January 2008 Commit Log

Number of Commits:

32

Number of Active Developers:

3

westram 2008-01-29 17:33 #32 Rev.: 5043

- warn about missing tree (not if tree is '????')

9 lines of code changed in 1 file:

• TOOLS: arb_export_tree.cxx (+9 -1)

westram 2008-01-29 17:33 #31 Rev.: 5042

- automatically convert MAC/DOS linefeeds

2 lines of code changed in 1 file:

• PERL_SCRIPTS/SPECIES: markSpecies.pl (+2)

westram 2008-01-29 17:06 #30 Rev.: 5041

- fixed indentation..

27 lines of code changed in 1 file:

• TOOLS: arb_export_tree.cxx (+27 -27)

westram 2008-01-24 18:11 #29 Rev.: 5040

- template to accept GDE/*/Makefile.xxx
- ignore .swp

2 lines of code changed in 1 file:

• util: arb_srclst.pl (+2)

westram 2008-01-24 18:03 #28 Rev.: 5039

- can also mark by acc etc.
- option to ignore leading/trailing spaces

57 lines of code changed in 1 file:

• PERL_SCRIPTS/SPECIES: markSpecies.pl (+57 -7)

westram 2008-01-24 10:39 #27 Rev.: 5038

- skip sequence selection for 'start arb'

1 lines of code changed in 1 file:

• GDEHELP/MENUS: start_arb.menu (+1)

westram 2008-01-24 10:39 #26 Rev.: 5037

- skip sequence selection for import

1 lines of code changed in 1 file:

• GDEHELP/MENUS: import.menu (+1)

westram 2008-01-24 10:39 #25 Rev.: 5036

- added tree-export + mention tree in comment of new tree
- export RAxML-style weights into extra file
- removed trailing spaces
- restrict to Protein alignments

18 lines of code changed in 1 file:

• GDEHELP/MENUS: raxmlprotein.menu (+18 -11)

westram 2008-01-24 10:39 #24 Rev.: 5035

- added tree-export + mention tree in comment of new tree
- export RAxML-style weights into extra file
- removed trailing spaces
- restrict to Nucleotide alignments

19 lines of code changed in 1 file:

• GDEHELP/MENUS: raxmldna.menu (+19 -11)

westram 2008-01-24 10:39 #23 Rev.: 5034

- added flag '-r' to export RAxML-style weights

163 lines of code changed in 1 file:

• TOOLS: arb_export_rates.cxx (+163 -65)

westram 2008-01-24 10:38 #22 Rev.: 5033

- added AWAR_GDE_FILTER

4 lines of code changed in 1 file:

• WINDOW: aw_awars.hxx (+4 -2)

westram 2008-01-24 10:38 #21 Rev.: 5032

- use defined AWAR

1 lines of code changed in 1 file:

• AWT: AWT_filter.cxx (+1 -1)

westram 2008-01-24 10:38 #20 Rev.: 5031

- updated

2 lines of code changed in 1 file:

• ARB_GDE: Makefile (+2)

westram 2008-01-24 10:38 #19 Rev.: 5030

- use defined AWARs

5 lines of code changed in 1 file:

• ARB_GDE: GDE_event.cxx (+5 -4)

westram 2008-01-24 10:38 #18 Rev.: 5029

- moved AWAR_GDE_FILTER to aw_awars.hxx

0 lines of code changed in 1 file:

• ARB_GDE: GDE_def.h (-1)

westram 2008-01-24 10:38 #17 Rev.: 5028

- mention seqtype '-'

7 lines of code changed in 2 files:

• ARB_GDE: GDE_ParseMenu.cxx (+6 -1), GDE_menu.h (+1 -1)

westram 2008-01-24 10:37 #16 Rev.: 5027

- defined AWARs for GDE interface

29 lines of code changed in 1 file:

• ARB_GDE: GDE_awars.h (new 29)

westram 2008-01-24 10:37 #15 Rev.: 5026

- when seqtype is "-"
. skips sequence-related parts
. loads different menu
. skip compression and filter elements
- use defined AWARs

50 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+50 -38)

meierh 2008-01-22 18:23 #14 Rev.: 5025

add and remove raxml menue files

48 lines of code changed in 3 files:

• GDEHELP/MENUS: raxml.menu (del), raxmldna.menu (new 23), raxmlprotein.menu (new 25)

meierh 2008-01-22 18:20 #13 Rev.: 5024

raxmldna raxmlprotein menues introduced

2 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+2 -1)

westram 2008-01-22 12:42 #12 Rev.: 5023

- fixed identifiers starting with '_' (these are reserved)

2 lines of code changed in 1 file:

• WINDOW: AW_status.cxx (+2 -2)

westram 2008-01-22 12:42 #11 Rev.: 5022

- include stdint.h (need uint32_t)

4 lines of code changed in 2 files:

• PROBE: PT_buildtree.cxx (+2), PT_io.cxx (+2)

meierh 2008-01-22 12:14 #10 Rev.: 5021

raxml7.0.0 introduce, RAxML5 removed

37908 lines of code changed in 39 files:

• GDE/RAxML: Makefile (+12 -26), Makefile.MPI (new 48), Makefile.PTHREADS (new 50), Makefile.gcc (new 48), RAxML-Manual.7.0.0.pdf (new 2203), README (del), Recommended_use.txt (del), axml.c (+5000 -11553), axml.h (+703 -243), bipartitionList.c (new 1326), categorizeGeneric.c (new 1285), cons.c (del), cons.h (del), consense.c (del), dnapars.c (del), evaluateGeneric.c (new 2382), evaluateGenericVector.c (new 1225), evaluatePartialGeneric.c (new 815), getopt.c (del), getopt.h (del), globalVariables.h (new 107), gpl.txt (del), makenewzGeneric.c (new 3119), models.c (new 1789), multiple.c (new 2310), newviewGeneric.c (new 5552), optimizeModel.c (new 2786), parsePartitions.c (new 922), phylip.c (del), phylip.h (del), phylip2.h (del), rapidBootstrap.c (new 437), raxmlParsimony.c (new 1814), rev_functions.c (+36 -7), searchAlgo.c (new 1630), softwaredisclaimer (del), topologies.c (new 761), treeIO.c (new 1548), unused_sources.tgz (del)

meierh 2008-01-18 18:50 #9 Rev.: 5020

outputs now RAxML_result.treefile instead of RAxML_parsimonyTree.treefile

16 lines of code changed in 1 file:

• GDEHELP/MENUS: raxml.menu (+16 -20)

baderk 2008-01-09 15:09 #8 Rev.: 5019

Fixed indention and changed the xml-structure of sequence quality entries
into a tree structure. (Still some work to do here...)
See ticket #13 for more information.

304 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+304 -384)

baderk 2008-01-08 15:56 #7 Rev.: 5018

Fixed possible error in sequence quality tool (missing filter entries may
be misinterpreted as sequence positions).

8 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_helix.h (+8 -8)

baderk 2008-01-08 11:32 #6 Rev.: 5017

Fixed intention only - no change in the content.

204 lines of code changed in 9 files:

• SEQ_QUALITY: SQ_GroupData.cxx (+15 -26), SQ_GroupData.h (+67 -80), SQ_ambiguities.h (+11 -21), SQ_functions.cxx (+1 -1), SQ_functions.h (+24 -33), SQ_helix.h (+34 -44), SQ_main.cxx (+37 -56), SQ_physical_layout.h (+14 -29), seq_quality.h (+1 -3)

baderk 2008-01-03 11:45 #5 Rev.: 5016

64bit conversion fix (int -> long).

1 lines of code changed in 1 file:

• ALIV3: a3_matrix.cxx (+1 -1)

baderk 2008-01-03 10:58 #4 Rev.: 5015

Code cleanup (readability).
Removed a growing memory leak which appears at each pt_server access.

11 lines of code changed in 1 file:

• PROBE: PT_match.cxx (+11 -9)

baderk 2008-01-03 10:56 #3 Rev.: 5014

Code cleanup and speedup (char -> uint32_t).

42 lines of code changed in 2 files:

• PROBE: PT_buildtree.cxx (+28 -10), PT_io.cxx (+14 -18)

baderk 2008-01-03 10:54 #2 Rev.: 5013

Cleanup (removed 'register' from typedefs).

9 lines of code changed in 1 file:

• ARBDB: adstring.c (+9 -9)

baderk 2008-01-03 10:53 #1 Rev.: 5012

Code cleanup and speedup (memcpy/memset instead of native code).

13 lines of code changed in 1 file:

• ARBDB: adseqcompr.c (+13 -46)

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