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, 45155 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, 4033 lines)

AWDEMO (0 files, 0 lines)

AWT (32 files, 12226 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, 6595 lines)

CORE (49 files, 9110 lines)

DBSERVER (3 files, 561 lines)

DIST (20 files, 7373 lines)

DUMMYINC (0 files, 0 lines)

EDIT (0 files, 0 lines)

EDIT4 (52 files, 28784 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, 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, 5521 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, 5519 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, 18077 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, 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, 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, 2362 lines)

SL (2 files, 95 lines)

ALILINK (7 files, 2364 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, 2997 lines)

DB_SCANNER (4 files, 749 lines)

DB_UI (5 files, 2069 lines)

FAST_ALIGNER (8 files, 5875 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, 1355 lines)

HELIX (6 files, 807 lines)

INSDEL (2 files, 2365 lines)

ITEMS (9 files, 1572 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, 257 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, 1125 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)

SOURCE_TOOLS (62 files, 10124 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, 8070 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, 5805 lines)

flags (1 files, 2 lines)

run (36 files, 14203 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)

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, 26018 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, 1533 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	1090 (100.0%)	15392 (100.0%)	14.1
westram	983 (90.2%)	14098 (91.6%)	14.3
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 (1.6%)	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 2019-05-27 09:49 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 13:57 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 10:54 Rev.: 17751

* ignore Makefile.old

1 lines of code changed in 1 file:

.gitignore (+1)

westram 2019-04-04 16:47 Rev.: 17742

* fix unnecessary typos.

31 lines of code changed in 1 file:

arb_OS_X.txt (+31 -31)

westram 2019-04-03 14:47 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 18:02 Rev.: 17727

* TAGS generation: remove older temporary files

4 lines of code changed in 1 file:

Makefile (+4 -1)

westram 2019-03-27 11:13 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 10:57 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 17:21 Rev.: 17696

* silence target 'tags'.

12 lines of code changed in 1 file:

Makefile (+12 -12)

westram 2019-03-18 19:07 Rev.: 17666

ignore leftover emacs autosave files.

1 lines of code changed in 1 file:

.gitignore (+1)

westram 2019-03-18 19:06 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 11:14 Rev.: 17656

* change names of ignored patch-files

3 lines of code changed in 1 file:

.gitignore (+3 -6)

westram 2019-03-07 18:30 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 13:10 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 20:39 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 15:22 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 10:12 Rev.: 17626

- accept gcc 8.3

1 lines of code changed in 1 file:

Makefile (+1 -1)

epruesse 2019-02-17 07:06 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 07:05 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 12:48 Rev.: 17620

* added gcc 7.4

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-11-25 20:19 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 18:56 Rev.: 17602

* updated README

41 lines of code changed in 1 file:

arb_README.txt (+41 -37)

westram 2018-10-31 10:52 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 19:19 Rev.: 17542

* allow compilation with gcc 6.5.0

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-10-17 14:21 Rev.: 17481

- updated

2 lines of code changed in 1 file:

arb_CHANGES.txt (+2 -1)

westram 2018-10-02 10:08 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 10:53 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 10:24 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 10:19 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 09:43 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 18:44 Rev.: 17345

* updated

3 lines of code changed in 1 file:

arb_CHANGES.txt (+3)

westram 2018-08-30 17:24 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 08:44 Rev.: 17277

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

16 lines of code changed in 1 file:

Makefile (+16 -13)

westram 2018-07-26 15:57 Rev.: 17272

* tested and accepted gcc 8.2

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2018-06-25 10:57 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 13:08 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 18:06 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 18:27 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 13:04 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 16:48 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)

(926 more)

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Most Recent Commits