+++ /dev/null
-
->>November 1, 1997
-
- --> v31t0
-
-version 31t of the fasta program package uses a more modular
-structure for comparison functions. In addition to modular functions
-to initialize, calculate and align sequences, v31 provides a modular
-function for creating the alignment display. This was required for
-fasty and fastf, which have very different alignment strategies from
-the other search programs.
-
->>February 13, 1998
-
-modified nascii[] so that 0, 1, 2 are no longer end of sequence
-characters.
-
-prss3 added. Unlike prss, prss3 uses -d # to specify the number of
-shuffles.
-
->>March 18, 1998
-
-First public release. Corrected problems with dropfz.c (which is
-used in fasty3, tfasty3). Makefile is well tested, but other Makefile's
-are not. PVM versions not tested.
-
->>March 19, 1998
-
-Problem with unthreaded tfastx3, tfasty3 caused by bug in complib.c
-fixed. All Makefiles (Makefile.alpha Makefile.sun, Makefile.sgi,
-Makefile.linux) have been tested and work properly. Threaded versions
-do not work on linux (yet). Function labeling problems with fasty3,
-tfasty3 corrected.
-
->>March 20, 1998
-
- --> v31t02
-
-Fixed problem with inconsistent openlib() calls that broke BLAST databases
-on some platforms.
-
->>March 27, 1998
-
- --> v31t04
-
-Fixed a long standing problem with fastx/tfastx and fasty/tfasty that
-caused various memory allocation problems and core dumps.
-
-The PVM version works again, but cannot produce alignments. The
-change in the location of the modular display functions will require
-significant changes in the pvm display functions. For the moment,
-showalign() has been commented out.
-
-Code tested on Macintosh without changes.
-
-Added some additional information in the results file.
-
-
-Please report bugs to wrp@virginia.edu
-
->>April 3, 1998
-
-Removed some debugging code in faatran.c now that fastx/fasty bugs
-seem corrected.
-
- FASTA --> v3.14
-
-Corrected uninitialized array elements in dropnfa.c.
-
->>April 10, 1998
-
-Added facility for specifying SRCH_URL (the URL string that will be
-used to re-search the database) and REF_RUL (the URL string that
-will be used to lookup the sequence) ini url_subs.c. This allows perl
-scripts to provide different databases for re-searching dynamically.
-
->>April 16, 1998
-
- --> v31t05
-
-Corrected problem with ignoring ','s in databases (','s are found in
-PIR).
-
->>April 18, 1998
-
-Corrected some problems with sequence names for Entrez lookups and
-re-searching databases.
-
-Made minor modifications to nxgetaa.c and compacc.c for compatibility
-with Borland 'C' compiler for Win32 systems. Including makefile.tc
-fasta.rsp, prss.rsp, and test.bat for Borland 'C'/win32.
-
->>April 24, 1998
-
- --> v31t06
-
-Fixed another bug in fasty3/tfasty3 alignment routines.
-
-Added additional information to the do_url1() (url_subs.c) function.
-The re-search URL can now reference the start, stop, and length of the
-library sequence to be re-searched with. For DNA library sequences,
-these values are always in nucleotides, even with tfasta/x/y.
-
-
->>May 12, 1998
-
-(no version change as v31t06 was not released prior to this)
-
-Correct nxgetaa.c GETLIB to deal correctly with BLAST NR database
-sequences with exceptionally long title lines.
-
-Fix bug with long -O results files.
-
->>May 18, 1998
-
- --> v31t07
-
-Corrected some bugs in information string lengths (e.g. gstring1,
-stat_str), disabling statistics with -z 0, translation of 'X' by
-saatran() (faatran.c) that caused problems with FASTX.
-
-A serious bug has been fixed in the FASTX alignment routines.
-For some pathological sequences, % identity increases from < 10%
-to 40%. The version number of the main program has not changed,
-but the version number of the fastx function has changed to 3.2.
-
->>June 19, 1998
-
- --> v31t08
-
-Corrected some problems with alignments with -m 10.
-
-Added -Z db_size option to modify apparent database size for
-expectation value calculation (used only for protein/protein FASTA and
-SSEARCH, FASTX, FASTY, TFASTX, and TFASTY).
-
->>July 1, 1998
-
- (no version change)
-
-Corrected size of lbnames[], lb_size[] in structs.h to accomodate MAX_LF
-files.
-
->>July 13, 1998
-
- --> v31t09
-
-Corrected problem in nxgetaa.c encountered when reading long sequences
-(that must be split) in fasta format.
-
-Corrected problem in statistics calculation encountered with a small number
-of very long DNA sequences.
-
->>July 17, 1998
-
- (no version change, date change for ssearch3)
-
-Corrected default expectation cutoff (it was 10, now it is 2.0) for
-DNA with ssearch3.
-
git://source.jalview.org / jabaws.git / blobdiff