source: branches/stable/GDE/TREEPUZZLE/ChangeLog

Last change on this file was 4640, checked in by westram, 17 years ago
  • proper 'clean'
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 13.6 KB
Line 
12007-05-30  Ralf Westram  <westram@bio.tum.de>
2
3        * Makefile: - proper 'clean'
4
52004-04-29  Ralf Westram  <Coder@ReallySoft.de>
6
7        * doc/manual.html: - removed umlauts
8
92003-09-19  Ralf Westram  <Coder@ReallySoft.de>
10
11        * src/util.c: - const fix
12
13Version  date           what has been changed
14
155.0       26.08.2000    - changes to manual, Makefile.in
16                        - cpREV hidden by -DCPREV flag
17                        - chi2test, quartio included into source code files
18                        - generic scr/Makefile.generic
19                        - src/makefile.com for VAX
20                        - AUTHORS, README, ChangeLog updated
21                        - INSTALL checked
22          27.08.2000    - test code excluded
23                        - '-randseed#' added for debugging purposes
24                        - ./data added to autoconf/automake
25                        - warning output if cmdline parameter unknown
26          11.10.2000    - fixed output of rate categories of sites before
27                          computing them
28                        - check whether rate categories were computed by
29                          1st user tree or NJ tree fixed in the output
30          12.10.2000    - invariant site model normalization fixed
31
32
33CODE FREEZE
34===========
35
365.0.a33   15.08.2000    - changes for autoconf/automake
37
385.0.a32   01.08.2000    - a FPE error fixed (badq == 0)
39                        - small error in -bestq fixed
40                        - fflush's added at several places
41
425.0.a31   01.08.2000    - comments added to tree structure sorting puzzle2.c
43                        - changes in configure.in, Makefile.in
44
455.0.a30   23.07.2000    - some debugging in checkquart
46                        - changed to autoconf
47
485.0.a29   13.07.2000    - some debugging in checkquart
49
505.0.a28   13.07.2000    - use best quartet topology option (-bestq) implemented
51
525.0.a27   13.07.2000    - further developement to checkquart
53                        - ascii/binary quartet values (-wqla/-wqlb)
54                        - typo correction
55
565.0.a26   11.07.2000    - fflush at all checktimer
57                        - further developement at checkquart
58                        - possibility to write quartet values to file (-wqlh)
59
605.0.a25   06.07.2000    - fflush at checktimer
61
625.0.a24   02.07.2000    - further debugging of checkquart
63
645.0.a23   02.07.2000    - further developement to checkquart
65
665.0.a22   29.06.2000    - checkquart added to makefile
67                        - bad quartet stats added after reading in *.allquarts
68
695.0.a21   27.06.2000    - site pattern statistics implemented and added to
70                          SEQUENCE ALIGNMENT section in puzzle report
71
725.0.a20   26.06.2000    - cpREV45 implemented
73
745.0.a19   26.06.2000    - for debugging purposes: typo "MPE" changed to "FPE"
75                        - fflush(stdout) added in chi2test
76
775.0.a18   20.06.2000    - checkquart implemented
78
795.0.a17   19.06.2000    - FPRINTF(STDOUTFILE and STDOUT definition changed
80                          and moved; fputid/fputid10 writes to STDOUT instead
81                          of stdout
82                        - ppuzzle checks slaves enough slave-processes
83                        - numquarts, num2quart, quart2num moved from ppuzzle.c
84                          to puzzle1.c
85                        - read/writeallquart implemented (undocumented feature)
86                          to be used by -wqf/-rqf at comandline
87                          -wqf = write quartet file (infilename.allquart) after
88                                 quartet evaluation
89                          -rqf = read quartet file (infilename.allquart), no
90                                 quartet evaluation, unless -wqf is used as
91                                 well, then quartets are written and read in
92                        - '-h' option at comandline -> printusage
93
945.0.a16   31.05.2000    - chi2test bug fixed
95                        - WAG matrix added, model choice adopted
96          13.06.2000    - date set to June 2000
97                        - author order changed to Schmidt, Strimmer, Vingron,
98                          v.Haeseler
99                        - CPU time output stopped, due to overflow errors
100          16.06.2000    - sequence composition chi2test moved before
101                          parameter output.
102                        - output of chi2test and bad quartet statistics split,
103                          to do the chi2test output earlier.
104
1055.0.a15   02.05.2000    - Names changed back from TREE-PUZZLE to PUZZLE
106          09.05.2000    - and to TREE-PUZZLE again ;-)
107
1085.0.a14   13.03.2000    - Changes to the manual.
109                        - Executable names changed to (p)treepuzzle.
110                          (changes in the makefiles)
111          15.03.2000    - Output of parameters after estimation added.
112
1135.0.a13   18.02.2000    - ALPHA version number removed from the code
114
1155.0.a12   18.02.2000    - CPU time measurement problems fixed for case where
116                          clock_t is an unsigned type.
117
1185.0.a11   17.02.2000    - time measure problems (CPU/wallclock) fixed
119                          not all features in addtimes are used at the moment.
120                        - unnecessary and unused routines removed fron source
121                          code.
122
1235.0.a10   20.01.2000    - Name changes from PUZZLE to TREE-PUZZLE
124                        - Chi2-fit model guessing for VT model added
125                        - little model printing bug fixed
126
1275.0.a9    22.12.1999    - VT Model incorporated (Mueller, Vingron (2000)
128                          JCB, to appear).
129                        - TODO: Chi2-fit model guessing for VT model
130
1315.0.a8    21.12.1999    - 'sys/times.h' and 'sys/types.h' removed from
132                          puzzle.h. They were neither ANSI conform nor
133                          necessary, but occured in the SUN man pages.
134                        - Definition and call of writetimesstat eliminated
135                          from the sequention version by compiler switched,
136                          and not just the function body as before.
137                        - '-O4' canged to '-O' to be more generic.
138
1395.0.a7    21.12.1999    - Macro constants introduced for data_optn
140                          (NUCLEOTIDE, AMINOACID, BINARY)
141                        - round robbing of datatype and AA model option changed
142                          in menu to make adjustment of the model possible by a
143                          determined sequence of letters:
144                          'd':  Auto -> Nucleotides
145                                     -> Amino acids
146                                     -> Binary states
147                                     -> Auto
148                          ('m' && data_optn == AMINOACID): 
149                                Auto -> Dayhoff
150                                     -> JTT
151                                     -> mtREV24
152                                     -> BLOSUM62
153                                     -> Auto
154                        - manual.html adjusted
155
1565.0.a6    20.12.1999    - new manual.html added
157
1585.0.a5    07.12.1999    - output bug fixed (bestrates were written before they
159                          were computed)
160
1615.0.a4    02.12.1999    - header file inclusion ajusted:
162                          added:  #include<string.h>
163                          changed from:  #include "ppuzzle.h"
164                                  to:    #ifdef PARALLEL
165                                         #  include "ppuzzle.h"
166                                         #endif
167
1685.0.a3    27.11.1999    - '-h' comandline option removed, because of problems
169                          with MPICH under LINUX
170                        - new memory leaks of 5.0.a2 closed in PP_Finalize
171
1725.0.a2    27.11.1999    - Cleanup of the source code
173                        - Measurement of CPU time added
174                        - Parallel load statistics added (quartets, trees, time)
175                          to puzzle report.
176                        - Cleanup debug messages
177                        - Comments "[...]" are removed from usertrees now.
178                        - single quotes will only be printed arount species
179                          names if -DUSEQUOTES is set at compiletime.
180                        - tree likelihood is printed infront of a tree as a
181                          comment, [ lh=-xx.xxxxx ](...);
182
1835.0.a1    26.11.1999    - Cleanup of the directories
184                        - Copyright changes
185                        - Version changes
186
187
188VERSION CHANGE
189==============
190
1914.1.a26   25.11.1999    - Makefile made universal for pauzzle and ppuzzle
192                        - lines not needed removed from puzzle.h
193
1944.1.a25   19.11.1999    - Output file prefixes for distances, trees, and
195                          puzzlereport changed in user trees analysis case
196                          to user tree file name
197                        - Temporary output of likelihood to treefile added
198
1994.1.a24   11.11.1999    - Output of puzzling step trees changed
200                          ptorder: [ orderno # % ID #UniqTopos #Steps ]PHYLIP
201                          pstep:   chunk #InChunk sum ID #UniqTopos #Steps
202                        - preliminary leap frog RNG implemented, i.e. uses
203                          the rand4 in the usual way in the sequential case.
204                          If run in parallel all rand4 are initialized with
205                          the same seed and started with PP_Myid-th random
206                          number. after that each process uses the every
207                          PP_NumProcs-th random number to make sure that these
208                          unique.
209
2104.1.a23   08.11.1999    - output of sequential and parallel version to *.pstep
211                          made identical
212
2134.1.a22   05.11.1999    - two different puzzle step tree outputs intruduced
214                          and added to the menu ("[ 1. 35 ](...);":
215                          - ordered unique tree list -> *.ptorder
216                            Format: "[ 1. 35 ]"  (Ordernumber, Amount)
217                          - chronological tree list  -> *.pstep
218                            Format: "[ 1. 35 ]"  (Chunknumber, Amount in chunk)
219                          (the last is a problem in parallel, because the come
220                          in chunks, as scheduled)
221                        - debugged the output
2224.1.a21   04.11.1999    - Makefile adjustments for other Plattforms
223                        - pstep tree output changed. unique treestructures
224                          printed to *.pstep file with a leading comment
225                          containing an order number and the ammount padded
226                          with blanks (e.g. "[ 1. 356 ]('mouse'...").
227                          output is done right before writing the puzzle file.
228                        - controlled MPI finish to the Quit menu option added
229
2304.1.a20   03.11.1999    - some garbage collection (free) added
231                        - makefile adjusted, OFLAGS for optimization added
232                          (ppuzzle/MPICH has problems with -O, so the
233                          ppuzzle is created without optimization)
234                          Some minor changes in the makefiles
235                        - still to do: garbage collection from 'internalnode'
236                          in master process
237
2384.1.a19   13.10.1999    - adding the output of standardized (i.e. sorted)
239                          puzzling step trees. Those are printed to the
240                          standard output at the moment. (Routines to sort
241                          and print the trees implemented)
242          14.10.1999    - routines for printing the sorted trees to a string.
243                          needed to send them between Master and Worker, and
244                          to have a unique key to sort and count the trees.
245          21.10.1999    - counting of sorted trees implemented by doubly linked
246                          list, sort routine, print to stdout
247          25.10.1999    - change place of writing distances to file right after
248                          distances have been computed.
249                        - output of puzzling step trees now with true name,
250                          not numbers
251          02.11.1999    - parallel counting and sending of puzzling step trees
252                        - some parallel sending bugs fixed
253
2544.1.a18   14.09.1999    - adding possibility to specify input file at
255                          command line, this specifies also the output
256                          filenames (puzzle output: *.puzzle; treefile:
257                          *.tree; distances: *.dist; Triangel EPS: *.eps;
258                          unresolved: *.qlist; puzzling step trees: *.pstep)
259                          If an unexisting name is given, one has to reenter
260                          the right name, but the wrong one is used as prefix.
261          15.09.1999    - sending back of bad quartets from slaves added
262                        - bug in quart2num fixed (not used before; was shifted
263                          by 1)
264                        - first version of a README added ;-)
265
2664.1.a17   03.08.1999    - Recv-Error in receiving DoPuzzleBlock fixed
267                        - double freeing of same MPI_Datatype fixed
268                        - changing of scheduling algorithm to smaller chunks
269                          in gss -> sgss
270          13.09.1999    - bug fixed in optimization routine in ml2.c:
271                          boundary check added
272
2734.1.a16   12.07.1999    - slight changes in verbosity levels
274                        - changed all printf to FPRINTF(STDOUTFILE to
275                          change easily from stdout to a file.
276
2774.1.a15   08.07.1999    - scheduler for both parallel parts
278                        - several small changes
279
2804.1.a14   25.06.1999    - computation of tree parallel, scheduler dependent,
281                          sending all biparts in one message instead of one
282                          by one
283                        - several small changes since a13 in sched.c, et al.
284
2854.1.a13   10.06.1999    - computation of tree parallel (chunk = #trees/#slaves)
286                        - scheduling schemes implemented for minimum chunk sizes
287
2884.1.a12   07.06.1999    - computation of quartets properly parallel
289                        - scheduling implemented
290                        - counting of quartets by slave ajusted
291                        - TODO: sending of bad quartets (array + list)
292                        - distinction between '1st user tree' and 'NJ tree'
293                          in result output removed again
294
2954.1.a11   28.05.1999    - PP_SendDoQuartBlock, PP_RecvDoQuartBlock,
296                          PP_SendQuartBlock, PP_RecvQuartBlock
297                        - mallocquartets() changed from global to local
298                          variables to be more flexible
299                        - Quartet computation moved to slave (badquartet
300                          handling missing: output, badquartet vector);
301                        - distinction between '1st user tree' and 'NJ tree'
302                          added in result output (puzzle1.c around l.1756)
303
3044.1.a10   20.05.1999    - num2quart, numquarts, quart2num introduced
305                        - parallel init/finalize, quartets computed on
306                          master and slave, compared -> equal -> all necessary
307                          parameter exported
308
3094.1.a9    19.05.1999    - 'dvector forg' removed from onepamratematrix
310                          cmdline, because it's not used in the function.
311
3124.1.a8    18.05.1999    - add _GAMMA_ (not necessary) to gamma.h and _PUZZLE_
313                          to puzzle.h to avoid dublicate includes, possible
314                          due to ppuzzle.h
315                        - ppuzzle added to makefile and to check
316                        - 1st parallel version but no slave computations
317                          only sending parameters and done signals.
318
3194.1.a7    18.05.1999    - export reevaluation of tree and evaluation of
320                          usertrees to evaluatetree.
321
3224.1.a6    17.05.1999    - -DNEWFORLOOP added to fixed.src, because the changed
323                          for loop structure changes the sequence of randomized
324                          quartets during likelihood mapping
325                        - change 'int main()' to 'int main(argc, argv)'
326                        - export more functionalities from main:
327                          memcleanup(), inputandinit(&argc, &argv)
328                        - grouping if's (excluding eachother) together in
329                          switch()
330                        - split treereavaluation and 1st usertree,
331                          evaluate all usertrees together (TODO: both,
332                          treereavaluation and usertrees in one loop)
333                        - MAKE CHECK added to ./makefile
334
3354.1.a5    16.05.1999    - adding Ždvector BrnlengthŽ to lslength cmdline to
336                          reduce globality of Brnlength. (Later better to *Tree)
337
3384.1.a4    11.05.1999    - structure of for loops changed in computeallquartets
339                          and recon_tree, so that the quarted addresses are in
340                          one contigous sequence (for a<b<c<d). This reduces
341                          swapping on low memory machines and is easier to
342                          parallelize.
343
3444.1.a3    07.05.1999    - export likelihood mapping from main to map_lklhd()
345                        - export tree reconstuction from main to recon_tree()
346
3474.1.a2    06.05.1999    - moving all quartet_(a)lklhd calls to a general
348                          purpose routine compute_quartlklhds()
349
3504.1.a1   06.05.1999     - Macro constants for typ_optn and puzzlemode
351                          for better readability.
352                        - Ring counter for typ_optn and puzzlemode in
353                          the menu realized with mod (%) instead of IF.
354                        - Possibility added to switch to a fixed random
355                          seed (-1) or/and fixed 'random' integers (0)
356                          by using -DFIXEDRANDSEED and -DFIXEDINTRAND options.
357
358
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