-
westram
2026-03-26 15:15
#5
Rev.: 19733
-
17 lines of code changed in 1 file:
-
PERL_SCRIPTS/ARBTOOLS/TESTS:
automatic.pl (+17 -14)
-
westram
2026-03-10 20:56
#4
Rev.: 19731
-
568 lines of code changed in 54 files:
-
Makefile (+3),
arb_CHANGES.txt (+2)
-
ARBDB:
ad_config.cxx (+1),
gb_cb.h (+1 -1)
-
ARB_GDE:
GDE.cxx (+1 -1)
-
DIST:
DI_view_matrix.cxx (+4 -4)
-
GENOM:
EXP_interface.cxx (-2),
GEN_interface.cxx (-2)
-
GL/glAW:
AW_window_ogl.cxx (+1 -2)
-
HELP_SOURCE/source:
mg_species.hlp (+17),
mg_species_configs.hlp (+14 -11),
nt_tree_select.hlp (+2 -2),
species_configs.hlp (+28 -19),
species_configs_highlight.hlp (+14 -9),
species_configs_saveload.hlp (+1 -1),
syncscroll.hlp (+2 -2)
-
MERGE:
MG_configs.cxx (+86 -85),
MG_main.cxx (+2 -2),
MG_species.cxx (+6 -4),
Makefile (+3),
merge.hxx (+4 -1),
needs_libs (+1 -2)
-
NTREE:
Makefile (+14 -5),
NT_branchAnalysis.cxx (+1 -1),
NT_cb.cxx (+10 -6),
NT_edconf.cxx (+44 -1036),
NT_extern.cxx (+23 -55),
NT_local_proto.h (+2 -3),
NT_sort.cxx (+2 -1),
NT_sync_scroll.cxx (+3 -5),
ad_trees.cxx (+3 -3),
needs_libs (+1)
-
PHYLO:
PH_display.cxx (+4 -4)
-
SL/APP:
app.cxx (+1 -1)
-
SL/DB_QUERY:
db_query.cxx (+32 -45),
db_query.h (-2)
-
SL/DB_UI:
ui_species.cxx (-2)
-
SL/MACROS:
macro_gui.cxx (+1 -1)
-
SL/TREEDISP:
TreeDisplay.cxx (+19 -3),
TreeDisplay.hxx (+16 -5)
-
SOURCE_TOOLS:
dep.4dummy (+3 -2),
dep.alltargets (+1),
dep.libtargets (+1),
generate_all_links.sh (+1)
-
WINDOW:
AW_button.cxx (+1 -1),
AW_root.cxx (+39),
AW_window.cxx (+106 -120),
aw_awar_defs.hxx (-1),
aw_root.hxx (+1),
aw_window.hxx (+15 -13)
-
lib/pictures:
ad_query.fig (-2),
mark_configs.fig (+15 -15)
-
lib/pictures/merge:
configs.fig (+12 -12),
species.fig (+4 -4)
-
westram
2026-03-10 13:11
#3
Rev.: 19708
-
469 lines of code changed in 230 files:
-
arb_CHANGES.txt (+8 -8),
arb_README.txt (+1 -1),
arb_install.sh (+1 -1)
-
ARBDB:
adali.cxx (+1 -1)
-
EDIT4:
ED4_main.cxx (+1 -1)
-
HELP_SOURCE/source:
FORM.hlp (+1 -1),
Protection.hlp (+3 -3),
aci.hlp (+2 -4),
acisrt.hlp (+1 -1),
ad_align.hlp (+1 -1),
ad_extended.hlp (+1 -1),
alignment.hlp (+10 -10),
arb_commands.hlp (+5 -6),
arb_db.hlp (+1 -1),
arb_edit4.hlp (+4 -4),
arb_export.hlp (+1 -1),
arb_export_nds.hlp (+1 -1),
arb_import.hlp (+2 -2),
arb_intro.hlp (+1 -2),
arb_merge.hlp (+2 -2),
arb_merge_into.hlp (+2 -2),
arb_merge_outof.hlp (+2 -2),
arb_merge_workflow.hlp (+6 -6),
arb_ntree.hlp (+8 -5),
arb_pars.hlp (+4 -4),
arb_pars_init.hlp (+1 -1),
asciiprint.hlp (+1 -1),
awt_csp.hlp (+1 -1),
bonds.hlp (+2 -2),
branch_analysis.hlp (+2 -2),
chimera_check.hlp (+1 -1),
color_loadsave.hlp (+4 -4),
color_props.hlp (+1 -1),
color_ranges.hlp (+1 -1),
colorize.hlp (+4 -4),
compare_taxonomy.hlp (+1 -1),
compare_topo.hlp (+1 -1),
consense_algo.hlp (+2 -2),
consense_tree.hlp (+1 -1),
consensus.hlp (+1 -1),
consensus_def.hlp (+1 -1),
console.hlp (+2 -2),
count_chars.hlp (+1 -1),
csp_2_gnuplot.hlp (+1 -1),
del_list.hlp (+7 -8),
di_clusters.hlp (+1 -1),
displayField.hlp (+1 -1),
dist.hlp (+3 -3),
e4.hlp (+2 -1),
e4_block.hlp (+1 -1),
experiment_info.hlp (+2 -2),
experiment_search.hlp (+2 -2),
export_format.hlp (+2 -2),
export_test.hlp (+1 -1),
field_shader.hlp (+1 -1),
gen_create.hlp (+2 -2),
gen_jump.hlp (+1 -1),
gene_extract.hlp (+2 -2),
gene_hide.hlp (+1 -1),
gene_info.hlp (+3 -3),
gene_map.hlp (+2 -2),
gene_mark.hlp (+1 -1),
gene_search.hlp (+4 -4),
gene_species_field_transfer.hlp (+1 -1),
gene_species_mark.hlp (+1 -1),
group_rename.hlp (+1 -1),
group_search.hlp (+1 -1),
group_trees.hlp (+1 -1),
helix.hlp (+4 -4),
import_test.hlp (+1 -1),
importift.hlp (+1 -1),
input_mask.hlp (+3 -1),
insdel.hlp (+1 -1),
insdel_sai.hlp (+1 -1),
iupac-codes.hlp (+1 -1),
macro.hlp (+1 -1),
macro_interruption.hlp (+1 -1),
manage_test.hlp (+2 -2),
mark.hlp (+23 -27),
mark_duplicates.hlp (+1 -1),
mark_list.hlp (+3 -3),
markbyref.hlp (+1 -1),
max_freq.hlp (+1 -1),
merge_species.hlp (+2 -2),
mod_field_list.hlp (+3 -3),
mode.hlp (+2 -2),
mode_group.hlp (+2 -2),
mode_info.hlp (+2 -2),
mode_length.hlp (+2 -2),
mode_lzoom.hlp (+3 -3),
mode_mark.hlp (+1 -1),
mode_move.hlp (+1 -1),
mode_pzoom.hlp (+3 -3),
mode_rotate.hlp (+2 -2),
mode_select.hlp (+1 -1),
mode_setroot.hlp (+2 -2),
mode_spread.hlp (+3 -3),
mode_swap.hlp (+2 -2),
mode_width.hlp (+2 -2),
mode_www.hlp (+2 -2),
move_groups.hlp (+1 -1),
multifurcate.hlp (+1 -1),
namesadmin.hlp (+1 -1),
newwindow.hlp (+8 -7),
next_neighbours.hlp (+1 -1),
next_neighbours_common.hlp (+2 -2),
next_neighbours_listed.hlp (+1 -1),
no_tree.hlp (+5 -5),
nt_align_select.hlp (+10 -10),
nt_keys.hlp (+1 -1),
nt_tree_marker_settings.hlp (+1 -1),
nt_tree_select.hlp (+1 -1),
nt_tree_settings.hlp (+1 -1),
nt_tree_settings_bootstrap.hlp (+1 -1),
nt_tree_settings_expert.hlp (+1 -1),
optimize.hlp (+1 -2),
organism_mark.hlp (+1 -1),
pa_quick.hlp (+1 -1),
pars.hlp (+2 -2),
pd_match_iupac.hlp (+1 -1),
pd_spec_param.hlp (+1 -1),
pfold.hlp (+5 -5),
pfold_sai.hlp (+1 -1),
ph_export_markerline.hlp (+2 -2),
phylo.hlp (+1 -1),
pm_spec_param.hlp (+1 -1),
pos_var_pars.hlp (+1 -1),
primer.hlp (+1 -1),
primer_new.hlp (+2 -2),
primer_result.hlp (+1 -1),
probe_param.hlp (+1 -1),
probeadmin.hlp (+1 -1),
probedesign.hlp (+1 -1),
probedesignresult.hlp (+1 -1),
probematch.hlp (+1 -1),
probespec.hlp (+5 -4),
props_nds.hlp (+3 -3),
props_www.hlp (+3 -3),
pt_server.hlp (+5 -5),
quit.hlp (+3 -2),
realign_dna.hlp (+1 -1),
rename.hlp (+1 -1),
rerepair.hlp (+2 -2),
resortbyother.hlp (+1 -1),
resorttree.hlp (+2 -2),
rst_log_zoom.hlp (+4 -5),
rst_phys_zoom.hlp (+1 -1),
saiProbe.hlp (+1 -1),
saicalc.hlp (+1 -1),
save.hlp (+6 -6),
savedef.hlp (+2 -1),
search_duplicates.hlp (+2 -2),
searching.hlp (+3 -3),
sel_box.hlp (+1 -1),
sel_fil.hlp (+5 -4),
selected.hlp (+4 -6),
selected_gene.hlp (+3 -3),
seq_quality.hlp (+1 -1),
set_color_of_listed.hlp (+3 -3),
set_protection.hlp (+1 -1),
sina_main.hlp (+1 -1),
sp_IDs.hlp (+1 -1),
sp_del_mrkd.hlp (+6 -5),
sp_info.hlp (+4 -4),
sp_info_locked.hlp (+1 -1),
sp_mark.hlp (+5 -4),
sp_search.hlp (+2 -3),
sp_sort_fld.hlp (+1 -1),
sp_sort_phyl.hlp (+2 -2),
sp_sp_2_ext.hlp (+1 -1),
spa_copy.hlp (+4 -4),
spa_create.hlp (+1 -1),
spa_delete.hlp (+5 -6),
spa_rename.hlp (+4 -4),
spaf_convert.hlp (+1 -1),
spaf_delete.hlp (+3 -2),
species_configs.hlp (+1 -1),
species_configs_highlight.hlp (+1 -1),
species_join.hlp (+2 -2),
split.hlp (+1 -1),
st_ml.hlp (+1 -1),
submission.hlp (+1 -1),
syncroots.hlp (+1 -1),
syncscroll.hlp (+1 -1),
tags.hlp (+1 -1),
tbl_boot2len.hlp (+1 -1),
tbl_justify.hlp (+1 -1),
tbl_reset.hlp (+1 -1),
tbl_scale.hlp (+1 -1),
ted_boot.hlp (+1 -1),
tkeep_mrkd.hlp (+1 -1),
topology_shader.hlp (+1 -1),
tr_export.hlp (+1 -1),
tr_import.hlp (+1 -1),
tr_jump.hlp (+5 -5),
tr_type_dendro.hlp (+1 -1),
tr_type_irs.hlp (+1 -1),
tr_type_nds.hlp (+2 -2),
tr_type_radial.hlp (+1 -1),
track_ali_changes.hlp (+1 -1),
translate_dna_2_pro.hlp (+1 -1),
tree2file.hlp (+1 -1),
tree2prt.hlp (+3 -3),
tree_group.hlp (+1 -1),
tree_pseudo.hlp (+1 -1),
tree_shading.hlp (+1 -1),
treeadm.hlp (+4 -4),
trees.hlp (+2 -3),
trm_boot.hlp (+1 -1),
trm_del.hlp (+1 -1),
trm_mrkd.hlp (+1 -1),
undo.hlp (+1 -1),
unmark_list.hlp (+3 -3),
vn_delete.hlp (+1 -1),
vn_import.hlp (+1 -1),
vn_search.hlp (+1 -1),
vn_suggest.hlp (+1 -1),
write_field_list.hlp (+7 -8),
xferset.hlp (+2 -2),
xterm.hlp (+1 -1)
-
MERGE:
MG_main.cxx (+1 -1),
MG_species.cxx (+2 -2)
-
NTREE:
NT_extern.cxx (+1 -1)
-
PERL2ARB:
ARB.pm (+1 -1)
-
SERVERCNTRL:
servercntrl.cxx (+2 -2)
-
SH:
arb (+1 -1),
example_batch_probe_match.sh (+1 -1)
-
SL/APP:
db_browser.cxx (+1 -1)
-
SL/TREE_READ:
TreeRead.cxx (+1 -1)
-
WINDOW:
AW_help.cxx (+1 -1)
-
westram
2026-03-10 13:00
#2
Rev.: 19707
-
28 lines of code changed in 6 files:
-
HELP_SOURCE/source:
Protection.hlp (+6 -3),
del_list.hlp (+5 -5),
gene_info.hlp (+4 -4),
security.hlp (+5 -4),
sp_info.hlp (+3 -4),
write_field_list.hlp (+5 -5)
-
westram
2026-03-10 12:56
#1
Rev.: 19706
-
73 lines of code changed in 6 files:
-
HELP_SOURCE/source:
arb.hlp (+51 -9),
nt_keys.hlp (+11),
pt_server.hlp (+8 -5)
-
NTREE:
NT_extern.cxx (+1 -1),
ad_ext.cxx (+1 -1)
-
SL/SAICALC:
saicalc.cxx (+1 -1)