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changes.txt
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CHANGES BETWEEN 4.1.2 and 4.1.2.1
New Features:
- Added support for NEXUS output in the portal binary.
Bugs Fixed:
- Output of NEXUS files when terminals are filtered,
or dynamic homology characters are not present could
produce errors or a file that POY itself could not
read (Felipe G. Grazziotin).
CHANGES BETWEEN 4.1.1. and 4.1.2
New Features:
- Added build (nj) to build a tree using the neighbor joining
algorithm. The algorithm implementation is deterministic, so
only one tree can be produce for each dataset.
- Added read (prealigned:(....., gap_opening:INT)) to read
prealigned sequences and assign each indel block a gap opening
cost.
- The build process now uses ocamlbuild instead of plain
Makefiles.
- The distributed binaries are the first to support plugins for
POY, but the feature is still experimental.
- Improved the NEXUS file format support, by adding the POY block,
which now includes: GAPOPENING, TCM, and WTSET. All the
characters in POY can now be stored in one NEXUS file that can
be reloaded later. The support for NEXUS files has improved to
allow more transparent interaction with other applications.
- POY now interprets all the ASSUMPTION block commands in NEXUS
files that the program can apply (e.g. EXSET, TYPESET, and
USERTYPE).
- Added report (nexus) and report (trees:(nexus)) to generate
output in nexus format.
- report ("out.ext", data, trees) produce NEXUS or hennig format
depending on ext. If the extension of the filename to which data
and trees are generated is "nexus" or "nex" then the data and
trees are generated in NEXUS format. If the extension is "hen",
"hennig", or "ss", then the format is Hennig86. For example,
report ("out.nexus", data,trees) is equivalent to report
("out.nexus", nexus, trees:(nexus)).
- Replace spaces with underscores in taxon names of NEXUS files.
- Added support to newick files with branch lengths. The branches
are ignored.
- Added support to 1~4 ranges.
- Bremer support values can output on the branches of a consensus
tree or any user provided input tree. (See the new commands
below.)
New Commands:
- report (nexus trees:(nexus)).
- transform (dynamic_pam:(locus:dcj:INT))
- report (supports:bremer:of_file:("file1", "file2", ...))
Features eliminated:
- Dropped ti and td
- ':' is not accepted in a taxon name, required for newick file
format. For example "mytaxon:1" is not an acceptable taxon name
anymore.
Bugs Fixed:
- Fixed issue 72.
- Fixed incorrect description of select (missing) in the
documentation.
- Annotated chromosomes could produce incorrect costs
- Fixed compilation problems of the portal
- Data.get_tcm2d error (Buz Wilson, Katrina Menard).
- Sankoff characters where not applied the user defined weight.
- Branch collapsing in Sankoff and Additive characters could be
incorrect.
- Tree scores with additive characters may be incorrect (Taran
Grant). This only happened if the additive character had state
7.
- search (constraint) and swap (constraint) have multiple fixes to
better guarantee the restrictions set by the constraint.
- 0 length branches now appear with 0 bremer support when bremer is
reported.
- Fixed compilation error in Mac OS X 64 bits using OCaml 3.11.0.
- The total rearrangement cost included indels for rearranged
elements.
CHANGES BETWEEN 4.1 and 4.1.1
Improvements:
- Simplified naming of single fragments and partitioned sequences:
now the number only appears if more than one fragment is loaded.
For example, if a file a.fas has only one fragment, the old
naming convention for that character was a.fas:0. The name for
the character is now a.fas.
- Improved the message for bad NEXUS files comming from Mesquite.
Bugs Fixed:
- search () used too much memory in some cost regimes, causing a
dramatic drop in the application performance when searching
those costs.
CHANGES BETWEEN 4.0.2911 AND 4.1
Improvements:
- Improved detection of inconsistencies in synonym files.
- ci and ri could fail with a Not_found error when static
homology characters where missing in an input file.
- The characters produced from an implied alignment keep
the name of the original sequence character. For example,
the first base in the implied alignment of chel.aln:0 gets
the name chel.aln:0:ia:0.
- Improved the graphical output, now in pdf format.
- If the synonyms file is not found, POY stops the script
execution.
- New command to report bremer values using multiple input files
containing trees collected during a search. For example, if a
user has 5 separate files containing trees collected
independently using swap (visited:"file1"), swap
(visited:"file2")..., swap (visited:"file5"), then the created
files can be used to produce the bremer support values using
report (supports:bremer:("file1", "file2", ..., "file5"))
- New command report (supports:[jackknife|bootstrap]:"FILE") and
report (graphsupports:[jackknife|bootstrap]:"FILE"). FILE
contains input trees, and the report contains those trees with
the corresponding support annotations.
- Added support for compression using the zlib library in bremer
files using swap (visited:"file"). The files produced can be
decompressed with gunzip.
- Removed the need to make depend before compiling any target.
Bugs Fixed:
- swap with non-additive characters can fail with segfault.
- swap (visited:"file") fails in windows.
- Diagnosis of Sankoff characters could fail.
- Sankoff characters diagnosis in XML did not print correct human
symbols.
- Bogus warning message when reading a list of trees.
- Compressed bremer files fail to use all of the trees.
- Additive characters do not appear in the diagnosis.
- Improved the precission of the maximum time when using search ()
- Fixed stack overflow / seg fault when reading a large number of
trees.
New Compilation Requirements:
- Made OCaml 3.10.2 or superior a requirement (due to Camlp4
bugs).
- POY now needs the zlib library.
CHANGES BETWEEN 2885 AND 2911
BUGS FIXED:
- Printing long trees in parenthetical notation could cause a crash.
- After compiling with --enable-xslt poy behaves as if not enabled.
- Transform (static_approx) with aa characters can fail.
- Test build/build9.poy fails.
- Issue#69 and some improvements to the Makefile rules.
- Multiple improvements and bugfixes in the swapers and tabu managers.
- Compressed files did not handle \r\n -> \n conversion in win32.
- Crash in Mac OS X - PPC.
- Fixed bug in the phastwinclad output.
- Hennig and Nexus parsers do not handle polymorphisms.
- Issue #67
- Iterative pass under affine and missing data could assing power sequences
(and therefore incorrect tree cost).
- Reading some very large files could cause a stack overflow error.
- Some input file channels where never closed, and many forks can be used.
- Windows fails on report (supports:bremer:"x")
- read (prealigned:("x", y)) some times fails.
- reading trees containing synonyms after rename () does not work.
- report (supports:bremer:"file") contained values for the root.
IMPROVEMENTS:
- Significant improvements in the performance of search (): it finds
better trees.
- Added -enable-xslt to the top configure for help purposes.
- Added support to make install DESTDIR=path
- Upon reading trees, POY verifies that all the loaded terminals are
present.
- Some times WinClada fails to read trees in Hennig format.
- Reduced memory consumption in XML conversion functions.
- Changed from Error to Warning the "You are loading a non-metric TCM"
message.
- Added XML file for SWAMI bioinformatics portals, and the companion
poy_server program.
CHANGES BETWEEN 2880 AND 2885:
- Bugfix: Reading some very large files could cause a stack
overflow error.
- swap (visited:"f") and report (supports:bremer:"f") compress the
file f.
- Bugfix: swap (visited) could print the wrong cost when only
static homology characters have been loaded (Taran Grant).
- New Arguments: report->searchstats, build->threshold,
build->lookahead, transform->max_kept_wag
- Improved the handling of the program arguments for better
execution in more implementations of MPI.
- Bugfix: Static approx fail to add gaps in non-affine sankoff
matrices.
- Bugfix: Make sure that characters that should be ignored
according to the Nexus and Hennig files are indeed ignored.
- Bugfix: help () did not work! Issue# 65.
- Multiple documentation improvements.
- Bugfix: Missing sequences could cause bogus 0-length branches in
the tree.
- Improved build (_mst).
- Bugfix: Duplicate character names in input files overwrite older
ones.
- Bugfix: Hennig/TNT parser do not accept empty comment in xread
command.
- Bugfix: The ncurses interface some times, misteriously,
internally deletes characters that are not deleted in the
screen, producing illegal commands.
- Improved error messages for Mesquite's TITLE command in NEXUS
files.
- Improved detection of Hennig/NONA/TNT files.
- Eliminated the full help on command errors. This is only
confusing.
- Improved the behavior of the GenBank file format parser.
- Bugfix: Equate within polymorphisms didn't parse in
Hennig/Nexus.
- Hennig parser now interprets the nstates command.
CHANGES BETWEEN 2870 AND 2880:
- Improved static approx for annotated chromosomes.
- Fixed multiple bugs in the implied alignment for chromosomal and genome characters
- Issue #55: Sorted the characters by code in report(crossreferences:names:("x")).
- Issue #57: Use non-additive characters in more cases after static approx.
- Fixed typo in report (memory) (Campations is Compactions).
- Issue #58: read ("unexistant") causes a hang in POY when running in parallel.
- Fixed bug in genome alignment
- Documentation update: Reference filed partially updated to reflect more uniform 2 intial format.
- Fixed Issue #56 and added set (iterative:false).
- Cleaned some harsh words in source code.
- Fixed cost matrix problem in the genome character
- Improved various details in the set (iterative:false) algorithm.
- Fixed Issue# 59 and removed bogus user messages.
- Added the options iterative:exact and iterative:approximate.
- Fixed Issue #60
- Modified heuristic of search (), and fixed diagnosis bug under iterative.
- Fix a bug in suffix tree creation.
- Bugfix: transform (weight) does not automatically update trees in memory.
- Improved the behavior of the tree selection under negative weights.
- Bugfix: accept negative values for random number generator seed.
- Minor fixes in report(data)
- Added seq.h header to eliminate a compile time warning.
- Added files to ignore from the documentation and compilation accessory files.
- Bugfix: Issue #61
- Bugfix: help (search) shows many results but not just the command search.
- Bugfix: help (search) shows a paragraph with vertical boxing (missing brackets).
- Bugfix: help (search) shows all the See Also items in one line.
- Added man pages.
- Bugfix: Issue #62
- Bugfix: The Fixed States field of report (data) is always empty.
- Handle negative segments in chromosomes when creating implied alignment
- Take into account inverted segments in annotated chromosomes
- Bugfix: Fixed a wrong case handling in the diagonal extension opening a gap.
- Simplified the execution of the changes introduced in the previous commit.
- The iterative algorithm now follows a postorder traversal.
- Added search->visited argument.
- Added search->constraint
- Fixed bug in file constraint ignored during break.
- Change kept_wag default value from 3 to 2
- Activated iterative algorithms for chromosome characters
- Improved 3D-chromosome and genome alignments
- Fixed bug in build with internal transform.
- Fixed bug in analyzer for expressions like build (10, transform (static_approx))
CHANGES BETWEEN 2635 AND 2870:
Improvements:
- Added a new initial assignment of sequences using fixed states.
- Added the new argument transform -> direct_optimization and
modified transform -> fixed_states.
- Multiple crashes in parallel execution have been corrected.
- Massive improvements in affine gap cost.
- Added filters for redundant tree evaluations during spr and tbr.
- Improved TBR.
- Changed the default swap strategy from alternate to TBR.
- Improved the command search ().
- Newick is the new default format for all the parenthetical tree
output functions.
- Reduced memory consumption by more than half for DH chars.
- Improvements in the performance of perturb operations.
- Added the command set->timer:INT.
- Limited number of rediagnosis performed during search.
- Improved the performance of swap(constraint).
- Disabled iterative in non-sequence chars.
- Modified the following arguments for better readability:
1. seq_to_breakinv -> custom_to_breakinv
2. breakinv_to_seq -> breakinv_to_custom
3. breakpoint -> locus_breakpoint
4. inversion -> locus_inversion
5. approx -> med_approx
6. sig_block_len -> min_loci_len
7. rearranged_len -> min_rearrangement_len
- Speedup tree fusing.
- Modified timeout's behavior (see documentation.)
- Moved the select (terminals) report from stdout to stderr, where
it belongs.
- Improved transform (static_approx) when using affine and sankoff
tcm's.
- Simplified representation of SankCS.t to reduce memory
consumption.
- Reduced the number of reports of the current search state.
- Improved tree fusing by not swapping those trees that are
already in the population.
Compilation Changes:
- New Configure Option: --enable-large-messages. See ./configure --help.
Bugs Fixed:
Bugfix:
Symptom:
Searches under gap_opening:x can fail with a segmentation
fault (Buz Wilson).
Problem:
The computation of the medians under affine is not atomic,
yet some heuristics assumed they where, breaking some
invariants.
Solution:
Store the complete median for use, and don't recompute the
individual medians.
Bugfix:
Symptom:
Certain scripts containing wipe () fail to be analyzed
(Lara Lopardo).
Problem:
The analyzer has a glitch for wipe () and use ().
Solution:
Analyze the portions separation by wipe () and use ()
independently.
Bugfix:
Symptom:
Orientation and init3D are true even if the user doesn't
set it to that value.
Problem:
We check if the list of options does not contain
`Orientation false or `Init3D false, but the default
selection contains an empty list, makeing this true.
Solution:
Check if the list of options contains `Orientation true
or `Init3D true.
Bugfix:
Symptom:
Reading an input tree when data some terminals have been
selected causes a Not_found error.
Problem:
We assign code in the tree by counting the number of
leaves instead of the number of taxa loaded in Data.d.
Solution:
Use the parameter in Data.d.
Bugfix:
Symptom:
transform (randomize_terminals) fails with a Not_found
error.
Problem:
We eliminate all the data and recompute the tree de novo.
But before recomputing we compare the nodes to see if
something really needs to be recomputed, the problem is
that some of the nodes are missing!
Solution:
force the update and if the error occurs, trigger the
update.
Bugfix:
Symptom:
report (diagnosis) may show some bogus character states.
Problem:
The reported characters remain classified in groups,
therefore, for some of the input characters, the reported
states may not match, thought the overall cost is correct.
Solution:
Reload the tree with the raw nodes, without
classification.
Bugfix:
Symptom:
transform () together with use () and store () may result
in empty datasets.
Problem:
The nodes are not necessarily regenerated when the data is
loaded back with the use () command.
Solution:
To avoid this problem, we store both the data and the
nodes, and use them when requested. This has 0 speed
penalty, and some memory penalty.
Bugfix:
Symptom:
If there are 0 characters loaded, a Random.int error is
raised when the calculate_support (bootstrap) command is
issued.
Problem:
We don't verify if the number of characters is greater
than 0 before doing the resample, and Random.int requires
a positive integer.
Solution:
If there are 0 characters, there is nothing to resample.
Just return the same array.
Bugfix:
Symptom:
Assertion failure when the input tree contains terminals
that don't exist in the input files.
Problem:
We don't verify the leaves before attempting to build the
tree, which has now a predefined set of codes. If the
input tree contains _more_ leaves than vertices require
the input data to produce a tree, the program will break
an assertion.
Solution:
Check the leaf names before attempting to load the tree.
Bugfix:
Symptom:
read ("bleh") produces a background File Not Found
messages in windows, which can appear anywhere in the
screen.
Problem:
We don't use proper handling of stderr in the windows port
for this kind of command.
Solution:
Redirect stdin, stderr, and stdout, ignoring the first two
completely in every architecture, by using not the system,
but directly OCaml's Unix module.
Bugfix:
Symptom:
Some times POY prints a large number instead of INF for
trivial Bremer support values.
Problem:
We check if the number is large, but floating point
comparison may fail.
Solution:
We now do a rough comparison for a number half of the
internal infinity number (Pervasives.float_of_int
(Pervasives.max_int / 4)) and if larger, then we assume it
is just infinity.
Fixed typo in Perturbing message (was Perburbing) (Buz Wilson).
Bugfix:
Symptom:
Reading a nexus file with comments inside the matrix
itself failed with Segmentation fault.
Problem:
We have an endless loop that causes an Stack Overflow
error, which can be a segmentation fault in some
architectures.
Solution:
Fix the endless loop by incrementing the counter before
making the recursive call.
Bugfix:
Symptom:
Reading UNALIGNED blocks in NEXUS files fails.
Problem:
Internally we convert the NEXUS matrix into a FASTA file,
but the generated file is ... incorrect.
Solution:
Make sure that the resulting file is correct.
Symptom:
read (aminoacids:("A")) transform (tcm:(1,1)) report (ia)
fails with a Not_found error (Boyan Alexandrov).
Problem:
The gap code is not the last code of the alphabet, which is an
assumption of the tcm generator.
Solution:
Exchange the integer code of the X and the gap.
Symptom:
Tree fusing fails when running static homology characters only
(Ward Wheeler).
Problem:
When using static homology characters only, no information is
attached to an edge, but the functions assume (and assert)
that there is indeed information associated with an edge.
Solution:
Generalize the code to consider the other possible set of
algorithms.
Fixed bug in the serialization of the three dimensional cost
matrices.
Symptom:
During parallel execution, if the dataset includes additive
characters, POY may crash (Fernando Marques).
Problem:
The serialization functions for additive characters did not
use proepr macros for 64 bit and 32 bit environments. They
also assumed that successive mem_malloc calls would produce
successive memory locations (clearly incorrect).
Solution:
Define the required macros to handle properly native integers,
and serialize and deserialize all the vectors independently.
Symptom:
poy script.txt when poy is compiled in parallel fails for the
following script:
read ("x")
build (10)
select ()
swap ()
report (trees)
with the Warning: "No trees in memory" (Fernando Marquez)
Problem:
The `GatherTrees command does not run the merging instructions
if only one process is being executed.
Solution:
For every branch of the tree exchange algorithm, run the
joiner set of instructions.
Symptom:
Issue 51 (loucrow and Fernando Marquez).
Problem:
The GatherTrees command had some bugs in the way it was
merging trees from different processes.
Solution:
Simply merge the stored_trees and trees fields from
Scripting.run and do not postprocess trees thanks to the
change described above.
Symptom:
Reading a NONA/TNT file produces trees rooted in the last
terminal of the file (Federico Lopez).
Problem:
The parser of NONA/TNT files, just as the Nexus parser,
produces the output in inverse order.
Solution:
Repeat the solution for Nexus files in 2635 with NONA/TNT
files.
Symptom:
select (terminals, "filename") outputs a table of included and
excluded for each slave.
Problem:
Although we filter output for slaves, table output is not
being filtered out.
Solution:
Filter the table output to include only output requests from
the slaves.
CHANGES BETWEEN 2602 AND 2635:
Bugfixes:
- read (prealigned:("file.txt", tcm:(1,1))) report (phastwinclad)
prints an error when file.txt contains fragments and some
fragments are missing (Julian Faivovich).
- Removed a bogus @ sign in the description of an input file type.
- An error appears for chromosome characters when iterative pass
is set before swap command.
- ./configure --enable-interface=readline; make fails under x86-64
linux (Dan Janies)
- The first taxon in a nexus file is treated as the last one
instead of honoring the input file order. This makes the last
terminal the effective default root for nexus files (Federico
Lopez).
- Fixed Issue #49
- Fixed Issue #48
- Fixed Issue #45
- Fixed Issue #40
- Fixed-Partial Issue #38
- Fixed Issue #37
- Fixed Issue #20
Improvements:
- subversion is not required to compile anymore and versions
compiled using the code.google.com site as well as the
downloaded source code have the correct build number.
- Added message to the Search Status showing the current tree cost
calculation algorithm.
- Made the selection of a root of a tree deterministic (for cost
calculations).
- Reduced the number of tree diagnosis during OnEachTree
operations and after reading an input file. This should reduce
considerably the execution time for non-trivial tree sizes.
CHANGES BETWEEN 2398 AND 2602:
------------------------------------------------------------------------
r2588 | andres | 2008-02-04 17:23:35 -0500 (Mon, 04 Feb 2008) | 8 lines
Bugfix:
Symptom:
Issue #36
Problem:
A newline is hinted to the pretty printer, but it is almost never used.
Solution:
Make the newline an obligatory one.
------------------------------------------------------------------------
r2587 | andres | 2008-02-04 14:24:53 -0500 (Mon, 04 Feb 2008) | 3 lines
Improvements: Hardcoded the machine that takes care of the generation of the
release binaries.
------------------------------------------------------------------------
r2586 | andres | 2008-02-04 14:23:57 -0500 (Mon, 04 Feb 2008) | 15 lines
Bugfix:
Symptom:
Running POY in parallel produces duplicated output for many functions.
Running POY in parallel in windows produces an MPI error message at the
end.
Problem:
We use the rank of the process to decide how to do IO. Only process 0
(the master), is allowed to produce output, otherwise it should be piped
through the master as plain messages. This is not being done properly in
the html interface which is used in the GUI based parallel execution.
Solution:
Make a uniform interface and set the rank when the parallel printer is
set upon the program initialization (Status.is_parallel).
------------------------------------------------------------------------
r2585 | andres | 2008-02-02 18:44:13 -0500 (Sat, 02 Feb 2008) | 4 lines
Bugfix:
A bogus test failure due to an incorrect cost stored in one of the test
files.
------------------------------------------------------------------------
r2584 | andres | 2008-02-02 10:45:36 -0500 (Sat, 02 Feb 2008) | 5 lines
Improvements:
Automatically cleanup the temporary files (to reduce the ammount of garbage
left after a test), and if not needed, leave the output going directly to
stdio so that the buildbot catches the results.
------------------------------------------------------------------------
r2583 | andres | 2008-02-01 18:19:19 -0500 (Fri, 01 Feb 2008) | 4 lines
Bugfix:
Modified the test_line program to properly signal buildbot when there is an
error in a batch of tests.
------------------------------------------------------------------------
r2582 | andres | 2008-02-01 17:02:19 -0500 (Fri, 01 Feb 2008) | 3 lines
Improvements:
Added compilation rules for poy_test at the top level.
------------------------------------------------------------------------
r2580 | andres | 2008-02-01 14:15:29 -0500 (Fri, 01 Feb 2008) | 4 lines
Improvements:
Added the new ocaml-flags options from the src/configure.ac to the topmost
configure file.
------------------------------------------------------------------------
r2579 | andres | 2008-02-01 14:15:05 -0500 (Fri, 01 Feb 2008) | 4 lines
Improvements:
Multiple improvements in the randomTree utility. See the --help for more
information about the new options and their behavior.
------------------------------------------------------------------------
r2578 | andres | 2008-02-01 13:30:09 -0500 (Fri, 01 Feb 2008) | 7 lines
Bugfix:
Symptom: Compiling with the html interface fails.
Problem: There is no Warning constructor in Status_html
Solution: Add the constructor.
------------------------------------------------------------------------
r2575 | vinh | 2008-01-30 08:36:23 -0500 (Wed, 30 Jan 2008) | 2 lines
Continue working on iterative pass for chromosome characters
------------------------------------------------------------------------
r2574 | andres | 2008-01-25 18:11:50 -0500 (Fri, 25 Jan 2008) | 5 lines
Improvements:
Added the constructor Status.Warning for warning messages. This resolves
Issue #24 in a clean manner.
------------------------------------------------------------------------
r2573 | andres | 2008-01-25 17:57:41 -0500 (Fri, 25 Jan 2008) | 6 lines
Bugfix:
Symptom: Issue #33
Problem: We don't add the files whose type is not autodetected to the list
of read files.
Solution: Add all the files whose type is specified by the user.
------------------------------------------------------------------------
r2572 | andres | 2008-01-25 17:46:33 -0500 (Fri, 25 Jan 2008) | 4 lines
Bugfix:
Symptom: Issue #34
Problem: We never handled these cases in the script postprocessing.
------------------------------------------------------------------------
r2571 | andres | 2008-01-25 10:09:56 -0500 (Fri, 25 Jan 2008) | 12 lines
Bugfix:
Symptom:
running tests with only one processor doesn't generate test_all.log
(Megan Harrison)
Problem:
The script uses Unix.waitpid () although tests with only
one processor have no children processes. This causes a
non-handled exception, skipping the necessary file concatenation
functions.
Solution:
If only 1 process is requested, skip the Unix.waitpid function.
------------------------------------------------------------------------
r2570 | andres | 2008-01-23 11:32:34 -0500 (Wed, 23 Jan 2008) | 4 lines
Improvements:
Added options for the selective compilation of windows binaries. Check bash
win32_build.sh --help for more information.
------------------------------------------------------------------------
r2569 | andres | 2008-01-23 11:05:32 -0500 (Wed, 23 Jan 2008) | 3 lines
Improvements:
Cleaned up the parallel execution message added in 2568.
------------------------------------------------------------------------
r2568 | andres | 2008-01-23 10:50:29 -0500 (Wed, 23 Jan 2008) | 4 lines
Improvements:
When executing in parallel, the initialization messages report the number of
processes being executed.
------------------------------------------------------------------------
r2567 | andres | 2008-01-23 09:56:15 -0500 (Wed, 23 Jan 2008) | 4 lines
Improvements:
Reduced the verbosity of the program by turning off the node loading status
messages.
------------------------------------------------------------------------
r2566 | andres | 2008-01-18 11:32:33 -0500 (Fri, 18 Jan 2008) | 2 lines
Removed the debugging flag which was committed by mistake.
------------------------------------------------------------------------
r2565 | andres | 2008-01-18 08:16:36 -0500 (Fri, 18 Jan 2008) | 5 lines
Bugfix:
The Makefile.local from the previous revision contained extra
definitions for clean using ::, but Makefile.in did not. This
rendered make useless. The problem is being fixed here.
------------------------------------------------------------------------
r2564 | andres | 2008-01-18 08:14:12 -0500 (Fri, 18 Jan 2008) | 4 lines
New Features:
Added the utility program randomTree to generate random trees,
in newick format, with branch lengths. Used for simulations.
------------------------------------------------------------------------
r2562 | vinh | 2008-01-17 22:07:00 -0500 (Thu, 17 Jan 2008) | 3 lines
Improvement:
Continue working on iterative pass for chromosome characters
------------------------------------------------------------------------
r2560 | andres | 2008-01-17 18:23:35 -0500 (Thu, 17 Jan 2008) | 3 lines
Improvements:
Added the windows parallel version to the compilation rules.
------------------------------------------------------------------------
r2558 | andres | 2008-01-17 18:00:16 -0500 (Thu, 17 Jan 2008) | 6 lines
Bugfix:
Symptom: A test of cd and pwd fails with no apparent reason.
Problem: The path is different in each machine being tested, therefore there
is no good reference file to compare with.
Solution: Remove the reference file.
------------------------------------------------------------------------
r2556 | andres | 2008-01-17 17:51:53 -0500 (Thu, 17 Jan 2008) | 6 lines
Bugfix:
Symptom: Test search07.poy fails.
Problem: We don't filter non-unionable characters before calling
auto_sequence_partition and auto_static_approx.
Solution: Filter them out!
------------------------------------------------------------------------
r2553 | andres | 2008-01-17 14:33:34 -0500 (Thu, 17 Jan 2008) | 15 lines
Bugfix:
Symptom:
Windows paths appear not to work properly and behave in strange manners
(like duplicating slashes when using ctrl-p) (ncurses interface).
Problem:
We worked around the slash problem as a scape character in the lexer by
escaping the individual characters. However, we are using now a special
purpose lexer that ignores escape sequences, and therefore, there is no
need to escape the slashes anymore.
In addition, we did not use a special character separator between unix
and win32.
Solution:
Pick the correct path separator according to the OS, and eliminate the
character escaping functions from the command line history in ncurses.
------------------------------------------------------------------------
r2551 | ilya | 2008-01-16 14:18:02 -0500 (Wed, 16 Jan 2008) | 12 lines
Documentation Update:
- Made substantial improvements and corrections
to the following documents:
- commands.tex
- allcommands.tex
- QuickStart.tex
- poyheuristics.tex
- poytutorials.tex
- Added a new figure and corrected an existing
figure for the 'Simple Search' section of the
QuickStart.tex
------------------------------------------------------------------------
r2550 | andres | 2008-01-15 12:22:53 -0500 (Tue, 15 Jan 2008) | 7 lines
Improvements:
Fixed the compilation procedures for Windows by removing the unelegant
steps.
Updated the source version of PDCurses to 3.3 (we where using 2.8). This
improves performance and overall experience for the end users.
------------------------------------------------------------------------
r2549 | andres | 2008-01-14 15:00:23 -0500 (Mon, 14 Jan 2008) | 3 lines
Bugfix:
Corrected a syntax error that did not permit compilation in OCaml 3.10.1.
------------------------------------------------------------------------
r2548 | andres | 2008-01-13 17:06:55 -0500 (Sun, 13 Jan 2008) | 4 lines
Bugfix:
Added some more missing test reference files, and updated the error message
of a test to match better the characteristics of the test.
------------------------------------------------------------------------
r2547 | andres | 2008-01-12 14:01:32 -0500 (Sat, 12 Jan 2008) | 4 lines
Improvements:
Replaced the poy_test program configuration from the readline to
the flat interface.
------------------------------------------------------------------------
r2546 | andres | 2008-01-12 13:56:58 -0500 (Sat, 12 Jan 2008) | 5 lines
Improvements:
Placed the LIBS environment at the end of every compilation rule which
needed it to eliminate compile-time errors due to undefined symbols (gcc's
linking sensibility). This was particularly important under windows.
------------------------------------------------------------------------
r2545 | andres | 2008-01-11 16:08:40 -0500 (Fri, 11 Jan 2008) | 2 lines
Reverting changes from revision 2544 which where made by mistake.
------------------------------------------------------------------------
r2544 | andres | 2008-01-11 16:07:44 -0500 (Fri, 11 Jan 2008) | 3 lines
Improvements:
Added the --with-ocaml-flags option to pass options for the OCaml compilers.
------------------------------------------------------------------------
r2543 | andres | 2008-01-11 16:07:08 -0500 (Fri, 11 Jan 2008) | 3 lines
Improvements:
Upon failure, during a test, the exception is raised not hidden.
------------------------------------------------------------------------
r2542 | andres | 2008-01-11 11:35:17 -0500 (Fri, 11 Jan 2008) | 10 lines
Bugfix:
Symptom:
No test successfully sends a reporting email.
Problem:
The recipient list should be extracted from the email header, however
the -t flag is missing from the sendmail command (this is required to
extract the recipient list).
Solution:
Add the -t flag in every sendmail call.
------------------------------------------------------------------------
r2541 | andres | 2008-01-11 11:34:07 -0500 (Fri, 11 Jan 2008) | 11 lines
Bugfix:
Symptom:
make poy_test fails with an unresolved dependency.
Problem:
status.ml is preprocesses by Camlp4, which means that it is filtered
from the default dependency check list. However, when it is included
back for dependency generation using Camlp4 as preprocessor, the mli is
not added again.
Solution:
Append status.mli to the dependency generation list after scripting.mli
------------------------------------------------------------------------
r2540 | andres | 2008-01-11 10:57:01 -0500 (Fri, 11 Jan 2008) | 4 lines
Improvements:
The log cleanup step of run_test will now eliminate not only test_all.xml
but all the process-specific logs.
------------------------------------------------------------------------
r2539 | andres | 2008-01-11 10:55:25 -0500 (Fri, 11 Jan 2008) | 3 lines
Bugfixes:
Fixed the new application tests so that they can be executed successfully.
------------------------------------------------------------------------
r2537 | megan | 2008-01-10 19:20:02 -0500 (Thu, 10 Jan 2008) | 4 lines
Tests Update:
Added missing data files gen5bp, gen11bp, gen20bp, Inv1.fas, Inv2.fas,
ua15.fas and the test file ann.
------------------------------------------------------------------------
r2535 | megan | 2008-01-10 09:05:04 -0500 (Thu, 10 Jan 2008) | 4 lines
Documentation:
Added description of iterative pass for chromosome characters and expanded
description of iterative pass in set command
------------------------------------------------------------------------
r2534 | megan | 2008-01-10 08:53:28 -0500 (Thu, 10 Jan 2008) | 3 lines
Tests Update:
Added test file "addons" with ci, ri, fasta and true cost tests
------------------------------------------------------------------------
r2533 | megan | 2008-01-10 08:40:40 -0500 (Thu, 10 Jan 2008) | 3 lines
Test update:
Added the test files ua_inv2.fas, gen, and unann
------------------------------------------------------------------------
r2532 | andres | 2008-01-09 09:36:18 -0500 (Wed, 09 Jan 2008) | 7 lines
Improvements:
Added support for concurrent test execution. Now a list of tests can be run
in parallel in multiple processors of the same machine.
The run_test.sh script now requires a fourth argument specifying the number
of processors to be used in the batch of tests.
------------------------------------------------------------------------
r2531 | andres | 2008-01-08 22:19:17 -0500 (Tue, 08 Jan 2008) | 5 lines
Bugfix:
Updated the Makefile.in to handle properly USEWIN32 != true as opposed to
USEWIN32 == false (which is never set). This bug was introduced during the
latest changes to properly execute the configure scripts in windows.
------------------------------------------------------------------------
r2530 | andres | 2008-01-08 22:17:04 -0500 (Tue, 08 Jan 2008) | 6 lines
Improvements:
Ported the tests to run properly in windows.
Multiple minor improvements to execute the tests and configuration scripts
in windows.
------------------------------------------------------------------------
r2529 | andres | 2008-01-08 18:00:58 -0500 (Tue, 08 Jan 2008) | 5 lines
Improvements:
Cleanup the *.win32 files that are not required anymore
Update the win32_build.sh script for the new compilation procedures under
windows.
------------------------------------------------------------------------
r2528 | andres | 2008-01-08 17:55:05 -0500 (Tue, 08 Jan 2008) | 4 lines
Updated support for configuration and compilation scripts under windows.
Updated version.ml to recognize properly the html interface flags.