-
westram
2011-12-23 16:13
#34
Rev.: 8327
-
13 lines of code changed in 2 files:
-
Makefile (+9 -3)
-
SOURCE_TOOLS:
export2sub (+4)
-
westram
2011-12-23 14:01
#33
Rev.: 8326
-
2 lines of code changed in 1 file:
-
UNIT_TESTER:
test_global.h (+2)
-
westram
2011-12-23 14:00
#32
Rev.: 8325
-
22 lines of code changed in 1 file:
-
TEMPLATES:
attributes.h (+22 -2)
-
westram
2011-12-23 13:57
#31
Rev.: 8324
-
3 lines of code changed in 3 files:
-
AISC:
Makefile (+1 -1)
-
NAMES_COM:
Makefile (+1 -1)
-
PROBE_COM:
Makefile (+1 -1)
-
westram
2011-12-23 13:56
#30
Rev.: 8323
-
50 lines of code changed in 1 file:
-
UNIT_TESTER:
test_unit.h (+50 -51)
-
westram
2011-12-23 13:56
#29
Rev.: 8322
-
7 lines of code changed in 2 files:
-
RNACMA:
AlignedSequenceLoader.cxx (+3 -2)
-
WINDOW:
aw_device.hxx (+4 -2)
-
westram
2011-12-23 13:44
#28
Rev.: 8321
-
3 lines of code changed in 1 file:
-
arb_build
2011-12-23 11:26
#27
Rev.: 8320
-
8 lines of code changed in 1 file:
-
westram
2011-12-21 13:04
#26
Rev.: 8319
-
112 lines of code changed in 21 files:
-
ARBDB:
adTest.cxx (+2 -2),
ad_core.cxx (-17),
ad_load.cxx (+1 -1),
ad_prot.h (+4 -30),
ad_save_load.cxx (+1 -1),
ad_t_prot.h (-16),
adali.cxx (-5),
adcomm.cxx (-4),
adfile.cxx (+1 -1),
aditem.cxx (+3 -12),
adlang1.cxx (+1 -1),
admath.cxx (-9),
adquery.cxx (+1 -1),
adsocket.cxx (+73 -68),
adstring.cxx (-18),
adtables.cxx (+7 -54),
adtools.cxx (+8 -21),
arbdb.cxx (+8 -149),
gb_prot.h (-1)
-
PERL_SCRIPTS/test:
Makefile (+1 -1)
-
SOURCE_TOOLS:
deadcode.pl (+1 -1)
-
westram
2011-12-21 12:17
#25
Rev.: 8318
-
68 lines of code changed in 6 files:
-
Makefile (+1 -4)
-
PERL_SCRIPTS/test:
Makefile (+1 -1),
check_arb.pl (new 15),
check_bioperl.pl (new 6),
check_lint.pl (new 4),
testScripts.pl (+41 -5)
-
westram
2011-12-21 12:01
#24
Rev.: 8317
-
1 lines of code changed in 1 file:
-
westram
2011-12-21 12:00
#23
Rev.: 8316
-
4 lines of code changed in 1 file:
-
ARBDB:
adGene.cxx (+4 -2)
-
westram
2011-12-20 16:54
#22
Rev.: 8315
-
13 lines of code changed in 3 files:
-
ARBDB:
adGene.cxx (+2),
adhash.cxx (+8 -1)
-
NTREE:
NT_extern.cxx (+3 -1)
-
westram
2011-12-20 16:35
#21
Rev.: 8314
-
1 lines of code changed in 3 files:
-
AISC_COM/AISC:
Makefile (+1 -5),
aisc_debug_globals.pa (del)
-
AISC_COM/C:
debug.c (del)
-
westram
2011-12-20 16:11
#20
Rev.: 8313
-
20 lines of code changed in 49 files:
-
AISC_COM/C:
client.c (+1 -187),
server.c (-3),
struct_man.c (-63)
-
ARBDB:
adExperiment.cxx (-5),
adGene.cxx (-15),
adcache.cxx (-12),
adstring.cxx (+1 -58),
adtree.cxx (-16),
arbdb.cxx (+1 -7)
-
AWT:
AWT_sel_boxes.cxx (-12)
-
AWTC:
AWTC_next_neighbours.cxx (-5)
-
CONSENSUS_TREE:
CT_hash.cxx (-33),
CT_part.cxx (-11)
-
CORE:
arb_msg.cxx (-4),
arb_strarray.cxx (+1 -5)
-
EDIT4:
ED4_main.cxx (+3 -15),
ED4_no_class.cxx (-8),
ED4_root.cxx (-32),
ED4_visualizeSAI.cxx (-3)
-
GL/glpng:
glpng.c (-145)
-
MERGE:
MG_species.cxx (-1)
-
MULTI_PROBE:
MP_main.cxx (-7),
MP_noclass.cxx (-20),
MP_permute.cxx (-38),
MP_probe_combi_statistic.cxx (-5)
-
NALIGNER:
ali_prealigner.cxx (-2)
-
NTREE:
AP_consensus.cxx (+2 -83),
AP_conservProfile2Gnuplot.cxx (+1 -1),
AP_cprofile.cxx (+1 -1),
Makefile (-1),
NT_extern.cxx (+1 -25),
ad_ali.cxx (+2 -5),
ad_transpro.cxx (-5),
ap_consensus.hxx (del),
nt_internal.h (+1)
-
PGT:
arb_interface.cxx (-8),
config_dialog.cxx (-21)
-
PHYLO:
PH_display.cxx (-10),
PH_main.cxx (+1 -1),
PH_matr.cxx (-124)
-
PROBE:
PT_etc.cxx (-40),
PT_prefixtree.cxx (+1 -32),
pt_prototypes.h (+1)
-
PROBE_DESIGN:
probe_design.cxx (-6)
-
PROBE_SET:
ps_detect_weak_differences.cxx (+2 -2)
-
SEQ_QUALITY:
SQ_functions.cxx (-119)
-
SL/NDS:
nds.cxx (-71)
-
SL/PRONUC:
AP_codon_table.cxx (-89)
-
SL/TREEDISP:
TreeCallbacks.cxx (-80)
-
westram
2011-12-20 15:49
#19
Rev.: 8312
-
3 lines of code changed in 3 files:
-
ARBDB:
adperl.cxx (+1 -1)
-
PERL2ARB:
ARB_ext.c (+1 -1),
Makefile.main (+1 -1)
-
westram
2011-12-20 15:33
#18
Rev.: 8311
-
131 lines of code changed in 8 files:
-
PROBE_SET:
Makefile (+4 -3),
ps_arb2asciipaths.cxx (+1 -1),
ps_convert_db.cxx (+2 -1),
ps_detect_weak_differences.cxx (+2 -1),
ps_get_probes.cxx (+1 -1),
ps_pg_specmap.hxx (new 62),
ps_pg_tree_functions.cxx (del),
ps_pg_tree_functions.hxx (new 59)
-
westram
2011-12-20 13:55
#17
Rev.: 8310
-
8 lines of code changed in 4 files:
-
ARBDB:
Makefile (+1),
admalloc.cxx (+1)
-
CORE:
arb_msg.cxx (+3 -3),
arb_msg.h (+3)
-
westram
2011-12-20 13:29
#16
Rev.: 8309
-
3085 lines of code changed in 244 files:
-
AISC:
aisc.c (+1 -1)
-
AISC_COM/C:
client.c (+13 -13),
client.h (-11),
server.c (+7 -4),
server.h (+2 -3),
struct_man.c (+8 -8),
struct_man.h (-8)
-
AISC_MKPTPS:
mkptypes.cxx (+2 -2)
-
ARBDB:
adChangeKey.cxx (+1 -1),
adExperiment.cxx (+1 -1),
adGene.cxx (+14 -14),
adRevCompl.cxx (+1 -2),
ad_config.cxx (+5 -6),
ad_config.h (-3),
ad_core.cxx (+39 -40),
ad_load.cxx (+10 -13),
ad_prot.h (+1 -27),
ad_save_load.cxx (+143 -139),
ad_t_prot.h (-5),
adali.cxx (+175 -175),
adcache.cxx (+1 -1),
adcomm.cxx (+1 -1),
adcompr.cxx (+7 -11),
adfile.cxx (+2 -2),
adhash.cxx (+31 -32),
adhashtools.cxx (+1 -1),
admap.cxx (+2 -2),
admatch.cxx (+1 -1),
adname.cxx (+1 -1),
adoptimize.cxx (+4 -6),
adquery.cxx (+5 -6),
adseqcompr.cxx (+13 -13),
adsocket.cxx (+6 -6),
adstring.cxx (+7 -11),
adsystem.cxx (+11 -10),
adtables.cxx (+1 -1),
adtree.cxx (+4 -5),
arbdb.cxx (+112 -111),
gb_prot.h (-56),
gb_t_prot.h (-14)
-
ARB_GDE:
GDE.cxx (+2 -4),
GDE_FileIO.cxx (+1 -2),
GDE_extglob.h (+2 -11),
GDE_global.cxx (+5 -80),
GDE_proto.h (-1)
-
AWT:
AWT_asciiprint.cxx (+10 -10),
AWT_canio.cxx (+1 -1),
AWT_db_browser.cxx (+4 -5),
AWT_input_mask.cxx (+2 -2),
AWT_map_key.cxx (+7 -4),
AWT_sel_boxes.cxx (+7 -7),
AWT_tables.cxx (+17 -17),
AWT_www.cxx (+3 -3),
awt.hxx (-3),
awt_input_mask_internal.hxx (-2),
awt_map_key.hxx (+4 -3),
awt_sel_boxes.hxx (-1)
-
AWTC:
AWTC_next_neighbours.cxx (+1 -1)
-
AWTI:
AWTI_export.cxx (+2 -2),
AWTI_import.cxx (+5 -5)
-
CONSENSUS_TREE:
CT_dtree.cxx (+1 -2),
CT_hash.cxx (+16 -19),
CT_hash.hxx (-2),
CT_ntree.cxx (+4 -4),
CT_part.cxx (+5 -5),
CT_part.hxx (-2),
CT_rbtree.cxx (+3 -3)
-
CONVERTALN:
embl.cxx (+20 -19),
genbank.cxx (+19 -19),
macke.cxx (+8 -8),
main.cxx (+1 -1),
prototypes.h (-7)
-
CORE:
arb_msg.cxx (+4 -4),
arb_msg.h (-4),
arb_signal.cxx (+1 -1),
arb_signal.h (-1),
arb_strarray.cxx (+1 -1),
arb_strarray.h (-1)
-
DIST:
DI_matr.cxx (+4 -4),
DI_view_matrix.cxx (+5 -5)
-
EDIT4:
ED4_ProteinViewer.cxx (+14 -14),
ED4_base.cxx (+1 -1),
ED4_block.cxx (+1 -1),
ED4_main.cxx (+5 -5),
ED4_manager.cxx (+11 -11),
ED4_naligner.cxx (+3 -3),
ED4_nds.cxx (+1 -1),
ED4_no_class.cxx (+5 -5),
ED4_root.cxx (+12 -12),
ED4_search.cxx (+1 -1),
ED4_terminal.cxx (+9 -9),
ED4_visualizeSAI.cxx (+1 -1),
ed4_block.hxx (-1),
ed4_class.hxx (-8),
ed4_defs.hxx (+2 -3)
-
GENOM:
EXP.hxx (-1),
EXP_interface.cxx (+17 -16),
EXP_local.hxx (-1),
EXP_main.cxx (+2 -2),
GEN.hxx (-3),
GEN_interface.cxx (+16 -17),
GEN_local.hxx (-2),
GEN_map.cxx (+47 -46),
GEN_nds.cxx (+3 -2)
-
GL/glpng:
glpng.c (+28 -28),
glpng.h (-12)
-
HELP_SOURCE:
arb_help2xml.cxx (+1 -1)
-
ISLAND_HOPPING:
align.cxx (+1 -1),
mem.cxx (+1 -1),
mem.h (+4 -5)
-
MERGE:
MG_adapt_ali.cxx (+1 -1),
MG_alignment.cxx (+9 -9),
MG_checkfield.cxx (+3 -3),
MG_configs.cxx (+5 -5),
MG_extendeds.cxx (+7 -7),
MG_main.cxx (+8 -8),
MG_species.cxx (+12 -12),
MG_trees.cxx (+5 -5),
merge.hxx (-1)
-
MULTI_PROBE:
MP_Window.cxx (+1 -1),
MP_externs.hxx (-3),
MP_main.cxx (+6 -6),
MP_noclass.cxx (+64 -68),
MP_permute.cxx (+2 -2),
MultiProbe.hxx (-1),
mp_proto.hxx (-2)
-
NALIGNER:
ali_global.cxx (+2 -2),
ali_main.cxx (+7 -7),
ali_prealigner.cxx (+1 -1)
-
NAMES:
names.cxx (+10 -3),
names.h (-9)
-
NTREE:
AP_consensus.cxx (+10 -12),
AP_conservProfile2Gnuplot.cxx (+2 -2),
AP_cprofile.cxx (+17 -16),
AP_pos_var_pars.cxx (+1 -1),
NT_concatenate.cxx (+69 -69),
NT_edconf.cxx (+8 -8),
NT_extern.cxx (+32 -32),
NT_import.cxx (+1 -1),
NT_ins_col.cxx (+1 -1),
NT_join.cxx (+2 -2),
NT_sort.cxx (+2 -2),
NT_validManual.cxx (+4 -4),
ad_ali.cxx (+11 -11),
ad_transpro.cxx (+4 -4),
ad_trees.cxx (+20 -20),
ap_conservProfile2Gnuplot.hxx (-1),
nt_cb.hxx (-32),
nt_internal.h (+1 -38)
-
PARSIMONY:
AP_tree_edge.cxx (+4 -4),
PARS_dtree.cxx (+2 -2),
PARS_main.cxx (+3 -3)
-
PGT:
analyze_window.cxx (+46 -46),
analyze_window.hxx (-4),
arb_interface.cxx (+31 -31),
arb_interface.hxx (+3 -12),
config_dialog.cxx (+287 -287),
config_dialog.hxx (-9),
dialog.cxx (+1 -1),
entry_sel_dialog.cxx (+56 -56),
entry_sel_dialog.hxx (-6),
file_import.cxx (+97 -101),
file_import.hxx (-3),
import_dialog.cxx (+429 -447),
main_dialog.cxx (+111 -109),
main_dialog.hxx (-11),
msgbox.cxx (+1 -1),
selection_dialog.cxx (+167 -166),
selection_dialog.hxx (-9)
-
PHYLO:
PH_display.cxx (+2 -2),
PH_main.cxx (+8 -8),
PH_matr.cxx (+6 -6),
phylo.hxx (-1)
-
PRIMER_DESIGN:
primer_design.cxx (+31 -31),
primer_design.hxx (-1)
-
PROBE:
PT_buildtree.cxx (+1 -1),
PT_debug.cxx (+2 -1),
PT_etc.cxx (+3 -3),
PT_main.cxx (+43 -43),
PT_match.cxx (+4 -4),
PT_prefixtree.cxx (+15 -15),
probe.h (-1),
pt_prototypes.h (-28)
-
PROBE_DESIGN:
SaiProbeVisualization.cxx (+3 -3),
probe_design.cxx (+12 -12)
-
PROBE_SET:
fb_test.cxx (+1 -1),
ps_arb2asciipaths.cxx (+2 -2),
ps_convert_db.cxx (+5 -5),
ps_detect_weak_differences.cxx (+17 -17),
ps_find_probes.cxx (+35 -35),
ps_get_probes.cxx (+4 -4),
ps_my2asciipaths.cxx (+2 -2),
ps_pg_tree_functions.cxx (+8 -8)
-
RNA3D:
RNA3D_Interface.cxx (+8 -8),
RNA3D_Interface.hxx (-5),
RNA3D_OpenGLEngine.cxx (+28 -28),
RNA3D_OpenGLEngine.hxx (-3)
-
RNACMA:
Cma.cxx (+32 -33)
-
SECEDIT:
SEC_graphic.cxx (+1 -1),
SEC_main.cxx (+3 -3)
-
SEQ_QUALITY:
SQ_functions.cxx (+7 -7),
SQ_functions.h (-11)
-
SERVERCNTRL:
servercntrl.cxx (+1 -1)
-
SL/AW_HELIX:
AW_helix.cxx (+1 -1)
-
SL/AW_NAME:
AW_rename.cxx (+1 -1),
AW_rename.hxx (-1)
-
SL/FAST_ALIGNER:
ClustalV.cxx (+2 -2),
fast_aligner.cxx (+3 -3),
seq_search.cxx (+1 -1),
seq_search.hxx (-2)
-
SL/GUI_ALIVIEW:
AWT_filter.cxx (+2 -2)
-
SL/HELIX:
BI_helix.cxx (+2 -2)
-
SL/ITEMS:
changekey.cxx (+1 -1),
item_sel_list.h (-1)
-
SL/NDS:
nds.cxx (+4 -3)
-
SL/PRONUC:
AP_codon_table.cxx (+3 -3),
AP_codon_table.hxx (-2)
-
SL/SEQIO:
seq_export.cxx (+2 -2)
-
SL/TREEDISP:
TreeCallbacks.cxx (+6 -6),
TreeCallbacks.hxx (-6),
TreeDisplay.cxx (+4 -4)
-
STAT:
ST_window.cxx (+1 -1)
-
TOOLS:
arb_a2ps.c (+77 -154),
arb_dnarates.cxx (+64 -64),
arb_gene_probe.cxx (+1 -1),
arb_primer.cxx (+9 -8),
arb_probe.cxx (+5 -3)
-
UNIT_TESTER:
TestEnvironment.cxx (+1 -1),
UnitTester.cxx (+1 -1)
-
WINDOW:
AW_button.cxx (+18 -21),
AW_debug.cxx (+1 -1),
AW_help.cxx (+2 -1),
AW_modal.cxx (+4 -4),
AW_nawar.cxx (+7 -7),
AW_preset.cxx (+14 -14),
AW_select.cxx (+1 -1),
AW_status.cxx (+3 -1),
AW_window.cxx (+4 -4),
AW_xfont.cxx (+3 -3),
aw_awar.hxx (+2 -4),
aw_nawar.hxx (+1 -2),
aw_preset.hxx (-4),
aw_root.hxx (-1),
aw_xfont.hxx (-1)
-
westram
2011-12-20 13:27
#15
Rev.: 8308
-
229 lines of code changed in 1 file:
-
SOURCE_TOOLS:
deadcode.pl (new 229)
-
westram
2011-12-13 15:01
#14
Rev.: 8302
-
49 lines of code changed in 4 files:
-
NTREE:
ad_transpro.cxx (+26 -15)
-
SL/PRONUC:
AP_codon_table.hxx (+8 -7)
-
SL/TRANSLATE:
Translate.cxx (+14),
Translate.hxx (+1)
-
westram
2011-12-12 16:52
#13
Rev.: 8300
-
21 lines of code changed in 11 files:
-
AISC_COM/AISC:
aisc_global.pa (+1 -1)
-
AISC_COM/C:
server.c (+1 -1)
-
ARB_GDE:
GDE_FileIO.cxx (+1 -1)
-
AWT:
AWT_config_manager.cxx (-1),
AWT_input_mask.cxx (+1 -1)
-
EDIT4:
ED4_secedit.cxx (+1 -1)
-
PARSIMONY:
GA_window.cxx (+1 -1)
-
PGT:
image_dialog.cxx (+1 -1),
plot.cxx (+14 -12)
-
WINDOW:
AW_device.cxx (-1),
AW_window.cxx (-1)
-
westram
2011-12-12 13:40
#12
Rev.: 8297
-
18 lines of code changed in 2 files:
-
Makefile (+16 -14)
-
SL:
Makefile (+2)
-
westram
2011-12-09 14:43
#11
Rev.: 8292
-
21 lines of code changed in 2 files:
-
PROBE:
PT_new_design.cxx (+20 -8),
probe.h (+1 -1)
-
westram
2011-12-09 14:02
#10
Rev.: 8291
-
1 lines of code changed in 1 file:
-
SL/TREEDISP:
TreeDisplay.cxx (+1 -1)
-
westram
2011-12-08 19:05
#9
Rev.: 8285
-
314 lines of code changed in 6 files:
-
ARBDB:
ad_prot.h (+160 -160),
ad_t_prot.h (+26 -26),
gb_prot.h (+102 -102)
-
NTREE:
nt_cb.hxx (-2),
nt_internal.h (+21 -18)
-
PROBE:
pt_prototypes.h (+5 -5)
-
westram
2011-12-08 19:04
#8
Rev.: 8284
-
21 lines of code changed in 3 files:
-
AISC_MKPTPS:
mkptypes.cxx (+17 -5)
-
NTREE:
AP_consensus.cxx (+4),
NT_cb.cxx (-2)
-
westram
2011-12-08 15:50
#7
Rev.: 8283
-
17 lines of code changed in 3 files:
-
Makefile (+1 -1),
arb_INSTALL.txt (+3 -3)
-
GL/glAW:
GLwDrawA.c (+13 -17)
-
westram
2011-12-07 15:47
#6
Rev.: 8280
-
314 lines of code changed in 1 file:
-
WINDOW:
AW_window.cxx (+314 -314)
-
westram
2011-12-07 15:33
#5
Rev.: 8279
-
140 lines of code changed in 4 files:
-
WINDOW:
AW_modal.cxx (+1 -1),
AW_window.cxx (+120 -100),
aw_window.hxx (+14 -3),
aw_window_Xm.hxx (+5 -2)
-
westram
2011-12-05 12:50
#4
Rev.: 8278
-
49 lines of code changed in 4 files:
-
WINDOW:
AW_nawar.cxx (+1 -1),
AW_window.cxx (+45 -45),
aw_nawar.hxx (+2 -1),
aw_window_Xm.hxx (+1 -1)
-
westram
2011-12-01 12:41
#3
Rev.: 8273
-
2 lines of code changed in 35 files:
-
Makefile (+1 -21)
-
ALIV3:
BI_helix.cxx (del),
BI_helix.hxx (del),
Makefile (del),
README (del),
a3.cxx (del),
a3_ali.cxx (del),
a3_ali.hxx (del),
a3_arbdb.cxx (del),
a3_arbdb.hxx (del),
a3_basen.c (del),
a3_basen.h (del),
a3_bihelix.cxx (del),
a3_bihelix.hxx (del),
a3_darray.cxx (del),
a3_darray.hxx (del),
a3_helix.cxx (del),
a3_helix.hxx (del),
a3_matrix.cxx (del),
a3_matrix.hxx (del),
a3_ptree.hxx (del),
a3_ptree1.cxx (del),
a3_ptree2.cxx (del),
a3_seq.cxx (del),
a3_seq.hxx (del),
a3_test_ptree.cxx (del),
a3_types.h (del),
ali_arbdb.cxx (del),
ali_arbdb.hxx (del),
needs_libs (del),
postree.cxx (del)
-
BINDEP:
needs_libs.aliv3 (del)
-
SOURCE_TOOLS:
dep.4dummy (+1 -2),
dep.alltargets (-2),
dep.libtargets (-1)
-
westram
2011-12-01 12:34
#2
Rev.: 8272
-
3 lines of code changed in 2 files:
-
EDIT4:
ED4_main.cxx (+2)
-
SECEDIT:
SEC_paint.cxx (+1 -1)
-
westram
2011-12-01 12:25
#1
Rev.: 8271
-
32 lines of code changed in 2 files:
-
WINDOW:
AW_button.cxx (+17 -17),
AW_window.cxx (+15 -15)