StatSVN - Directory [root]

[root]

AISC (16 files, 3892 lines)

AISC_COM (1 files, 16 lines)

AISC (8 files, 2074 lines)

C (15 files, 2740 lines)

AISC_MKPTPS (4 files, 1872 lines)

ALEIO (0 files, 0 lines)

ALIV3 (0 files, 0 lines)

ARBDB (85 files, 44758 lines)

EXAMPLES (0 files, 0 lines)

ARBDB2 (0 files, 0 lines)

ARBDBPP (0 files, 0 lines)

ARBDBS (0 files, 0 lines)

ARBDB_COMPRESS (0 files, 0 lines)

ARB_GDE (16 files, 4031 lines)

AWDEMO (0 files, 0 lines)

AWT (32 files, 12319 lines)

AWTC (6 files, 1048 lines)

AWTI (10 files, 2871 lines)

BERGEY (0 files, 0 lines)

BINDEP (36 files, 167 lines)

BINDINGS (2 files, 267 lines)

PERL (4 files, 1028 lines)

PYTHON (4 files, 147 lines)

BUGEX (1 files, 188 lines)

CAT (0 files, 0 lines)

CHIP (0 files, 0 lines)

CONSENSUS_TREE (13 files, 2235 lines)

CONVERTALN (36 files, 6584 lines)

CORE (46 files, 8555 lines)

DBSERVER (3 files, 561 lines)

DIST (20 files, 7371 lines)

DUMMYINC (0 files, 0 lines)

EDIT (0 files, 0 lines)

EDIT4 (52 files, 28713 lines)

EISPACK (7 files, 29479 lines)

GDE (2 files, 145 lines)

AxML (5 files, 5977 lines)

CLUSTAL (13 files, 4954 lines)

CLUSTALW (33 files, 21348 lines)

CORE (0 files, 0 lines)

FASTDNAML (7 files, 6447 lines)

FASTTREE (3 files, 10124 lines)

HGL_SRC (0 files, 0 lines)

LOOPTOOL (0 files, 0 lines)

MAFFT (1 files, 55 lines)

mafft-7.053-without-extensions (0 files, 0 lines)

core (0 files, 0 lines)

scripts (0 files, 0 lines)

mafft-7.055-with-extensions (4 files, 309 lines)

core (90 files, 75630 lines)

extensions (3 files, 72 lines)

mxscarna_src (21 files, 6911 lines)

probconsRNA (20 files, 7594 lines)

vienna (6 files, 11842 lines)

MOLPHY (0 files, 0 lines)

doc (0 files, 0 lines)

utl (0 files, 0 lines)

MUSCLE (1 files, 38 lines)

src (190 files, 34747 lines)

unused (3 files, 548 lines)

MrBAYES (1 files, 45 lines)

mrbayes_3.2.1 (31 files, 114639 lines)

PHYLIP (66 files, 71352 lines)

doc (42 files, 21478 lines)

PHYML (22 files, 15180 lines)

PHYML20130708 (2 files, 64 lines)

phyml (18 files, 22760 lines)

bin (0 files, 0 lines)

doc (17 files, 24532 lines)

examples (5 files, 1255 lines)

lg4x (5 files, 142 lines)

src (68 files, 78797 lines)

PROBCONS (1 files, 23 lines)

probcons (17 files, 6323 lines)

RAxML (31 files, 72525 lines)

RAxML8 (5 files, 698 lines)

SATIVA (5 files, 493 lines)

sativa (3 files, 1494 lines)

epac (8 files, 2380 lines)

ete2 (1 files, 185 lines)

SUPPORT (10 files, 2584 lines)

TREEPUZZLE (6 files, 854 lines)

data (0 files, 0 lines)

doc (3 files, 1653 lines)

src (18 files, 17676 lines)

GDEHELP (10 files, 774 lines)

DATA_FILES (0 files, 0 lines)

FASTA (0 files, 0 lines)

GENBANK (1 files, 1500 lines)

MATRIX (9 files, 258 lines)

HELP_PLAIN (3 files, 135 lines)

HELP_WRITTEN (8 files, 750 lines)

MENUS (19 files, 2018 lines)

PHYLIP (0 files, 0 lines)

GENOM (17 files, 5520 lines)

GENOM_IMPORT (18 files, 2818 lines)

GFX (2 files, 1079 lines)

GL (1 files, 61 lines)

glAW (10 files, 1498 lines)

glpng (4 files, 715 lines)

HEADERLIBS (7 files, 205 lines)

HELP_SOURCE (16 files, 3795 lines)

genhelp (6 files, 200 lines)

oldhelp (343 files, 25879 lines)

prompt (1 files, 31 lines)

seer (0 files, 0 lines)

ISLAND_HOPPING (12 files, 2104 lines)

JAVALIB (0 files, 0 lines)

MERGE (16 files, 5517 lines)

MULTI_PROBE (21 files, 6003 lines)

NALIGNER (26 files, 7913 lines)

NAMES (4 files, 1535 lines)

NAMES_COM (8 files, 297 lines)

NIELS_F77 (0 files, 0 lines)

NTREE (43 files, 18070 lines)

ORS_CGI (0 files, 0 lines)

ORS_COM (0 files, 0 lines)

ORS_SERVER (0 files, 0 lines)

PARSIMONY (19 files, 8885 lines)

PERL2ARB (10 files, 1224 lines)

PERLTOOLS (3 files, 1092 lines)

PERL_SCRIPTS (0 files, 0 lines)

ACI (1 files, 30 lines)

ARBTOOLS (2 files, 625 lines)

DOCUMENTED (0 files, 0 lines)

IFTHELP (4 files, 254 lines)

TESTS (1 files, 3 lines)

BIOPERL (2 files, 119 lines)

GENERAL (1 files, 99 lines)

GENOME (3 files, 452 lines)

IFTHELP (0 files, 0 lines)

MACROS (1 files, 158 lines)

MAUS (0 files, 0 lines)

SAI (2 files, 159 lines)

SPECIES (3 files, 329 lines)

lib (1 files, 80 lines)

test (5 files, 212 lines)

PGT (0 files, 0 lines)

xslt (0 files, 0 lines)

PHYLO (11 files, 2150 lines)

PRIMER_DESIGN (20 files, 3030 lines)

PROBE (25 files, 10726 lines)

PROBE_COM (8 files, 446 lines)

PROBE_DESIGN (11 files, 6533 lines)

PROBE_SERVER (0 files, 0 lines)

PROBE_GROUP (0 files, 0 lines)

PROBE_GROUP_DESIGN (0 files, 0 lines)

TREE_MERGE (0 files, 0 lines)

WORKER (0 files, 0 lines)

PROBE_SET (32 files, 6863 lines)

PROBE_WEB (0 files, 0 lines)

CLIENT (0 files, 0 lines)

SERVER (0 files, 0 lines)

READSEQ (9 files, 5275 lines)

RNA3D (20 files, 4636 lines)

Attic (0 files, 0 lines)

OPENGL (0 files, 0 lines)

data (0 files, 0 lines)

images (0 files, 0 lines)

RNACMA (10 files, 1466 lines)

SECEDIT (28 files, 8537 lines)

SEER (0 files, 0 lines)

SEQ_QUALITY (12 files, 2457 lines)

SERVERCNTRL (4 files, 559 lines)

SH (33 files, 2357 lines)

SL (2 files, 95 lines)

ALILINK (6 files, 2328 lines)

ALIVIEW (4 files, 177 lines)

AP_TREE (8 files, 2369 lines)

ARB_TREE (4 files, 559 lines)

AW_HELIX (4 files, 361 lines)

AW_NAME (5 files, 1058 lines)

CB (7 files, 1126 lines)

CONSENSUS (3 files, 1730 lines)

DB_QUERY (5 files, 2997 lines)

DB_SCANNER (4 files, 736 lines)

DB_UI (5 files, 2067 lines)

FAST_ALIGNER (8 files, 5873 lines)

FILE_BUFFER (0 files, 0 lines)

FILTER (6 files, 901 lines)

FILTSEQEXP (3 files, 649 lines)

GROUP_SEARCH (3 files, 4170 lines)

GUI_ALIVIEW (9 files, 1342 lines)

HELIX (6 files, 807 lines)

INSDEL (2 files, 2362 lines)

ITEMS (9 files, 1572 lines)

ITEM_SHADER (5 files, 2380 lines)

LOCATION (4 files, 611 lines)

MACROS (10 files, 1867 lines)

MATRIX (4 files, 336 lines)

NDS (3 files, 1083 lines)

NEIGHBOURJOIN (5 files, 557 lines)

PRONUC (8 files, 2771 lines)

PTCLEAN (4 files, 264 lines)

PVP (2 files, 484 lines)

QUERY (3 files, 666 lines)

REFENTRIES (4 files, 527 lines)

REGEXPR (4 files, 370 lines)

ROOTED_TREE (0 files, 0 lines)

SEQIO (5 files, 1125 lines)

SEQUENCE (10 files, 1757 lines)

TRANSLATE (4 files, 346 lines)

TREEDISP (10 files, 7351 lines)

TREE_ADMIN (4 files, 345 lines)

TREE_READ (5 files, 1235 lines)

TREE_WRITE (4 files, 576 lines)

SOURCE_TOOLS (62 files, 10036 lines)

COMPILE_COMPAT (4 files, 129 lines)

docs (1 files, 79 lines)

release (2 files, 384 lines)

STAT (9 files, 2160 lines)

TEMPLATES (43 files, 7957 lines)

TEST (0 files, 0 lines)

TESTAWT (0 files, 0 lines)

TESTVECTORFONT (0 files, 0 lines)

TOOLS (27 files, 11964 lines)

TREEGEN (17 files, 1459 lines)

TREE_COMPRESS (0 files, 0 lines)

TRS (0 files, 0 lines)

UNIT_TESTER (22 files, 5722 lines)

flags (1 files, 2 lines)

run (34 files, 13969 lines)

consense (0 files, 0 lines)

1 (7 files, 475 lines)

2 (5 files, 894 lines)

3 (4 files, 1543 lines)

4 (3 files, 146 lines)

6 (1 files, 49 lines)

diff (4 files, 72 lines)

display (25 files, 17274 lines)

distance (3 files, 69 lines)

fakehome (0 files, 0 lines)

general (6 files, 90 lines)

help (3 files, 933 lines)

homefake (0 files, 0 lines)

.arb_prop (1 files, 1 lines)

impexp (38 files, 4437 lines)

pars (22 files, 828 lines)

tools (22 files, 475 lines)

trees (1 files, 27 lines)

xsub (4 files, 511 lines)

sockets (0 files, 0 lines)

valgrind (2 files, 179 lines)

WETC (3 files, 114 lines)

WINDOW (75 files, 26013 lines)

XML (4 files, 500 lines)

XML_IMPORT (2 files, 46 lines)

IMP_TREE (9 files, 592 lines)

bin (2 files, 211 lines)

doc (1 files, 85 lines)

etc (6 files, 5366 lines)

fig2dev (0 files, 0 lines)

dev (0 files, 0 lines)

lib (8 files, 12081 lines)

BUGS (2 files, 69 lines)

addlibs (1 files, 14 lines)

arb_default (7 files, 694 lines)

desktop (4 files, 21 lines)

dtd (2 files, 92 lines)

export (14 files, 130 lines)

gde (2 files, 25 lines)

icons (0 files, 0 lines)

import (9 files, 680 lines)

nonformats (7 files, 783 lines)

inputMasks (9 files, 343 lines)

macros (4 files, 126 lines)

.checks (3 files, 675 lines)

ARB (0 files, 0 lines)

SEQ_DATA (1 files, 111 lines)

motifHack (3 files, 322 lines)

pixmaps (0 files, 0 lines)

nas (3 files, 17 lines)

pictures (94 files, 5171 lines)

PARS (0 files, 0 lines)

awt (19 files, 589 lines)

awtc (2 files, 37 lines)

consensus (2 files, 880 lines)

cpro (2 files, 76 lines)

demo (0 files, 0 lines)

edit4 (16 files, 1377 lines)

etc (0 files, 0 lines)

faligner (3 files, 149 lines)

findcorr (0 files, 0 lines)

merge (12 files, 488 lines)

pars (3 files, 177 lines)

phylo (3 files, 60 lines)

query (5 files, 133 lines)

seer (0 files, 0 lines)

unused (0 files, 0 lines)

demo (0 files, 0 lines)

findcorr (0 files, 0 lines)

window (1 files, 30 lines)

pixmaps (84 files, 3509 lines)

edit (20 files, 602 lines)

unused (0 files, 0 lines)

icons (7 files, 273 lines)

unused (0 files, 0 lines)

merge (1 files, 48 lines)

pgt (0 files, 0 lines)

print (6 files, 239 lines)

unused (0 files, 0 lines)

seer (0 files, 0 lines)

unused (0 files, 0 lines)

protein_2nd_structure (0 files, 0 lines)

rna3d (5 files, 4617 lines)

images (22 files, 0 lines)

sellists (9 files, 98 lines)

submit (3 files, 1061 lines)

ptpan (4 files, 57 lines)

util (18 files, 1534 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	1080 (100.0%)	15261 (100.0%)	14.1
westram	973 (90.1%)	13967 (91.5%)	14.3
oldcode	9 (0.8%)	760 (5.0%)	84.4
epruesse	33 (3.1%)	281 (1.8%)	8.5
boehnel	4 (0.4%)	75 (0.5%)	18.7
yadhu	17 (1.6%)	74 (0.5%)	4.3
meierh	12 (1.1%)	24 (0.2%)	2.0
richter	4 (0.4%)	19 (0.1%)	4.7
baderk	17 (1.6%)	18 (0.1%)	1.0
spanfeln	1 (0.1%)	11 (0.1%)	11.0
foerster	2 (0.2%)	11 (0.1%)	5.5
arb_build	1 (0.1%)	8 (0.1%)	8.0
aboeckma	2 (0.2%)	5 (0.0%)	2.5
jobb	1 (0.1%)	4 (0.0%)	4.0
artemov	2 (0.2%)	2 (0.0%)	1.0
littschw	1 (0.1%)	1 (0.0%)	1.0
lai	1 (0.1%)	1 (0.0%)	1.0

Most Recent Commits

westram 2019-03-18 18:07 Rev.: 17666

ignore leftover emacs autosave files.

1 lines of code changed in 1 file:

.gitignore (+1)

westram 2019-03-18 18:06 Rev.: 17665

allow to build single unit and run its tests.

use
{{{
cd $ARBHOME;setenv UNIT PROBE/PROBE; makeloc oneunit
}}}
for tcsh or
{{{
cd $ARBHOME; export UNIT=PROBE/PROBE; makeloc oneunit
}}}
for bash.

22 lines of code changed in 1 file:

Makefile (+22 -5)

westram 2019-03-13 10:14 Rev.: 17656

* change names of ignored patch-files

3 lines of code changed in 1 file:

.gitignore (+3 -6)

westram 2019-03-07 17:30 Rev.: 17651

* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@17627:17650

1 lines of code changed in 1 file:

.gitignore (+1)

westram 2019-03-06 12:10 Rev.: 17645

update doxygen docs:

- updated obsolete setting using "doxygen -u".
- use Helvetica font for dot-gfx generated by doxygen.
- activates conf-mode in emacs.

1701 lines of code changed in 1 file:

Doxyfile (+1701 -776)

westram 2019-03-04 19:39 Rev.: 17641

* reintegrates 'mix' into 'trunk'
- improve git/svn interoperability
* adds: log:branches/mix@17637:17640

3 lines of code changed in 1 file:

.gitignore (+3)

westram 2019-03-04 14:22 Rev.: 17634

* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

35 lines of code changed in 1 file:

.gitignore (new 35)

westram 2019-02-26 09:12 Rev.: 17626

- accept gcc 8.3

1 lines of code changed in 1 file:

Makefile (+1 -1)

epruesse 2019-02-17 06:06 Rev.: 17625

Honor $AR env variable if set (make defaults to 'ar')

1 lines of code changed in 1 file:

Makefile (+1 -1)

epruesse 2019-02-17 06:05 Rev.: 17624

Add xerces-c-dev to ubuntu build deps

1 lines of code changed in 1 file:

arb_UBUNTU.txt (+1)

westram 2018-12-23 11:48 Rev.: 17620

* added gcc 7.4

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-11-25 19:19 Rev.: 17618

* full update from child 'fix' into 'trunk'
- fixes undefined variables in makefiles
- fixes perl tests
* adds: log:branches/fix@17599:17617

82 lines of code changed in 1 file:

Makefile (+82 -43)

westram 2018-11-08 17:56 Rev.: 17602

* updated README

41 lines of code changed in 1 file:

arb_README.txt (+41 -37)

westram 2018-10-31 09:52 Rev.: 17593

* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

4 lines of code changed in 2 files:

Makefile (+1 -1), arb_CHANGES.txt (+3 -1)

westram 2018-10-26 18:19 Rev.: 17542

* allow compilation with gcc 6.5.0

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-10-17 13:21 Rev.: 17481

- updated

2 lines of code changed in 1 file:

arb_CHANGES.txt (+2 -1)

westram 2018-10-02 09:08 Rev.: 17424

* fix compilation w/o config.makefile (=auto-generation from template)
- was broken by [17375]

8 lines of code changed in 1 file:

Makefile (+8 -6)

westram 2018-09-18 09:53 Rev.: 17375

* make sure that either {{{DARWIN=1}}} or {{{LINUX=1}}} in config.makefile

6 lines of code changed in 1 file:

Makefile (+6)

westram 2018-09-13 09:24 Rev.: 17367

* allow parallel calls to 'make tags'
- uses build-unique temporary files to avoid conflicts

11 lines of code changed in 1 file:

Makefile (+11 -10)

westram 2018-09-13 09:19 Rev.: 17366

* provide a build specific ID (ARBBID)
- different in each call to make
- constant in recursive calls (and submakefiles)

9 lines of code changed in 1 file:

Makefile (+9)

westram 2018-09-13 08:43 Rev.: 17365

* svn-ignore temporary files used by target 'tags' (solves problems with some of my scripts)

2 lines of code changed in 1 file:

Makefile (+2 -2)

westram 2018-09-02 17:44 Rev.: 17345

* updated

3 lines of code changed in 1 file:

arb_CHANGES.txt (+3)

westram 2018-08-30 16:24 Rev.: 17342

* reintegrates 'group' into 'trunk'
- implements #780
* adds: log:branches/group@17162:17190,17261:17341

27 lines of code changed in 1 file:

Makefile (+27 -19)

westram 2018-07-27 07:44 Rev.: 17277

* activate {{{-Wmultistatement-macros}}} for gcc 8++

16 lines of code changed in 1 file:

Makefile (+16 -13)

westram 2018-07-26 14:57 Rev.: 17272

* tested and accepted gcc 8.2

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-06-25 09:57 Rev.: 17114

* only refer to {{{/etc/bash.bashrc}}} (for global alias)
* add howto-edit-global-bashrc for unintended sysadmins :)

7 lines of code changed in 1 file:

arb_install.sh (+7 -3)

westram 2018-06-15 12:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

2 lines of code changed in 1 file:

arb_CHANGES.txt (+2 -1)

westram 2018-05-04 17:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-04-30 17:27 Rev.: 16936

* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

0 lines of code changed in 1 file:

Makefile (-2)

westram 2018-04-20 12:04 Rev.: 16904

* reintegrates 'pvp' into 'trunk'
- fixes #782
- implements #701
* adds: log:branches/pvp@16882:16903

9 lines of code changed in 2 files:

Makefile (+3), arb_CHANGES.txt (+6 -3)

westram 2018-04-11 15:48 Rev.: 16880

* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879

9 lines of code changed in 1 file:

Makefile (+9)

westram 2018-04-05 11:09 Rev.: 16873

* fix typos ("neither")

1 lines of code changed in 1 file:

arb_install.sh (+1 -1)

westram 2018-01-25 18:46 Rev.: 16827

* add gcc 7.3.0 (compiled out-of-the-box)

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2017-11-28 17:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2017-11-19 15:19 Rev.: 16683

* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

37 lines of code changed in 1 file:

Makefile (+37 -18)

westram 2017-11-17 12:54 Rev.: 16668

* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

0 lines of code changed in 1 file:

Makefile (-4)

westram 2017-11-14 14:36 Rev.: 16653

* reintegrates 'gcc' into 'trunk' (fixes defect part of #752)
- allow compilation with gcc 7.x series (accepting 2 clang-test-results for gcc 7.x)
- vectorization:
* in {{{SL/CONSENSUS/chartable.cxx}}} works again with gcc 7.x (broken for 6.x series)
- checker: added syntax to exclude a range of versions
* check new 7.x vectorizations + fix vectorization-counts
* adds: log:branches/gcc@16578:16635,16649:16652

4 lines of code changed in 1 file:

Makefile (+4 -3)

westram 2017-11-12 14:53 Rev.: 16649

* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

3 lines of code changed in 1 file:

arbsrc_README_gcc.txt (+3 -10)

westram 2017-11-06 13:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

11 lines of code changed in 1 file:

Makefile (+11 -23)

westram 2017-10-29 17:41 Rev.: 16582

* refuse to compile with gcc 4.6.4
- fails to compile inplace ctors (working with {{{gcc 4.4.3, 4.6.x && x!=4, 4.7++}}})
- compiler detection fails (gcc segfaults when attempting to dump predefined variables). suppress error @ caller.
* link to GccVersionInfo

10 lines of code changed in 1 file:

Makefile (+10 -3)

(917 more)

Directory [root]

Lines of Code

Developers

Most Recent Commits