StatSVN - Directory [root]

[root]

AISC (16 files, 3904 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, 45387 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, 12224 lines)

AWTC (6 files, 1048 lines)

AWTI (10 files, 3131 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, 6595 lines)

CORE (50 files, 9204 lines)

DBSERVER (3 files, 561 lines)

DIST (20 files, 7372 lines)

DUMMYINC (0 files, 0 lines)

EDIT (0 files, 0 lines)

EDIT4 (52 files, 28782 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, 22761 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, 702 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, 5524 lines)

GENOM_IMPORT (18 files, 2798 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 (344 files, 26091 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, 5832 lines)

MULTI_PROBE (21 files, 6008 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, 18182 lines)

ORS_CGI (0 files, 0 lines)

ORS_COM (0 files, 0 lines)

ORS_SERVER (0 files, 0 lines)

PARSIMONY (19 files, 8889 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, 2152 lines)

PRIMER_DESIGN (20 files, 3032 lines)

PROBE (25 files, 10725 lines)

PROBE_COM (8 files, 446 lines)

PROBE_DESIGN (11 files, 6535 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, 6865 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, 4638 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, 8545 lines)

SEER (0 files, 0 lines)

SEQ_QUALITY (12 files, 2459 lines)

SERVERCNTRL (4 files, 559 lines)

SH (33 files, 2363 lines)

SL (2 files, 95 lines)

ALILINK (7 files, 2363 lines)

ALIVIEW (4 files, 177 lines)

AP_TREE (8 files, 2375 lines)

ARB_TREE (4 files, 569 lines)

AW_HELIX (4 files, 363 lines)

AW_NAME (5 files, 1058 lines)

CB (7 files, 1126 lines)

CONSENSUS (3 files, 1730 lines)

DB_QUERY (5 files, 3010 lines)

DB_SCANNER (4 files, 791 lines)

DB_UI (5 files, 2061 lines)

FAST_ALIGNER (8 files, 5877 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, 1356 lines)

HELIX (6 files, 807 lines)

INSDEL (2 files, 2366 lines)

ITEMS (9 files, 1599 lines)

ITEM_SHADER (5 files, 2392 lines)

LOCATION (4 files, 611 lines)

MACROS (10 files, 1867 lines)

MATRIX (4 files, 336 lines)

NDS (3 files, 1085 lines)

NEIGHBOURJOIN (5 files, 557 lines)

PRONUC (8 files, 2771 lines)

PTCLEAN (4 files, 256 lines)

PVP (2 files, 484 lines)

QUERY (3 files, 666 lines)

REFENTRIES (4 files, 526 lines)

REGEXPR (4 files, 370 lines)

ROOTED_TREE (0 files, 0 lines)

SEQIO (5 files, 1218 lines)

SEQUENCE (10 files, 1757 lines)

TRANSLATE (4 files, 346 lines)

TREEDISP (10 files, 7359 lines)

TREE_ADMIN (4 files, 345 lines)

TREE_READ (5 files, 1235 lines)

TREE_WRITE (4 files, 576 lines)

XFERGUI (2 files, 1293 lines)

XFERSET (3 files, 2156 lines)

SOURCE_TOOLS (63 files, 10416 lines)

COMPILE_COMPAT (4 files, 129 lines)

docs (1 files, 79 lines)

release (2 files, 384 lines)

STAT (9 files, 2162 lines)

TEMPLATES (44 files, 8108 lines)

TEST (0 files, 0 lines)

TESTAWT (0 files, 0 lines)

TESTVECTORFONT (0 files, 0 lines)

TOOLS (27 files, 11973 lines)

TREEGEN (17 files, 1459 lines)

TREE_COMPRESS (0 files, 0 lines)

TRS (0 files, 0 lines)

UNIT_TESTER (22 files, 5807 lines)

flags (1 files, 2 lines)

run (39 files, 17711 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 (39 files, 4469 lines)

pars (22 files, 828 lines)

pvp (4 files, 63 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, 26102 lines)

XML (4 files, 500 lines)

XML_IMPORT (2 files, 46 lines)

IMP_TREE (9 files, 592 lines)

bin (2 files, 215 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, 18 lines)

pictures (96 files, 3558 lines)

PARS (0 files, 0 lines)

awt (19 files, 599 lines)

awtc (2 files, 46 lines)

consensus (2 files, 368 lines)

cpro (2 files, 72 lines)

demo (0 files, 0 lines)

edit4 (16 files, 819 lines)

etc (0 files, 0 lines)

faligner (3 files, 139 lines)

findcorr (0 files, 0 lines)

merge (12 files, 473 lines)

pars (3 files, 184 lines)

phylo (3 files, 67 lines)

query (5 files, 131 lines)

seer (0 files, 0 lines)

unused (0 files, 0 lines)

demo (0 files, 0 lines)

findcorr (0 files, 0 lines)

window (1 files, 24 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, 1537 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	1104 (100.0%)	15474 (100.0%)	14.0
westram	997 (90.3%)	14180 (91.6%)	14.2
oldcode	9 (0.8%)	760 (4.9%)	84.4
epruesse	33 (3.0%)	281 (1.8%)	8.5
boehnel	4 (0.4%)	75 (0.5%)	18.7
yadhu	17 (1.5%)	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 (1.5%)	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 2019-10-10 18:16 Rev.: 18168

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18159:18167

4 lines of code changed in 1 file:

Makefile (+4 -1)

westram 2019-10-07 14:01 Rev.: 18148

* update

1 lines of code changed in 1 file:

arb_CHANGES.txt (+1)

westram 2019-10-03 09:08 Rev.: 18140

* full update from child 'fix' into 'trunk'
- improve target 'cleanRelinkable'
- fix crash in inotify file tracker (occurred when moving a tracked file)
- minor tweaks for fts
* adds: log:branches/fix@18131:18139

3 lines of code changed in 1 file:

Makefile (+3 -1)

westram 2019-10-01 09:30 Rev.: 18128

* reintegrates 'fix' into 'trunk'
- effectively merges [17619]
* adds: log:branches/fix@17596,17618:18127

49 lines of code changed in 1 file:

arb_README.txt (+49 -34)

westram 2019-09-27 10:26 Rev.: 18121

- doc target 'cleanRelinkable'

1 lines of code changed in 1 file:

Makefile (+1)

westram 2019-09-26 17:39 Rev.: 18120

* add new target 'cleanRelinkable':
- removes libs, executables + tests to reduce size of WC (esp. in sanitized builds).
- avoid 'cleanRelinkable' causes rebuild (esp. rebuild of RaxML8).
* fix bogus-error when target 'clean' in UNIT_TESTER got called.

6 lines of code changed in 1 file:

Makefile (+6)

westram 2019-09-24 17:52 Rev.: 18119

* cosmetic

2 lines of code changed in 1 file:

Makefile (+2 -1)

westram 2019-09-24 17:28 Rev.: 18118

* disable {{{AddressSanitizer}}} for gcc 4.8.x ({{{LeakSanitizer}}} wont work, build fails on 14.04)

Note: fixed build on lorkin

2 lines of code changed in 1 file:

Makefile (+2 -1)

westram 2019-09-24 15:40 Rev.: 18117

* reset SANITIZE if no sanitizer survived its restricting rules

4 lines of code changed in 1 file:

Makefile (+4)

westram 2019-09-20 12:12 Rev.: 18104

* log change #562.

2 lines of code changed in 1 file:

arb_CHANGES.txt (+2 -1)

westram 2019-09-17 14:46 Rev.: 18092

* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090

3 lines of code changed in 1 file:

Makefile (+3)

westram 2019-09-17 14:13 Rev.: 18088

* reintegrates 'fts' into 'trunk'
* adds:
- log:branches/fts@17653,17655:17717,17724:18087
- [17925/branches/gui]

3 lines of code changed in 1 file:

Makefile (+3)

westram 2019-08-16 12:05 Rev.: 18014

* always dump missed loop vectorizations.
* if gcc regards a loop optimization as "too expensive", source requires IRRELEVANT_LOOP-comment
=> this revision fails compilation with 9.x series.

1 lines of code changed in 1 file:

Makefile (+1 -2)

westram 2019-08-13 12:19 Rev.: 18009

* accept gcc 9.2.0

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2019-05-27 08:49 Rev.: 17904

* workaround SuSE build problem
- for whatever reasons SuSE delivers a gcc which identifies as 7.4.1 (no such version has been released yet)
* IIRC the same did happen with gcc 5.3.1
- generally ignore subversions (in top level compiler check) for gcc-major>=5

6 lines of code changed in 1 file:

Makefile (+6 -1)

westram 2019-05-10 12:57 Rev.: 17877

* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

40 lines of code changed in 1 file:

Makefile (+40 -9)

westram 2019-04-07 09:54 Rev.: 17751

* ignore Makefile.old

1 lines of code changed in 1 file:

.gitignore (+1)

westram 2019-04-04 15:47 Rev.: 17742

* fix unnecessary typos.

31 lines of code changed in 1 file:

arb_OS_X.txt (+31 -31)

westram 2019-04-03 13:47 Rev.: 17738

* reintegrates 'config' into 'trunk'
* adds: log:branches/config@17733:17737

25 lines of code changed in 2 files:

Makefile (+17 -78), config.makefile.template (+8 -12)

westram 2019-04-02 17:02 Rev.: 17727

* TAGS generation: remove older temporary files

4 lines of code changed in 1 file:

Makefile (+4 -1)

westram 2019-03-27 10:13 Rev.: 17703

* provide stacktraces for {{{UndefinedBehaviorSanitizer}}}
- similar as done for {{{AddressSanitizer}}} and {{{LeakSanitizer}}}
- add verbose-flags to debug code that filters logfiles and rewrites stacktrace into message-format ({{{FILE:LINE: MESSAGE}}})
- fix paths of stacktraces (expand+reduce pathprefixes; trace enter/leave directory messages)

1 lines of code changed in 1 file:

Makefile (+1)

westram 2019-03-27 09:57 Rev.: 17701

* fix build/test of single unit
- failed to test after clean

11 lines of code changed in 1 file:

Makefile (+11 -9)

westram 2019-03-25 16:21 Rev.: 17696

* silence target 'tags'.

12 lines of code changed in 1 file:

Makefile (+12 -12)

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)

(940 more)

Directory [root]

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Most Recent Commits