readme.v34t0

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

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