacc.c, getseq.c, doinit.c initfa.c, initsw.c, and
-nmgetlib.c to support automatic sequence type detection.
-
->>July 28-31, 2002
-
-(1) The various Makefile's have been "normalized". The fast*34[_t]
- (Makefile.34m.common[_sql]), Makefile.pvm4[_sql], and
- Makefile.mpi4[_sql] make files all use a common set of filenames,
- described in Makefile.fcom. This greatly simplifies adding
- programs, but requires that all *.o files be deleted when moving
- from fast*34* to pv34comp* to mp34comp*.
-
-(2) showalign.c/p_showalign.c have been merged into mshowalign.c
- showbest.c/manshowbest.c have been merged into mshowbest.c. Some
- of the related files (showun.c, manshowun.c, have not been merged
- or tested).
-
-(3) Code for ranking scores with valid e_value's incorporated.
-
-(4) Bug fixes in p2_complib.c, so that fasts34/fasts34_t/pvcompfs
- provide identical statistics.
-
->>July 26, 2002
-
-Makefile.pvm4_sql and Makefile.pvm4 have been substantially simplified
-by providing the worker program name from the h_init() function in the
-initfa.c/initsw.c files.
-
->>July 24, 2002
-
-Substantial modifications to param.h, structs.h to ensure that no
-sequence specific information is kept in struct pstruct. This
-structure now holds the pam[] matrix, and other scoring parameters,
-but nothing that is dependent on aa0. The aa0 dependent stuff (nm0,
-Lambda, K, etc) is now stored in struct mngmsg. This was mostly done
-to support the pv34comp* programs, which have separate mngmsg
-structures but the same pstructs.
-
-The fasts34, fasts34_t, and pv34compfs/c34.workfs have all been tested
-successfully.
-
->>July 19, 2002
-
-Fix an old bug in the calculation of E()-values in DNA databases
-longer than 2147483647 residues on machines with 32-bit longs.
-
-
->>July 28-31, 2002
-
-(1) The various Makefile's have been "normalized". The fast*34[_t]
- (Makefile.34m.common[_sql]), Makefile.pvm4[_sql], and
- Makefile.mpi4[_sql] make files all use a common set of filenames,
- described in Makefile.fcom. This greatly simplifies adding
- programs, but requires that all *.o files be deleted when moving
- from fast*34* to pv34comp* to mp34comp*.
-
-(2) showalign.c/p_showalign.c have been merged into mshowalign.c
- showbest.c/manshowbest.c have been merged into mshowbest.c. Some
- of the related files (showun.c, manshowun.c, have not been merged
- or tested).
-
-(3) Code for ranking scores with valid e_value's incorporated.
-
-(4) Bug fixes in p2_complib.c, so that fasts34/fasts34_t/pvcompfs
- provide identical statistics.
-
->>July 26, 2002
-
-Makefile.pvm4_sql and Makefile.pvm4 have been substantially simplified
-by providing the worker program name from the h_init() function in the
-initfa.c/initsw.c files.
-
->>July 24, 2002
-
-Substantial modifications to param.h, structs.h to ensure that no
-sequence specific information is kept in struct pstruct. This
-structure now holds the pam[] matrix, and other scoring parameters,
-but nothing that is dependent on aa0. The aa0 dependent stuff (nm0,
-Lambda, K, etc) is now stored in struct mngmsg. This was mostly done
-to support the pv34comp* programs, which have separate mngmsg
-structures but the same pstructs.
-
-The fasts34, fasts34_t, and pv34compfs/c34.workfs have all been tested
-successfully.
-
->>July 8, 2002
-
-Modifications to comp_lib.c, initfa.c and new scaleswt.c, tatstats.c
-to support FASTS with Tatusov statistics.
-
-last_params() has been introduced to allow aa0 dependent changes in m_msg/pstr.
-
-sortbest() has been moved into initfa.c/initsw.c to make it function specific.
-
-find_z() takes an additional parameter, escore.
-
-The do_work() results structure, beststr, and stat_str all accommodate
-escores as well as integer scores (stat_str also saves segn and segl
-but doesn't need them).
-
-In scaleswt.c, process_hist() now knows much more about Tatusov statistics.
-
-last_stats() provided to accommodate rank-based statistical corrections.
-
-scale_scores() is the last function to modify the beststr scores
-(final calculation of E-value).
-
-Some sortbest*() calls and some bptr[i]->zscore=find_zp() loops have
-been moved into scale_scores();
-
->>July 3,5, 2002
-
-Modifications to allow mySQL comments (--) in "library.sql 16" files.
-Thus, a first line of:
-
- --host seqdb user password;
-
-is read by FASTA as the login information to a mySQL server, but is
-ignored by mySQL. "DO" commands in FASTA mySQL files can also be
-rendered invisible to mySQL in this way. See "do.sql".
-
-Modifications to mysql_lib.c to allow very long SQL statements. The
-buffer is now dynamically reallocated in 4Kb chunks.
-
-The fasta3.1 man page has been updated and re-organized.
-
->>June 26, 2002
-
-Minor modifications to nmgetaa.c (openlib()) to use the same arguments
-for searching and PRSS. PRSS needs access to all of m_msg, but
-searches do not. Other small fixes to comp_mlib.c, towards the goal
-of merging comp_mlib.c and comp_lib.c.
-
->>June 25, 2002
-
-Modify the statistical estimation strategy to sample all the sequences
-in the database, not just the first 60,000. The histogram is still
-based only on the first 60,000 scores and lengths, though all scores
-an lengths are shown. The fit to the data may be better than the
-histogram indicates, but it should not be worse.
-
-Currently, this modification is available only if the -DSAMPLE_STATS
-option is defined.
-
->>June 23, 2002 CVS fa34t11d4
-
-Fix a very long-standing bug in fasty/tfasty that caused 'NNN' to be
-translated as 'S', rather than 'X'. fastx/tfastx has done this
-correctly for many years, but the fasty/tfasty code that I received
-from Zheng Zhang was not implemented correctly (my fault, his code was
-fine).
-
->>June 19, 2002
-
-Added "-C #" option, where 6 <= # <= MAX_UID (20), to specify the
-length of the sequence name display on the alignment labels. Until
-now, only 6 characters were ever displayed. Now, up to MAX_UID
-characters are available.
-
->>May 30, 2002 CVS fa34t11d3
-
-Fixed problem with programs using the default -E cutoff when -b was
-provided. With this implementation, -E can override -b, but -b
-overrides the default -E.
-
-Fixed problem with 64-bit file offsets in param.h (change USE_FSEEK0
--> USE_FSEEKO, include -D_LARGEFILE_SOURCE and -D_LARGEFILE64_SOURCE
-in Makefile.linux_sql). Put limits on alignment display length (200
-chars). More checks for null returns from SQL queries.
-
->>Apr 17, 2002 CVS fa34t11d2
-
-Fixed bug in mm_file.h/ncbl2_mlib.c that caused the SGI version to be
-unable to read blast2 format files.
-
-Changed "mp_*" tags to "pg_*" for -m 10 option.
-
->>Mar 30, 2002
-
-Fix embarrassing bug in revcomp() (getseq.c) that failed to complement
-the central nucleotide in a sequence with an odd number of residues.
-
-Small changes to dropfs.c for more segments.
-
->>Mar 16, 2002
-
-Added create_seq_demo.sql, nt_to_sql.pl to show how to build an SQL
-protein sequence database that can be used with with the mySQL
-versions of the fasta34 programs. Once the mySQL seq_demo database
-has been installed, it can be searched using the command:
-
- fasta34 -q mgstm1.aa "seq_demo.sql 16"
-
-mysql_lib.c has been modified to remove the restriction that mySQL
-protein sequence unique identifiers be integers. This allows the
-program to be used with the PIRPSD database. The RANLIB() function
-call has been changed to include "libstr", to support SQL text keys.
-Due to the size of libstr[], unique ID's must be < MAX_UID (20)
-characters.
-
-A "pirpsd.sql" file is available for searching the mySQL distribution
-of the PIRPSD database. PIRPSD is available from
-ftp://nbrfa.georgetown.edu/pir_databases/psd/mysql.
-
->>Mar 6, 2002
-
-Fix showbest.c showbest() to report pst.zdb_size as database size.
-Fix dropnfa.c spam() to address off-by-one on end of run, and double
-counting on backwards scan. Fix dropnfa.c do_fasta() to fix another
-problem introduced by -S. Changes to comp_lib.c to ensure that both
-the beginning and end of the query and library sequence have '\0'
-present. Changes to initfa.c, initsw.c to ensure that a match to a
-lower-case letter with -S gets exactly the same score as a match to an
-'X'. Changes to mmgetlib.c to work with 64-bit longs in *.xin files.
-
->>Feb 26, 2002
-
-Fixes to doinit.c, initfa.c, initsw.c to allow DNA matrices using the
-"-s dna.mat" option. A new matrix, "d50ry.mat" is available that
-scores +5 for a match, -2 for a transition, and -5 for a
-transversion. "d50ry.mat" corresponds to DNA PAM50 with transitions
-twice as common as transversions. When "-s dna.mat" is used, "-n"
-MUST be used as well.
-
-Query sequence names ("aa", "nt") should be more accurate.
-
->>Feb 22, 2002
-
-Fix to getseq.c to allow "plain" sequence files.
-
->>Feb 12, 2002
-
-Minor fix to res_stats.c.
-
->>Jan 28, 2002
-
-Fixes to resurrect res_stats.c. res_stats (cc -o res_stats
-res_stats.c scaleswn.c -lm) takes the output from a current "-R
-file.res" file and calculates statistical significance - this allows
-one to take exactly the same set of scores (and lengths) and calculate
-statistical estimates using different strategies.
-
->>Jan 24, 2002
-
-modifications to mmgetlib.c, ncbl2_mlib.c to more robustly read memory
-mapped files (*.xin, map_db) on machines lacking "native" 64-bit
-longs. If the machine provides some definition for a 64-bit long
-(e.g. "long long", "int64_t"), things should work. 64-bit offsets into
-memory mapped files work properly on Alpha, SGI, i386 Linux, and
-MacOSX. The current implementation depends either on 64 bit longs
-(Compaq Alpha's pre 4.0G) or the <sys/inttype.h> file. Makefile,
-Makefile.alpha, and Makefile.linux have been modified.
-
-Modifications to nmgetlib.c, mmgetlib.c to provide GI numbers and
-Accession versions for Genbank searches. If the GI:123456 number is
-available, it will be used and the description line will be formatted:
-
- gi|123456|gb|ACC1234.1|LOCUS description
-
-This should help FAST_PAN runs, where the version of a sequence
-changes frequently.
-
->>Jan 10, 2002
-
-Modifications to p2_complib.c, p2_workcomp.c to more reliably allocate
-space for library sequence descriptions on the master and workers.
-
->>Jan 2-3, 2002 CVS fa34t10c/fa34t10d3
-
-Fixes to comp_lib.c to support Macintosh and Windows/Turbo-C
-compilation. New Makefile.tc. Macintosh version supports both
-"Classic" and "Carbon" environments.
-
-"<values.h>" has been replaced with the more modern "<limits.h>"
-
-Fixes to p2_complib.c to support n_libstr (libstr length) in GETLIB().
-
-comp_thr.c, complib.c removed.
-
->>Dec 16, 2001
-
-Complete integration of comp_mlib.c with both the unthreaded and
-threaded programs. Comp_mlib allows fasta34 and fasta34_t to compare
-a database with a second database, just as pv34compfa does. Using
-multiple queries with fasta34_t is not as efficient as pv34compfa (and
-it cannot use networks of Unix workstations), but it is much easier to
-use and install.
-
-With the comp_mlib.c option, fasta34 cannot automatically recognize
-DNA sequences, just as pv34compfa no longer recognizes DNA sequences.
-You must use the "-n" option to search with DNA sequences. The other
-programs (fastx34, tfastx34, etc) "know" the type of the query and
-database sequences, so "-n" is only required for fasta34(_t).
-
->>Dec 14, 2001 CVS tag fa34t10b
-
-Fix problems reading DNA databases in blast2 format.
-
->>Dec 11, 2001
-
-Changes to spam() in dropnfa.c so that, for DNA sequences, the
-previous behavior for finding the boundaries of a local alignment
-region use the same algorithm as previous versions of fasta. For
-protein sequences, the algorithm will extend the local region beyond
-the "ktup" boundaries if a better score can be found. For DNA
-sequences, this raises the noise rather than increasing sensitivity,
-so it is turned off and "ktup" boundaries are respected. The old,
-"ktup" boundary algorithm is available with -DNOSPAM_EXT.
-
-This version also includes a working res_stats.c, which can be used to
-test various statistical estimates on exactly the same set of scores.
-
-Fixed problems with -m 9 percent identity for fastx/fasty/tfastx/tfasty.
-These errors have been present since -m 9 was implemented.
-
->>Dec 10, 2001
-
-Fix to map_db.c to work correctly with files > 2 Gb when 64-bit longs
-are available. It is not yet designed to work with ftello() and other
-offset types.
-
->>Nov 11,21, 2001 CVS tag fa34t10a, fa34t10d1
-
-Substantial changes to revcomp(), getseq(), and other functions to
-correct problems with -S on DNA sequences. Sequences with lower case
-nucleotides were not recognized or reverse complemented properly.
-
-Fix to dropnfa.c (v34t07, Nov 21, 2001) bg_align() to re-initialize
-static globals - this fixes a problem encountered with pv34compfa. A
-new main program, comp_mlib.c has been added to the CVS archive,
-although it is not referenced in any of the Makefile. comp_mlib.c
-works like p2_complib.c and compares a library against another
-library.
-
->>Nov 4, 2001
-
-Change to dropnfa.c spam () while(1) -> while(lpos <= dmax->stop).
-This fixes a problem with ktup=1 on Suns only, so far.
-
->>Oct 4, 2001 CVS tag fa34t10
-
-Add comp_lib.c file, which merges complib.c (unthreaded) and
-comp_thr.c (threaded) code into one file.
-
-Modifications to nmgetlib.c, mmgetaa.c to allow Genbank flatfile
-format without DESCRIPTION or ACCESSION lines.
-
-Additional fix for -S with ktup=1.
-
->>Sept. 24, 2001
-
-Fix to have correct gap-penalties for short scoring matrices with
-tfastx/fastx.
-
->>Sept. 10, 2001 CVS tag fa34t05d6
-
-Fix a bug introduced by -S fix in fa34t05d5. Also, try to remove
-changes in p34compfa compared to pv4compfa output.
-
->>Sept. 6, 2001 CVS tag fa34t05d5
-
-Fix the -S dropnfa/fx/fz2 bug that was not actually fixed in
-fa34t05d4. Incorporate the correct scaleswn.c refered to in
-fa34t05d4.
-
->>Sept. 5, 2001 CVS tag fa34t05d4
-
-Fix problem with m_msg.quiet that prevented interactive prompts for
-ktup, file name, etc with threaded programs.
-
-Fix serious bug in dropnfa.c/dropfx.c/dropfz2.c that caused -S to work
-improperly on sequences with effective length of 3 or less.
-
-Change to scaleswn.c to make mle_cen(), mle_cen2() more robust to cases
-where the top and bottom scores are the same.
-
-Change p2_complib.c to avoid compiler complaints with (void *)wstage2p=NULL
-on some platforms.
-
->>Aug. 30, 2001 CVS tag fa34t05d3
-
-Fixed problem with uthr_subs.c for Suns, but changed Makefile.sun to
-use pthreads rather than Sun Unix threads. Removed SQL stuff from
-Makefile.mpi4/pvm4 and added Makefile.mpi4_sql/pvm4_sql.
-
-fa34t05d2 - fix to map_db.c to provide *sascii.
-
-fa34t05d1 - fixes to ibm_pthr_subs.c and Makefile.ibm from IBM.
-
->>Aug. 20, 2001 CVS tag fa34t05d0
-
-The pvm/mpi complib programs have been substantially updated with
-release 3.4. See readme.v34t0 for more information. With version
-3.4, the MPI programs are mp34comp*, mu34comp*, etc.
-
-A major effect of this change is to disable automatic sequence type
-(protein/DNA) recognition with pv34compfa/mp34compfa. By default,
-protein libraries are assumed. Thus, pv34compfa/mp34compfa require
-the "-n" command line option when running pv34compfa/mp34compfa on DNA
-sequence libraries. This issue does not occur with the other
-programs, which will recognize the appropriate sequence type, because
-it is determined by the program (e.g. pv34compfx requires
-DNA:protein).
-
-Fixed substantial problem with 64-bit file offsets for Linux in
-complib.c/comp_thr.c, p2_complib.c. This problem, solved by Doug
-Blair, was preventing the threaded versions from working properly in
-memory mapped mode.
-
-In all earlier versions of fasta, when very long sequences were
-searched, the sequence length reported was that of the "chunk" that
-was actually searched (typically 80,000-query_length) rather than the
-actual library sequence length. The peculiar behavior now changed,
-and the full length of the library sequence, not the sequence chunk,
-is reported as the library sequence length. Note that chunks are
-still used, however, which can cause the same alignment to be shown
-twice. In addition, the "-m 9" output format has changed to report
-the coordinates of the query and library sequence (see below), which
-may be different from 1-sequence_length because the the query and
-library sequences may have been extracted from larger sequences. Four
-additional fields have been added, "pn0", "px0","pn1", "px1" that are
-the positions in for the beginning (pn0/1) and end (px0/1) of they
-query/library sequence. pn0/1 would typically be changed with the
-"@C:#" directive, described below.
-
-Changes to doinit.c/initfa.c/initsw.c to provide a new function -
-f_lastenv() - that allows function-specific adjustments to parameters
-after the command line options have been read but before the first
-sequence is read. This change solved problems with "mp/pv34compfx -S".
-
-fasts34/tfasts34 now recognize that 'I/L' are the same, as are 'Q/K'
-(which are apparently indistinguishable by Mass-Spec). The latter
-identity is on by default, but can be turned off with "-h 0".
-
-The MPI/PVM versions of the programs have been tested extensively with
-compfa, compfx, and comptfx. Makefile.mpi4 now works properly.
-Changes to p2complib.c to support the PVM option "-T 1-4", which
-allows one to run on nodes 1-4 of a (presumably larger) PVM virtual
-machine. This option has no effect on the mp34comp* programs. The
-old "-T 4" to run on 4 nodes, is also available. If each node has 2
-cpu's, as indicated in the "pvmd hostfile", both CPU's will be used
-for a total, in this example, of 8 processes. This allows one to
-specify a large PVM machine and use separate parts of it
-independently.
-
-Changes to nmgetlib.c to fix problems with longer dates in GCG files
-(Y2K). Fixes to faatran.c for extended alphabets and 'X's. Various
-code clean-ups to make "gcc -Wall" a little bit (not much) happier.
-
-This is the first distributed fasta34 version.
-
-================
->>Aug 9, 2001 CVS tag fa34t05
-
-Corrections to initfa.c to allow -S to work with tfastx/y.
-Fix to manshowbest.c for query position with -m 9.
-
->>July 18, 2001 CVS tag fa34t04
-
-Various changes to complib.c, comp_thr.c, p2_complib.c, showbest.c,
-showalign.c to deal with overlapping alignments in long sequences that
-have been segmented. When long sequences are segmented (lcont>0), the
-eventual total length (n1tot_v) is saved at beststr->n1tot_p. If
-there was no lcont, then beststr->n1tot_p = NULL, and beststr->n1
-should be used as the sequence length. This has the advantage of
-requiring space only when long sequences are encountered, and
-requiring only one integer for several segments.
-
-m_msg.noshow has been removed.
-
-The -m 9 format has been changed - 5 fields have been added, 4
-(pmn0/pmx0/pmn1/pmx1) provide the beginning and end coordinates of the
-query and library sequence; the last (fs) reports the number of
-frameshifts. The names of the alignment boundaries have been changed
-from min0/max0/min1/max1 to amn0/amx0/amn1/amx1 (Alignment miN/maX).
-
-The SQL format has been extended to provide for statements that do
-things but do not generate results, such as creating and selecting into a temporary table, e.g.:
-================
- do
- create temporary table seq_pos (
- id int unsigned not null auto_increment primary key,
- prot_id int unsigned not null default 0,
- start int unsigned not null default 0,
- length int unsigned not null default 0,
- )
- ;
- do
- insert into seq_pos (prot_id, start, length)
- select id, 11, len-10
- from protein, annot
- where len > 100
- and annot.protein_id = protein.id
- and annot.pref=1
- ;
- select seq_pos.id,
- substring(protein.seq, start, length),
- concat("@C:", start, " ", descr)
- from protein, seq_pos, annot
- where protein.id = annot.protein_id
- and protein.id = seq_pos.prot_id
- and annot.pref = 1
- ;
- select prot_id,
- concat("@C:", start, " ", descr)
- from seq_pos, annot
- where annot.protein_id = seq_pos.prot_id
- and seq_pos.id = #
- and annot.pref = 1
- ;
-================
-
- In the current implementation, these statements must start with "DO"
-as the first two characters on the line, and come immediately after a
-line ending with ';'. The text from "DO" to the next ";", excluding
-the "DO", is executed when the database connection is made.
-
-===== >>July 12, 2001
-
-The allocation of the work_info data structure used to send
-information to the worker threads has been changed. The old method
-worked, possibly by accident.
-
-A bug in p2_complib.c that caused E()-values to be calculated
-improperly for the first query sequence has been fixed.
-
->>July 11, 2001 --> fa34t02
-
-It is now possible to specify output coordinates in library sequences
-by including the string: "@C:number" on the description line, e.g.
-
- >gtm1_human gi|12345 human glutathione transferase M1 @C:21
-
-would label the first residue in the library sequence "21" rather than
-"1". This capability has been included to provide accurate
-coordinates for searches done against subsequences generated by an SQL
-query. For example, one could use a query of the form:
-
- SELECT protein.id, substring(protein.seq,11,length(protein.seq)-20),
- concat(protein.name," @C:11 ",protein.descr)
- FROM protein;
-
-to generate a sequence set with each sequence starting with residue
-11. Without the "@C:11" option on the description line, the program
-would number the alignment positions starting at 1, even though the
-first residue of the sequence really started at 11. "@C:11" allows
-one to correct the coordinate system.
-
-Currently, "@C:offset" is available only with library type 1 (fasta
-format) and 16 (mySQL).
-
-The SQL-generated database with "@C:offset" can be used with both the
-fast*34(_t) programs and with pv34comp*. However, the SQL syntax is
-used differently in the fasta34 and pv34compfa programs. fast*34(_t)
-requires three SQL statements during a search: (1) a statement to
-generate a large set of library sequences; (2) a statement to generate
-a description of a single sequence, given a unique identifier provided
-by (1); and (3) a statement to generate a single sequence given a
-unique identifier provided by (1). For fast*34 searches, the third
-(3) SQL statement must provide the "@C:offset" information in the
-third results field for the offset to be used. It is optional in (1)
-and (2).
-
-The pv34comp* programs only require one SQL statement, statement (1)
-above, which must provide three fields, a unique identifier, the
-sequence, and a complete description that must include "@C:offset" if
-substrings are used. If SQL queries (2) and (3) are provided, they
-are ignored. Thus, the same files can be used by both programs, but
-the "@C:offset" is required in different SQL queries by the fast*34
-and pv34comp* programs.
-
-Other changes:
-
-Re-incorporation of GAP_OPEN option; fix to Altschul-Gish stats when
-GAP_OPEN is used.
-
-Re-incorporation of A. Mackey's spam() improvement in dropnfa.
-
-Fixes to include file ordering to allow fast*34(_t) pv34comp* programs
-to compile.
-
-Fix to lascii[] for SQL database queries.
-
-Fix to an old bug in comp_thr.c to send individual worker_info
-structures to threads (does not fix LINUX threads problems, however).
-
-=====
->>July 9, 2001
-
-Considerable changes to support no-global library functions.
-
-(1) Separate ascii/sequence mapping arrays are used by the
- query-reading (qascii), library-reading (lascii), and sequence
- comparison function (pascii) routines. As a result, there is no
- longer a need for tgetlib.o/lgetlib.o - lgetlib.o can serve both
- functions.
-
-(2) This also allows us to remove all #ifdef TFAST/FASTX conditionals
- from complib.c/comp_thr.c/p2_complib.c. We no longer need
- tcomp_thr.o, comp_thrx.o, etc. We still have a variety of
- p2_complib.o variations to support the different c34.work* files.
-
-(3) Because non-global openlib/getlib functions are available, exactly
- the same open/get functions are available for reading both the
- query and reference libraries in pv34comp* programs. The
- host-specific openlib/getlib functions in hxgetaa.c are now
- provided by nmgetlib.c, etc. This has two effect:
-
- (a) it is now possible to compare a query database generated by an
- SQL query to a library database generated by a different SQL
- query.
-
- (b) pv34comp* has lost (at least in this version) the ability to
- automatically detect the query sequence type. To search with a
- DNA query, you MUST use "-n".
-
-(4) the resetp() function is now responsible for almost all of the
- function sepcific (TFAST/FASTX/etc) initializations. All of the
- function specific code has been removed from complib.c/comp_thr.c
- and most of it has been moved to initfa.c/resetp().
-
-(5) manageacc.c has been merged into compacc.c (mostly prhist()).
-
-=====
->>June 1, 2001
-
-Many changes to accommodate a new - no global variable - strategy for
-reading sequence databases. Every time a file is opened, a struct
-lmf_str is allocated which can be used for memory mapped files, ncbl2,
-files, and mysql files.
-
-In addition, an open'ed file has a default sequence type: DNA or
-protein, or one can open a file in a mode that will allow the sequence
-type to be changed.
-
-=====
->>May 18, 2001 CVS: fa33t09d0
-
-A new compile time parameter - -DGAP_OPEN, is available to change the
-definition of the "-f gap-open" parameter from the penalty for the
-first residue in a gap to a true gap-open penalty, as is used in BLAST
-and many other comparison algorithms. This will probably become the
-default for fasta in version 3.4.
-
-Fixes to conflicts between "-S" and "-s matrix". When a scoring
-matrix file was specified, lower-case alignments were not displayed
-with -S (although the scores were calculated properly).
-
-More extensive testting of mysql_lib.c (mySQL query-libraries) with
-the pv4comp* and mp4comp* programs.
-
-=====
->>April 5, 2001 CVS: fa33t08d4b3
-
-Changes in nmgetlib.c and ncbl2_mlib.c to return long sequence
-descriptions for PCOMPLIB (pv4/mp3comp*). Also fix p2_complib.c to
-request DNA library for translated comparisons.
-
-Fix for prss33(_t) to read both sequences from stdin.
-
-=====
->>March 27, 2001 CVS: fa33t08d4
-
-Modifications to allow 64-bit fseek/ftell on machines like Sun,
-Linux/Intel, that support -D_FILE_OFFSET_BITS=64, -D_LARGE_FILE_SOURCE
-off_t, and fseeko(), ftello() with the option -DUSE_FSEEKO. Machines
-with 64-bit long's do not need this option. Machines with 32-bit
-longs that allow files >2 Gb can do so with 64-bit file access
-functions, including fseeko() and ftello(), which work with off_t file
-offsets instead of long's.
-
-=====
->>March 3, 2001 CVS: fa33t08d2
-
-Corrected problems in nmgetaa.c and mysql_lib.c with parallel
-programs, and one serious problem with alternate DNA scoring matrices
-(initfa.c, initsw.c) not being set properly. A subtle problem with
-the merge of scaleswn.c and scaleswg.c is fixed.
-
->>February 17, 2001
-
-Modified mysql_lib.c to use "#", rather than "%ld", to indicate the
-position of the GID. This change was made because sprintf() cannot be
-used reliably to generate an SQL string, as '"' and '%' are used in
-such strings.
-
-=====
->>January 17, 2001
-(no version change, date change)
-
-Minor fixes to initfa.c, initsw.c to deal with DNA scoring matrices
-properly. "-n -s dna.mat" is required for the sequence/matrix to be
-recognized as DNA.
-
->>January 16, 2001
--->v34t00
-
-Merge of the main CVS trunk - fa33t06 with the latest release branch,
-fa33t08.
-
-In addition, PCOMPLIB mods have been made to mysql_lib.c. Because
-p2_complib.c gets sequence description information during the first
-read of the database, the mysql_query must be changed to return:
-result[0]=GID, result[1]=description, result[2]=sequence. In the
-PCOMPLIB case, the other SQL queries (for GID description, sequence)
-are not necessary but must still be provided.
git://source.jalview.org / jabaws.git / blobdiff