1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725
|
Mon, 6 Sep 2004
* stopgap release: mcl-04-250
* mclpipeline/mclblastine used stale mcl options (-do log). Fixed.
* Moved graph directory one level higher.
* Rewrote mcx option parsing, GNU-style now accepted.
Tue, 17 Aug 2004
* mcl-04-230 released.
* Fixed bug in the interpretation function. In rare cases (where
an attractor systems had cardinality exceeding one) it would split
a cluster.
* Fixed some very dumb and slack code in the library.
100-fold speed increase in mcxsubs block extraction - the slack-bugs
(slugs?) where *that* slack.
Sped up applications doing much vector calculus by replacing cute
initializer-callback-equipped mcxNAlloc invocations with plain mcxAlloc.
* Fixed mcxdeblast bug surfacing in the combination of --m9 and
--tab=<tab-file> options.
* 64-bit compatibility testing and auditing. Not exhaustive.
* Moved doc directory one level higher.
* Signal mcl!
Premature exit of the main iteration (and mcl) can be enforced by
sending mcl the ALRM signal. It will interpret the last iterand as a
clustering. This can be useful in the extremely rare case where
an input graph contains the 3x3 flip-flop state as a subgraph
(after centering, notably). I recently encountered this when
clustering a very sparse homology graph (to arrive at orthology)
using -c 4.
* Tentative addition to option parsing. GNU-style equivalence
of --I=3 and -I 3. Horrors!
mcl foo.mci --I=3 --scheme=6 --te=8
thus works. On trial.
* Immediately after it has finished a run, mcl can optionally reread
the input graph, and generate performance characteristics for
the graph/clustering pair. It can also check whether all clusters
correspond to connected components in the input graph.
* Removed the ugly -do and -dont options.
Use
Option Default Previous
--force-connected=X 0 (new)
--check-connected=X 0 (new)
--keep-overlap=X 0 -do keep-overlap
--append-log=X 1 -do write-log
--show-log=X 0 -do show-log
--analyze=X 0 -do clm
Where X can be any string in 1/y/Y/0/n/N/1.
* Added clmclose, for retrieving connected components from a graph,
and for testing whether the domains in a cluster file or domain file
correspond to connected components in a given graph.
* --apropos output looks better.
Wed, 7 Jul 2004
* mcl-04-189 released.
* Tim Hughes found a bug in mcxassemble, arising from an embarassing
typo in the underlying library code - fixed.
* Joost van Baal pointed out some issues with the LICENSE.
It has been reworded to nicely ask scientists to behave properly.
Sat, 3 Jul 2004
* mcl-04-185 released.
Mainly fixes for small glitches and documentation updates, and the new
general purpose application mcxdump for dumping matrix/tab file
combinations. Nothing breathtaking.
* Added mcxdump, to do a wider range of dump chores (than clmformat
already does).
* mcl --apropos now dumps one-line descriptions of *all* options,
even the very obscure and never-use-them options.
This option will propagate to all siblings in the near future,
as a result of a rewrite of the option-parsing module.
* Updated THANKS; Enter Andreas Kahari (OpenBSD port, compile warnings),
Jason Stajich (mcxdeblast work), and Tim Hughes (bug reports).
* Applied mcxdeblast patchlet by Jason Stajich to support parsing
WU-BLAST format.
* Fixed a bug in the zoem macro definition file output by clmformat,
reported by Tim Hughes.
* The mcxdeblast --m9 option now actually works with the ncbi blast -m 9
option (i.e. skip comments lines).
* Fixed several documentation glitches spotted by Joost van Baal.
* Added (somewhat terse and makeshift) remarks on the role of zoem in
mclpipeline/mclblastline manuals, after Joost pointed out that the
mclblastline/mclpipeline zoem dependency (via clmformat) was not well
documented.
Tue, 22 Jun 2004
* mcl-04-174 released.
* Integrated Jason Stajich's tabular blast format parser.
Restructured mcxdeblast to a great extent.
Use --m9 to expect tabular BLAST format.
With mclblastline, use --blast-m9.
* mcxdeblast had its default settings changed to resemble those of
tribemcl.
* mclblastline explicitly uses the mcxassemble '-r max' option; it can be
be overruled e.g. by issuing --ass-r=add.
* clmformat.zmm: Get rid of spurious braces, update special rules to
pass evaluation.
* NOTE
mclpipeline was streamlined. All mcl-related options now start with
--mcl, e.g. --mcl-I=3.0, --mcl-scheme=6, etc. Consult the manual pages if
needed. All format-related options start with --fmt, all assembly related
options start with --ass. Any of the --mcl, --ass, --fmt options not
recognized by mclpipeline will simply be stripped of the prefix and
passed on to the corresponding program. To use the clmformat
--dump-pairs option (which is not in the mclpipeline/mclblastline manual)
with mclpipeline, use --fmt--dump-pairs.
* clmformat acquired the --dump-pairs option, for dumping one cluster/node
pair per single line.
* mcxsubs syntax accepts 3%5 syntax, implying the list 3,8,13,18 and so on.
The syntax can be repeated, e.g. 3%5,6%13 . Use this for quickly thinning
out a matrix. mcxsubs also acquired the options
-dfac <num>
-cfac <num>
-rfac <num>
--rand-discard
--rand-merge
--rand-intersect
--rand-exclusive
for randomizing subdomain selection, and
--spec-cols
--spec-rows
--spec-doms
for omitting the final restriction to subdomains of the input matrix.
Refer to the manual page for more information.
Then, the --reread option was renamed --from-disk.
* More jury grades!
Wed, 14 Apr 2004
* mcl-04-105 released.
* Bumped the gratuitous version tag to 1.004. It has been a long time
since the previous release and much work has been done.
- clmformat has gotten a pretty zoem face
- native binary format was revived and integrated into mcxsubs
(making it orders of magnitudes faster if binary format is used)
- the MCL IO library has seen a lot of work
- the underlying utility libraries have seen much work as well
- a bug in the loop weight assignment spotted by Abel Ureta-Vidal
was fixed
- the mcl '-v clusters' verbosity option is new
- so is the '-dump dag' option
- mcxsubs now supports simultaneous extraction of
(possibly overlapping) blocks
- the environment variables MCLXASCIIDIGITS, MCLXIOVERBOSITY,
MCLXIOFORMAT, and MCLXASCIIFLAGS have arrived
- mcxarray documentation finally got written
- and various other fixes for glitches went in, thanks to Joost
van Baal for some of those
* Revived binary format. Reading matrices is roughly 30 times faster
in binary format. For an average MCL run, this may result in a 10% gain
in speed or more.
Treat with care; binary format is not portable across some subcollection
of processors/compilers/filesystems.
Both binary and ascii input now support reading subgraphs directly
from disk, which is foremost important for mcxsubs.
* mcxsubs is now *much* faster if applied to binary format
and the --reread option is used. The speed gain may be 400-fold.
* Big rewrite of clmformat. All the formatting code was taken out,
and clmformat now outputs logical formatting statements.
These are in the zoem language, so for using clmformat one
needs to install the zoem package, obtainable from
http://micans.org/zoem/src/zoem-latest.tar.gz
The good thing is that lay-out can now be changed by editing
a single zoem macro definition file.
* The default of assigning loop weights has changed.
It is now set to equal the maximum weight found in the list of
neighbours. The old behaviour can be regained by specifying -cma 100.
NOTE
The new default will, with identical inflation value and
compared with the old default, result in slightly more granular
(more fine-grained) clusterings. This can optionally
be compensated for by increasing the inflation value a little.
* The new -cma <num> option accepts a number inbetween 0 and 100.
Think of it as a fraction f expressed as a percentage. It sets the loop
value to the weighted average
f * ctr + (1-f) * max
where ctr is the 'center' of a list of entries (the sum of entries
squared divided by the squared sum of entries) and max is the maximum
of that list.
The loop value thus obtained is multiplied by the value given
to the -c option (which stands default at 1.0).
* Improved interpretation interfaces for overlapping clusterings;
Added mcl '-dump dag' option, and some changes to clmimac. Use clmimac
to interpret matrices obtained either with '-dump ite' or '-dump dag' as
clusterings. For early mcl iterands, such clusterings may possibly
contain overlap.
* Added mcxarray documentation, it is now installed.
* Added clmps utility, which is by default not yet installed and
has no manpage yet. It outputs the body of a PostScript file.
* Added '-v clusters' for reporting on intermediate clusters.
However, if you are *really* interested in intermediate clusterings,
you should use '-dump ite' and the clmimac application.
* All mcl applications (should) respect the environment variable
MCLXASCIIDIGITS, setting the number of digits after the decimal point
that should be written for native ascii format. The special value -1
indicates that no value should be written at all (upon further reads the
default value 1.0 will be used). This is relevant only for ascii format.
* All mcl applications (should) respect the environment variable
MCLXIOFORMAT, which regulates whether matrices are written in binary
or ascii format. Consult the mcl manual page for how it works.
* All mcl applications (should) respect the environment variable
MCLXIOVERBOSITY, which regulates whether a progress bar is printed
during matrix I/O. Consult the mcl manual page for how it works.
* Added 'b:' tag to mcxsubs syntax for retrieving block diagonal matrix
(where blocks can optionally overlap). Some groundwork in the library
for enabling this.
* Added two more pruning schemes; set the default scheme index
to four rather than two.
* Added mcl -in-gq <val> option, for removing any edges in the
input graph whose weight is below <val>.
* Fixed bug in clminfo (spotted by Abel Ureta-Vidal), causing the
singleton count to be wrong sometimes.
Fri, 03 Oct 2003
* mcl-03-276 released.
* added clmmate manual page. Use it to find best pairs of
clusters between two clusterings (use the -twins option).
* fixed mcxmap functional bug.
* mcxassemble and mcxdeblast were improved, including fixes and
suggestions from (at different stages) Abel Ureta-Vidal and
Dinakarpandian Deendayal.
* The documentation now uses the zoem manual NAME macro (recently added),
so that the troff output is apropos (whatis, man -k) compatible.
* fixed trivial bug in mclpipeline.
Tue, 02 Sep 2003
* mcl-03-245 released (mainly a maintenance release).
* Fixed bug which caused mcl and siblings to crash or go haywire (exit
for the wrong reaon) when presented with non-conforming input. The bug
was introduced during the previous IO module rewrite that brought raw
matrix format and mcxassemble. So versions >= 03-154 probably feature
this bug.
* Added mcxarray for creating cosine or pearson matrix from microarray
data. Not yet installable, no manpage, -h gives manual.
* Added speed/complexity section to mclfaq.
* Fixed clmmeet, which appeared to be broken since 03-010.
* Added mclgraga, a simple script for granularity gauging. Use as in
clmformat -icl cluster-fu -dump - | mclgraga --range=0,10,2000 (and in
other ways as well). It's not installable though and has no manpage.
One has to copy it from the source distribution
* Changed mclgrep to be not installable; one has to copy it from
the source distribution. It has no manpage either.
* clmformat has -dump <stream>, -pi <infl>, -dump-node-sep <sep> options.
* clminfo has -pi <infl>, -ap (append performance measures),
-ag (append granularity measurs), -do/dont <header|rule> options.
Fri, 04 Jul 2003
* mcl-03-185 released (maintenance release).
* Added mclgrep, which can grep sections from an mcl file.
e.g. 'mclgrep clm foo' will display 'clm' section(s) in the file foo,
if present. Handy for comparing granularity and performance
characteristics.
* Behold the mcl '-do clm' option; it will include performance criteria
and granularity characteristics in the cluster output file.
* Fixed embarassing clminfo bug (introduced in mcl-03-178).
* Fixed mcx broken interactive mode (introduced in mcl-03-178).
Fri, 27 Jun 2003
* mcl-03-178 released (maintenance release).
* Fixed a bug causing the jury marks, the jury synopsis, and the
pruning percentages to be wrong.
* Added several new features, yet to be documented here
(documented in the manual pages though).
Look for the mcl -do and -dont options.
Tue, 03 Jun 2003
* mcl-03-154 released.
* Encouraged the version number up to 1.003.
* Added mcxassemble, clmformat, mclpipeline, mclblastline, mcxdeblast.
Removed clmconf, its functionality was assimilated by clmformat.
* Added -pi <pre-inflation> option to mcl for skewing input weights.
* Added automatic output naming facilities to mcl. By default (if the
-o option is not used) it will write to out.fname.suf, where fname is the
name of the input file, and suf is automatically constructed. The -ap and
-aa options allow further customization.
For example:
mcl small.mci -I 3 -c 2.5 -pi 0.8 -scheme 5
will result in a file named
out.small.mci.I30s5c25pi08
It is possible to obtain the file name corresponding with a given run
by using the -az option.
* Removed longtime deprecated -a option.
* mclpipeline implements a generic pipeline implementing the
stages from data file (application-specific input) until
formatted output (clusters represented in terms of
application-specific labels).
* mclblastline implements a particular mcl pipeline tailored
to BLAST files.
* mcxdeblast added, for parsing BLAST files (beta version).
* display results in readable form using clmformat.
* Added mcxassemble, which takes as input simple raw cooccurrence
data in a very free format, and turns it into mcl matrix format.
Options for adding, maxing, multiplying, and discarding repeated
entries as well as repeated vectors.
Nodes can be relabeled by specifying a map file. This makes it
easy and fast e.g. to do a one-pass Blast file parse, write the
cooccurrence data and a prefered node labeling, and then construct
the final matrix. The setup for transforming application-specific
data into raw data is this:
- Parse cooccurrence data from some external format.
- Transform cooccurrence data to raw mcl data as you parse.
- When done, write out required header and domain information
to a separate file. The domain information can be built during
the parsing stage.
- Use mcxassemble to construct a valid matrix from the raw data
and the header information.
- Nodes can be relabeled as needed using a separate map file,
which takes the form of a very thin matrix file.
* mcxmap uses the new permutation/relabeling mechanism; permutations
are now fully supported.
* IO internals underwent major rewrite in order to support mcxassemble
raw data munging and mapping functionality (in mcxmap and mcxassemble)
* Vector part of impala library was made somewhat safer;
new mclpAR* type for dealing with multisets of ivps.
* # now acts as a comment within the (mclmatrix ... ) section,
onwards from the begin keyword.
* MCL should be straigthforward to compile under Wintel using Cygwin,
as now verified by SvD (small fix was needed; log2 seems defined
as macro under cygwin).
* clean-ups in underlying util and impala libraries.
* implemented
-DVALUE_AS_DOUBLE and
-DINDEX_AS_LONG compiler options.
The first for matrix entries cq edge weights, the second
for matrix indices cq node identifiers.
* revamped
-DRUNTIME_INTEGRITY compiler option.
* clm apps now have --version option.
Fri, 10 Jan 2003
* mcl-03-010 released.
This is a MAJOR overhaul, with increased power in the MCL libraries and
utilities. The mcl family can now deal with a much more general
representation of matrices/graphs. This is detailed in several benefits
listed below. There is a drawback: mcl itself is now approximately 15-20
percent slower than before (measured on not so large graphs). Some of
this loss can perhaps be recouped by forthcoming changes; regardless,
the benefits were deemed to far outweigh this minor performance loss.
* Increased version number to 1.002. The difference between versions
1.001 and 1.002 is much larger than that between versions 1.001 and
1.002 - the version numbering scheme is very minimalistic.
* mcl's input format was extended (existing graphs are still acceptable).
See mcx(5) / mcxformat.html.
* mcl's internals were rewritten to allow fully sparse matrix/graph
representation. Formely, the nodes of a graph had to be indexed
sequentially, starting at zero. This is no longer the case.
mcl can now internally deal with sparsely indexed graphs.
Example:
| (mclheader
| mcltype matrix
| dimensions 12x12
| )
| (mcldoms
| 11 22 33 44 55 66 77 88 99 123 456 789 $
| )
| (mclmatrix
| begin
| 11 22 66 77 123 $
| 22 11 33 55 $
| 33 22 44 55 $
| 44 33 88 99 456 $
| 55 22 33 77 88 $
| 66 11 123 $
| 77 11 55 123 $
| 88 44 55 99 456 $
| 99 44 88 456 789 $
| 123 11 66 77 $
| 456 44 88 99 789 $
| 789 99 456 $
| )
Besides being useful from a user-point of view, this new setup is a
first step in enabling mcl for grid or cluster computing.
Look at the mcx(5) / mcxformat.html page for more information.
* mcl sibling programs are able to handle clusterings in which the
clusters have nonconsecutive identifiers.
* The low level API is now totally permissive of all kinds of domain
combinations. It is up to higher levels to enforce domain identity or
subsumption etc. Also,
The low level API leaves it up to the caller whether a node is not
represented because it is not part of the domain or whether it is not
represented because it has no neighbours. It is up to the higher levels
to decide.
The low level API (and most of the higher level API) allows 0x0, Kx0,
and 0xK matrices. mcl will happily cluster a 0x0 graph.
* renamed the src/nonema directory to src/impala (permanently).
renamed src/intalg to src/taurus (tentatively).
* renamed mcximac to clmimac.
* added mcxmap
* added clmresidue
* clmdist can now also compute the Jacquard index and the variance of
information measure (the -mode option). Its output looks nicer and can be
changed using the -parts, -digits, -width, --nolegend, and --noindex
options.
* The underlying library code for clminfo was thoroughly cleansed.
An untraced FPEfault was reported for earlier versions; hopefully
that is now gone.
* mcl now accepts
-sort revsize (default, large clusters first)
-sort size (small clusters first)
-sort lex (lexicographical ordering)
-sort none (clusters as found by interpretation routine)
* mcxsubs now
- acts on rectangular matrices as well.
- can select on value (being >=/> low and/or <=/< high).
- can remap the domain of a selected matrix to range 0-N-1,
for only columns, only rows, or both columns and rows.
- can make the selected matrix characteristic.
- can transpose the final result.
- has fairly horrid looking specification strings.
It can be used for removing tough nodes from a graph, where toughness is
measured according to output resulting from running mcl with '-dump
chr'.
* fixed problem with documentation in mcl-02-277.
verbatim env in html looked rotten under IE.
Fri, 4 Oct 2002
* mcl-02-277 released.
Mostly a maintenance release. Perhaps the extra FAQ entry is most
noteworthy. Read e.g. http://micans.org/mcl/doc/mclfaq.html#checksymmetry
A new release featuring support for removal/projection of tough nodes is
in the pipeline. That release will be more interesting.
* Added faq {How do I check that my graph/matrix is symmetric/undirected?}
Please do check this people!
* Several additions and fixes in the util library, nothing much affecting
mcl.
* Added field to '-dump chr' output (loop value before rescaling).
* Removed unnecessary 'thou shalt not have values < 0' commandment.
* Some small doc additions.
Fri, 21 Jun 2002
* mcl-02-172 released.
* Fixed --log output format error.
* Some autotools fixes, and some changes in documentation generation
(immaterial for mcl users).
* [Joost] configure.ac.in: added AM_MAINTAINER_MODE: by default,
don't rebuild e.g. Makefile.in from Makefile.am. Default users are
not maintainers.
Thu, 30 May 2002
* mcl-02-150 released.
* Applied valgrind to mcl, and fixed all memory leaks thus found.
Standard computation paths are clean (if no errors). Inserted several
clean-up routines.
* Retrofitted this file to include version 02-095.
* [Joost] Added acinclude.m4, including acx_pthread.m4 by Steven G.
Johnson and Alejandro Forero Cuervo, so that we'll build out-of-the-box
on systems like Tru64Unix/OSF1 which need special compiler flags when
dealing with pthread stuff. Thanks to Martin Mokrejs for reporting the
bug.
* Fixed bug present in version 02-095 and 02-116, caused by
the computation of the average of inhomogeneity over all vectors
and a very buggy mclVectorMaxValue -- it removes all zero entries from
vectors. Bug, reported by Martin Mokrejs, manifested itself when
inhomogeneity was exactly zero for all vectors,
* Compiled mcl with checkergcc, and tested a few computation paths.
No errors found.
* [Anton] Updated tribe software after bug report by Maring Mokrejs.
* [Joost] Separated Zoem from mcl, modularized util and separated it
as well. It is still tacked on in the distribution though.
* [Joost] Enabled --enable-tribe, the tribe module written by Anton
Enright.
* [Anton] Inserted tribe software.
* Removed -dump att option, added more general -dump chr option.
Fri, 26 Apr 2002
* mcl-02-116 released, bumped version number to 1.001.
* Added mcximac utility for interpreting MCL iterands as clusterings.
* Automated versioning; documents and --version sensitive apps
now generate consistent date and version tags.
Fri, 05 Apr 2002
* mcl-02-095 released.
* Added mclfaq document (supported in html, roff, ps).
* Added --log option to mcl, appends a log section to
the clustering output. MUST-DO for large graphs. It is not a default
because I don't want to scare new users. This option works with
--expand-only as well. Logging includes information on kept mass, vector
footprints, recoveries, selections, and time taken by expansion.
* -nw, -nl, -nj, --log, --show-log, -how-much-ram, --jury-charter are new.
* Added extensive window monitoring of mass averages for the worst k
instances, k=1,2,5,10,20,50 .. 20000, 50000.
* The mcl -h output is now less frightening, or so I hope.
* Added 'jury synopsis' remark classifying the pruning quality.
It is meant as indication only. Pruning quality is now measured
in the following flavours:
perfect exceptional superior excellent good acceptable mediocre poor
bad lousy miserable awful wretched atrocious
* Streamlined command line parsing a lot, using new util/opt.[ch].
Separated parsing from validation; the framework should be usable for
setting parameters when calling mcl parts from code.
* Modularized the mcl code a lot. It is now close to being
usable as shared object code with all the command-line functionality
still accessible.
moved the lion's part of shmcl/mcl.c to mcl/alg.c. Created
mcl/alg.[ch], mcl/proc.[ch], mcl/procinit.[ch] mcl/inflate.[ch],
mcl/expand.[ch], removed mcl/params.[ch] mcl/mcl.[ch].
shmcl/mcl.c looks acceptable again.
* Added util/opt.[ch] util/err.[ch] mcl/init.[ch],
added mcxHashMerge to util/hash.[ch], streamlined error messages in
terms of mcxErr, mcxWarn, mcxTell.
* Rewrote the mcl manual page so that all pruning-related options
are now in a separate section.
* Documented existing --dense and --thick flags (unlikely
you need them though).
* Cleaned up html documentation a lot. It should now look good in
most browsers. Moved from <dl> to <table>
* Began first ever so slight reworking of taurus. renamed Ilist to mcxIL
and its 'list' member to 'L'. Terse!
* Compiled zoem util mcl shmcl shcl shmcx shmx nonema
with gcc -pedantic -Wall -ansi, and fixed all the nitty gritty stuff
thus found, including an erroneous pthread_create argument cast and two
functions whose declaration was hidden (not in the header file).
Mon, 04 Mar 2002
* mcl-02-063 released.
* Fixed the missing '#include <string.h>' in taurus/ilist.c,
and fixed the bug caused by #defining TRUE and FALSE without
checking whether they were previously defined.
Wed, 27 Feb 2002
* mcl-02-058 released.
* Mcl-related changes are all updates in the documentation,
plus small changes in the underlying 'util' library. No functional
changes.
* Zoem has changed significantly since the previous release.
It needs to be separated from mcl. (zoem is the tool with which mcl
documentation is generated).
Fri, 15 Feb 2002
* mcl-02-047 released.
Tue, 5 Feb 2002
* mcl-02-035 released.
Wed, 12 Dec 2001
* mcl-20011211 released.
|