August 2013 Commit Log

Number of Commits:
73
Number of Active Developers:
3
westram 2013-08-28 16:23 Rev.: 10513


* DRYed PHYML interface (Amino vs DNA)

46 lines of code changed in 2 files:

westram 2013-08-28 16:19 Rev.: 10512


* helper target to ease refactoring ARB_GDEmenus

20 lines of code changed in 1 file:

westram 2013-08-28 15:41 Rev.: 10511


* swap order (first DNA, then Amino) to match other tools in this menu

33 lines of code changed in 1 file:

westram 2013-08-28 15:38 Rev.: 10510


* split menu-sources for both versions of phyml

236 lines of code changed in 3 files:

westram 2013-08-28 15:29 Rev.: 10509


* remove trailing '3' in fastdnaml.menu (was ignored by arb_read_tree)
* split menu-sources for phylip_ml and phyml

345 lines of code changed in 4 files:

westram 2013-08-28 15:16 Rev.: 10508


* PHYML20130708 Makefile
- did not always make final target ($(ARBHOME)/bin/phyml...)
- define complete dependency chain => no matter what is deleted from WC, it should be rebuild now
- no longer trigger configure-call by stamp (let it depend on Makefile, i.e. as long as Makefile is not changed, configure will be called exactly once)
- do auto-clean before configure
- directly call 'make install' (does build as well)

21 lines of code changed in 1 file:

westram 2013-08-27 13:10 Rev.: 10499


- added assertions against entering functions when error is exported (gb_search + GB_searchOrCreate_string)

4 lines of code changed in 1 file:

westram 2013-08-27 12:10 Rev.: 10498


* changelog tree fixes

3 lines of code changed in 1 file:

westram 2013-08-27 11:40 Rev.: 10497


* replaced 'consense tree' by 'consensus tree' (user-visible terminology)
* added documentation for ARBs consensus tree algorithm

195 lines of code changed in 10 files:

westram 2013-08-26 16:49 Rev.: 10494


* reintegrate 'nds'
* replaces broken revision [10485]

375 lines of code changed in 10 files:

westram 2013-08-26 16:14 Rev.: 10492


* fix compile error :/

1 lines of code changed in 1 file:

westram 2013-08-26 16:13 Rev.: 10491


* fixed callback IDs of genome-NDS window

10 lines of code changed in 1 file:

westram 2013-08-26 11:51 Rev.: 10488


* revert broken revision [10485]

(fixed by [10494])

132 lines of code changed in 9 files:

westram 2013-08-26 10:15 Rev.: 10485


* mask some non-printing characters from NDS output (esp. LFs and TABs)
- motivation: gtk renders LFs at tree tips (resulting in overlapping leaf names)
- replace LF/CR by '#' and TAB by one space; replace other chars < ASCII 32 by '?'
- affects:
* displays (tree-tips, edit4 info-area)
* exported files (trees, calc-sheets, distance matrixes)
* link edit4 against NDS (edits should use code from NDS, not its own code!)

(reverted by [10488]; superseded by [10494])

193 lines of code changed in 9 files:

westram 2013-08-25 14:09 Rev.: 10482


* Tree IO (patch reintegrates branch 'tree')
- added unit test (!TreeReader, export/import consistency for most export-parameters combinations)
- refactorings: moved more behavior into !TreeReader; deny access to class internals
- improved error messages/warnings
* show error-position in input data when bailing out
* warn about unused data behind tree
* trees < 2 species produce error now
- behavior
* fixed export/import of bootstrap values (expect ':' as separator; avoiding misinterpretation of group names starting with digits)
* auto-name unnamed nodes
* supports bootstrap values specified as percent (e.g. '12.5%')
* no longer interpret {{{''}}} as escape sequence for a single {{{'}}}
* no longer remove leading '_' from leaf-/groupnames (no idea why this was done)
- fixes:
* export+import of tree using double quotes often resulted in leaf-/groupnames enclosed in double-quotes (or more often failed to load completely)
* name of root-node was lost after import.
* better support for single-node subtrees, e.g. '(leafname)'. Nodes were skipped.
* deadlock occurring when tree file was truncated somewhere in the middle.
* leaks stuffed

1051 lines of code changed in 18 files:

westram 2013-08-23 12:30 Rev.: 10479


* async GDE build
- pass down make flags (esp. -j) into subdirectories
- enclose subbuilds in $(SEP) as in main ARB Makefile (showing enter/exit timestamp for each subdir)
- mafft: build/clean core+extensions async
- mrbayes:
* define proper rules to make target 'mb' work with -j (no idea why that is needed)
* do not clear MAKEFLAGS in caller Makefile
- speedup for 'build' (on 8 cores)
* after GDE clean: 60s -> 30s
* after MrBAYES clean: 44s -> 17s

39 lines of code changed in 6 files:

westram 2013-08-22 12:11 Rev.: 10476


* reverted [10467] and [10466] (build failed for 'cent5')

6631 lines of code changed in 3 files:

westram 2013-08-21 13:55 Rev.: 10467


* ~~do not pack 'configure' into source tarball~~

(reverted by [10467])

1 lines of code changed in 1 file:

westram 2013-08-21 13:50 Rev.: 10466


* ~~'configure' is modified by compiling on a machine with different autoconf version~~
- ~~removed 'configure' from SVN; delete it on 'clean'~~
- ~~call autoconf before configure~~

(reverted by [10467])

3 lines of code changed in 2 files:

westram 2013-08-20 10:51 Rev.: 10458


- attempt to fix (randomly occurring) compile error
- creation of subdir 'obj' was triggered parallel to obj-compilation (now triggered '''before''')

5 lines of code changed in 1 file:

westram 2013-08-20 09:28 Rev.: 10457


- .awk is source

1 lines of code changed in 1 file:

aboeckma 2013-08-15 11:48 Rev.: 10456

Added rudimentary fasttree menu (need to know which options to use)

41 lines of code changed in 2 files:

aboeckma 2013-08-15 10:37 Rev.: 10455

Added !MrBayes custom command file menu

75 lines of code changed in 2 files:

aboeckma 2013-08-15 09:12 Rev.: 10454

Added !MrBayes help

99 lines of code changed in 2 files:

aboeckma 2013-08-14 14:35 Rev.: 10448

mafft changed default value for offset

7 lines of code changed in 1 file:

aboeckma 2013-08-14 14:28 Rev.: 10447

Added mrBayes gde menu

114 lines of code changed in 2 files:

aboeckma 2013-08-14 14:27 Rev.: 10446

mafft preserve case

1 lines of code changed in 1 file:

aboeckma 2013-08-14 14:09 Rev.: 10445

Allow numbers with positive exponent in newick tree

1 lines of code changed in 1 file:

epruesse 2013-08-14 13:43 Rev.: 10444

rename buttons in species information window
- DETACH -> "New window..."
(more easy to understand, detach was a mystery to many)
- GET -> "Update"
- do not shout (CLOSE -> Close, etc.)

38 lines of code changed in 3 files:

westram 2013-08-13 14:32 Rev.: 10441


* completely disabled TAB check for GDE and READSEQ

2 lines of code changed in 1 file:

westram 2013-08-13 14:23 Rev.: 10440


merge from tree [10434] [10436]

67 lines of code changed in 5 files:

westram 2013-08-13 14:17 Rev.: 10439


- no longer attempt to rm ./GDE/MAFFT/mafft-7.055-with-extensions/core

1 lines of code changed in 1 file:

aboeckma 2013-08-13 11:06 Rev.: 10435

Ignore tabs in !FastTree

1 lines of code changed in 1 file:

aboeckma 2013-08-13 10:35 Rev.: 10433

Added fasttree2 source (no menu, yet)

10116 lines of code changed in 2 files:

aboeckma 2013-08-13 10:01 Rev.: 10432

Added two missing switches to phyml

54 lines of code changed in 1 file:

aboeckma 2013-08-13 10:00 Rev.: 10431

Added nbproject to arb_srclist ignore

1 lines of code changed in 1 file:

westram 2013-08-12 13:38 Rev.: 10428


* added libreadline-dev (completes r10420)

1 lines of code changed in 1 file:

westram 2013-08-12 13:35 Rev.: 10427


- fix for concurrent builds ('install' depends on 'muscle')

2 lines of code changed in 1 file:

epruesse 2013-08-12 13:27 Rev.: 10426

always estimate gamma distribution parameter for phyml dna

1 lines of code changed in 1 file:

epruesse 2013-08-08 16:24 Rev.: 10423

fix bug introduced in r10422 ... there really is no way around a loop
to replicate the "readlink -f" behavior

25 lines of code changed in 1 file:

epruesse 2013-08-08 14:29 Rev.: 10422

slight cleanup of bin/arb startup script
- avoid readlink (not present on OSX)
- put quotes around arguments (file/directory names with spaces)
- use $SHELL instead of always sh

28 lines of code changed in 1 file:

aboeckma 2013-08-08 13:40 Rev.: 10421

Fixed bug in mafft makefile

5 lines of code changed in 2 files:

epruesse 2013-08-07 18:53 Rev.: 10420

- work around linking bug in centos5
- add libreadline-dev to ubuntu depends

9 lines of code changed in 2 files:

epruesse 2013-08-07 14:48 Rev.: 10418

fix !MrBayes makefile (libs need to be in LDLIBS when using implicit rules)

1 lines of code changed in 1 file:

epruesse 2013-08-07 14:44 Rev.: 10417

re-enable make buildins for !MrBayes (unset MAKEFLAGS)

1 lines of code changed in 1 file:

aboeckma 2013-08-07 13:47 Rev.: 10416

Added mr bayes (no menu yet)

114499 lines of code changed in 32 files:

epruesse 2013-08-07 12:52 Rev.: 10414

make probcons compile on ubuntu >12.04 (added another cstring include)

1 lines of code changed in 1 file:

aboeckma 2013-08-07 10:29 Rev.: 10413

Make arb_srclist happy

1 lines of code changed in 4 files:

aboeckma 2013-08-07 10:25 Rev.: 10412

Removed muscle version file. Cannot make it work with arb_srclist

2 lines of code changed in 2 files:

aboeckma 2013-08-07 10:03 Rev.: 10411

make probcons compile on linux (added cstring include )

3 lines of code changed in 3 files:

aboeckma 2013-08-07 09:51 Rev.: 10410

Ignore probcons in tab break check

1 lines of code changed in 1 file:

aboeckma 2013-08-06 11:58 Rev.: 10409

Updated raxml to current version

63104 lines of code changed in 46 files:

aboeckma 2013-08-06 10:41 Rev.: 10408

Moved PROBCONS to NO_DEPENDS section.

1 lines of code changed in 1 file:

aboeckma 2013-08-02 10:45 Rev.: 10407

integrated probcons

47 lines of code changed in 1 file:

aboeckma 2013-08-02 10:15 Rev.: 10406

svn ignore probcons files

1 lines of code changed in 1 file:

aboeckma 2013-08-02 10:13 Rev.: 10405

added probcons

6336 lines of code changed in 18 files:

aboeckma 2013-08-02 09:40 Rev.: 10403

minimalistic help file for mafft

82 lines of code changed in 2 files:

aboeckma 2013-08-02 09:09 Rev.: 10402

working muscle integration(now someone needs to tell me what parameters are usefull)

70 lines of code changed in 2 files:

epruesse 2013-08-01 16:41 Rev.: 10400

don't check MUSCLE or MAFFT for tabs

2 lines of code changed in 1 file:

aboeckma 2013-08-01 14:35 Rev.: 10394

(hope)fully working mafft integration

3 lines of code changed in 1 file:

aboeckma 2013-08-01 14:18 Rev.: 10393

build muscle as part of gde

1 lines of code changed in 1 file:

aboeckma 2013-08-01 14:03 Rev.: 10392

remove binary

0 lines of code changed in 1 file:

aboeckma 2013-08-01 14:02 Rev.: 10390

added muscle sourcles amd makefile

35297 lines of code changed in 198 files:

westram 2013-08-01 13:42 Rev.: 10388


* GDE menus
- added new keyword 'intyped'
* default value ('basic') preserves previous behavior
* value 'detailed' saves "typed sequences"
* restriction: all inputdata-files (of one item) need to use the same 'intyped'-value

101 lines of code changed in 6 files:

westram 2013-08-01 13:36 Rev.: 10387


* dup overwritten buffer

3 lines of code changed in 1 file:

westram 2013-08-01 11:47 Rev.: 10385


* GDE menus
- fail if an unknown command is found
- restrict use of 'item:' and 'menumeta:'
- print parse error messages in parseable format

19 lines of code changed in 1 file:

westram 2013-08-01 11:31 Rev.: 10384


* more detailed errors while loading GDE menus

23 lines of code changed in 2 files:

westram 2013-08-01 11:27 Rev.: 10383


- cosmetics

20 lines of code changed in 1 file:

westram 2013-08-01 11:23 Rev.: 10382


- fixed some locals

24 lines of code changed in 1 file:

westram 2013-08-01 11:14 Rev.: 10381


* mafft
- fix savetest
- ignore all mafft-stuff in bin

1 lines of code changed in 1 file:

westram 2013-08-01 11:05 Rev.: 10380


* GDE menus
- added simple unit-test loading menu file

20 lines of code changed in 3 files:

aboeckma 2013-08-01 10:31 Rev.: 10379

MAFFT menu (without sequence type)

64 lines of code changed in 1 file:

aboeckma 2013-08-01 10:31 Rev.: 10378

Generate mafft links

9 lines of code changed in 1 file:

July 2013 »

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