Directory HELP_SOURCE/source/

Total Files:
347
Deleted Files:
2
Lines of Code:
22422

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HELP_SOURCE/source/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 725 (100.0%) 3430 (100.0%) 4.7

Most Recent Commits

westram 2025-08-13 10:25 Rev.: 19532


* reintegrates 'help' into 'trunk'
- tweak arb documentation:
* automatically link
- ticket references to arb bug tracker (only affects html version).
- found URLs.
* page titles
- warn about long titles.
- introduce {{{SUBTITLE}}}s (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
* cleanup header sections in all helpfiles.
* fix and/or update several help files.
* document syntax of help sources.
* build issues:
- when xml validation fails, next build no longer uses invalid xml => keeps failing.
- remove output files on error (including files below {{{ARBHOME/lib}}}).
- pipe output through logs to ensure proper wrapping in {{{Entering/Leaving}}} lines.
- moves {{{Tree admin}}} + {{{NDS}}} menu entries to top of menu
* adds: log:branches/help@18783:19531

2796 lines of code changed in 664 files:

  • HELP_SOURCE/source: FAQS.hlp (new), FORM.hlp (new), Protection.hlp (+7 -7), aaali.hlp (new), accessibility_sai.hlp (new), aci.hlp (+5 -5), acisrt.hlp (new), ad_align.hlp (+7 -7), ad_extended.hlp (+8 -8), advice.hlp (+7 -7), alignment.hlp (new), ap_stack.hlp (new), arb.hlp (+18 -18), arb_commands.hlp (+10 -10), arb_db.hlp (new), arb_edit4.hlp (new), arb_envar.hlp (+7 -7), arb_export.hlp (new), arb_export_nds.hlp (+8 -8), arb_gde.hlp (new), arb_import.hlp (new), arb_intro.hlp (+15 -13), arb_merge.hlp (new), arb_merge_into.hlp (new), arb_merge_outof.hlp (+9 -9), arb_merge_workflow.hlp (new), arb_ntree.hlp (new), arb_pars.hlp (new), arb_pars_init.hlp (+8 -8), arb_secedit.hlp (new), asciiprint.hlp (new), awt_csp.hlp (+7 -7), bonds.hlp (new), bootstrap.hlp (new), branch_analysis.hlp (new), bugtracker.hlp (new 30), checkfield.hlp (new), chimera_check.hlp (new), cluster_group.hlp (+8 -8), color.hlp (+11 -11), color_loadsave.hlp (new), color_props.hlp (new), color_props_groups.hlp (new), color_ranges.hlp (+7 -7), colorize.hlp (new), compare_taxonomy.hlp (+7 -7), compare_topo.hlp (new), concatenate.hlp (+6 -7), consense_algo.hlp (+4 -4), consense_tree.hlp (+8 -8), consensus.hlp (+10 -10), consensus_def.hlp (+4 -4), console.hlp (+5 -5), copyNpaste.hlp (new), count_chars.hlp (+7 -7), csp_2_gnuplot.hlp (+7 -7), del_list.hlp (new), di_clusters.hlp (new), displayField.hlp (new), dist.hlp (+18 -18), dssp_ift.hlp (+11 -11), e4.hlp (new), e4_background_priority.hlp (new), e4_block.hlp (new), e4_consensus.hlp (+7 -7), e4_defaults.hlp (new), e4_get_species.hlp (new), e4_mode.hlp (new), e4_modsai.hlp (+9 -9), e4_options.hlp (new), e4_replace.hlp (+6 -6), e4_search.hlp (+7 -7), ecoliref.hlp (new), ed4_flags.hlp (+6 -6), ed4_nds.hlp (new), exec_bug.hlp (new), experiment_info.hlp (new), experiment_search.hlp (+7 -7), export_format.hlp (new), export_test.hlp (+5 -5), extended.hlp (+8 -9), faligner.hlp (new), field_sel_new.hlp (+8 -8), field_shader.hlp (new), gde_flat_ift.hlp (+5 -5), gde_menus.hlp (new), gen_create.hlp (+9 -9), gen_disp_style.hlp (+7 -7), gen_jump.hlp (+8 -8), gen_mode.hlp (+5 -5), gen_new_view.hlp (new), gen_options.hlp (new), gene_extract.hlp (new), gene_hide.hlp (new), gene_info.hlp (+6 -6), gene_map.hlp (+8 -8), gene_mark.hlp (new), gene_mode.hlp (new), gene_search.hlp (new), gene_species.hlp (+10 -10), gene_species_field_transfer.hlp (new), gene_species_mark.hlp (new), genes.hlp (new), glossary.hlp (+13 -13), group_by_field.hlp (new), group_rename.hlp (+7 -7), group_search.hlp (+5 -5), group_trees.hlp (+5 -5), helix.hlp (new), helixsym.hlp (+10 -10), help.hlp (new), import_test.hlp (new), importift.hlp (+8 -8), input_mask.hlp (+8 -8), input_mask_format.hlp (+9 -9), input_mask_new.hlp (new), insdel.hlp (+9 -9), insdel_sai.hlp (new), islandhopping.hlp (+7 -7), iupac-codes.hlp (new), keeled_groups.hlp (+4 -4), kernlin.hlp (new), macro.hlp (+7 -7), man_arb_edit4.hlp (new), manage_test.hlp (new), manual.hlp (+5 -5), mark.hlp (new), mark_duplicates.hlp (new), mark_genes.hlp (new), mark_list.hlp (new), markbyref.hlp (+5 -5), matrix_settings.hlp (new), max_freq.hlp (new), merge_species.hlp (+7 -7), mergetaggedfield.hlp (new), mg_alignment.hlp (new), mg_extendeds.hlp (new), mg_names.hlp (+4 -4), mg_preserve.hlp (+10 -8), mg_species.hlp (+4 -4), mg_species_configs.hlp (+8 -8), mg_trees.hlp (new), mg_xfer_field_of_listed.hlp (+4 -4), mg_xfer_field_of_sel.hlp (new), missbase.hlp (new), mod_field_list.hlp (+10 -10), mode.hlp (new), mode_group.hlp (new), mode_info.hlp (new), mode_kernlin.hlp (+9 -9), mode_length.hlp (+7 -7), mode_lzoom.hlp (+8 -8), mode_mark.hlp (+5 -5), mode_move.hlp (+8 -8), mode_nni.hlp (+9 -9), mode_optimize.hlp (+10 -10), mode_pzoom.hlp (new), mode_rotate.hlp (new), mode_select.hlp (new), mode_setroot.hlp (+8 -8), mode_spread.hlp (+8 -8), mode_swap.hlp (+9 -9), mode_width.hlp (+8 -8), mode_www.hlp (+8 -8), move_groups.hlp (new), mp_params.hlp (+5 -5), multifurcate.hlp (new), multiprobe.hlp (+10 -10), multiproberesults.hlp (+5 -5), namesadmin.hlp (+6 -6), ne_align_seq.hlp (+9 -9), nekey_map.hlp (new), newwindow.hlp (new), next_neighbours.hlp (new), next_neighbours_common.hlp (new), next_neighbours_listed.hlp (new), nni.hlp (new), no_tree.hlp (+6 -10), nt_align_select.hlp (new), nt_keys.hlp (+7 -7), nt_tree_marker_settings.hlp (+5 -5), nt_tree_select.hlp (new), nt_tree_settings.hlp (+7 -7), nt_tree_settings_bootstrap.hlp (+6 -6), nt_tree_settings_expert.hlp (new), optimize.hlp (+5 -5), organism_mark.hlp (new), organisms.hlp (new), pa_add.hlp (+7 -7), pa_bootstrap.hlp (new), pa_branchlengths.hlp (new), pa_globopti.hlp (new), pa_kernlin.hlp (new), pa_locopti.hlp (new), pa_mixtree.hlp (new), pa_optimizer.hlp (new), pa_partial.hlp (new), pa_quick.hlp (new), pa_reset.hlp (new), pa_value.hlp (+20 -20), pars.hlp (+9 -10), partial_sequences.hlp (+7 -7), pd_match_iupac.hlp (+8 -8), pd_spec_param.hlp (+8 -8), pfold.hlp (+9 -9), pfold_props.hlp (new), pfold_sai.hlp (+13 -11), ph_export_markerline.hlp (+7 -7), phylo.hlp (+9 -9), pm_spec_param.hlp (+7 -7), pos_var_pars.hlp (+7 -7), primer.hlp (new), primer_new.hlp (+6 -6), primer_result.hlp (new), probe_param.hlp (new), probeadmin.hlp (+8 -8), probedesign.hlp (+9 -9), probedesignresult.hlp (+14 -14), probematch.hlp (+5 -5), probespec.hlp (+4 -4), prop_configs.hlp (new), prop_configs_edit.hlp (new), props_frame.hlp (+7 -7), props_nds.hlp (+11 -11), props_www.hlp (+7 -9), proteinViewer.hlp (+9 -9), pt_server.hlp (new), questions.hlp (+7 -7), quit.hlp (+7 -7), realign_dna.hlp (new), reg.hlp (new), rename.hlp (+5 -5), rerepair.hlp (+7 -7), reset_win_layout.hlp (+7 -7), resortbyother.hlp (+15 -15), resorttree.hlp (new), rna3d_changeMolecule.hlp (new), rna3d_dispBases.hlp (+9 -9), rna3d_dispHelices.hlp (+10 -10), rna3d_dispMolecule.hlp (new), rna3d_general.hlp (+12 -10), rna3d_mapSeqData.hlp (new), rst_log_zoom.hlp (+8 -8), rst_phys_zoom.hlp (new), saiProbe.hlp (+7 -7), saicalc.hlp (+6 -6), save.hlp (+4 -4), save_matrix.hlp (new), savedef.hlp (+7 -7), scandb.hlp (new), search_duplicates.hlp (new), search_equal_fields.hlp (+9 -9), searching.hlp (new), sec_bonddef.hlp (+5 -5), sec_display.hlp (+7 -7), sec_imexport.hlp (+7 -7), sec_keys.hlp (+7 -7), sec_main.hlp (+10 -10), sec_mode.hlp (+14 -14), sec_props.hlp (new), secedit_imexport.hlp (+9 -9), security.hlp (+8 -8), sel_box.hlp (new), sel_fil.hlp (new), selected.hlp (new), selected_gene.hlp (new), seq_quality.hlp (+7 -7), sequence_colors.hlp (new), set_color_of_listed.hlp (new), set_protection.hlp (new), sina_main.hlp (+6 -7), sp_IDs.hlp (+5 -5), sp_del_mrkd.hlp (+9 -9), sp_info.hlp (new), sp_info_locked.hlp (+6 -6), sp_mark.hlp (+8 -8), sp_search.hlp (new), sp_sort_fld.hlp (new), sp_sort_phyl.hlp (+8 -8), sp_sp_2_ext.hlp (new), spa_copy.hlp (+4 -4), spa_create.hlp (new), spa_delete.hlp (new), spa_rename.hlp (+4 -4), spaf_convert.hlp (+7 -7), spaf_create.hlp (new), spaf_delete.hlp (+8 -8), spaf_reorder.hlp (+8 -8), species.hlp (+4 -4), species_configs.hlp (+8 -8), species_configs_highlight.hlp (new), species_configs_saveload.hlp (+7 -7), species_join.hlp (+5 -5), srt.hlp (new), st_ml.hlp (+6 -6), submission.hlp (new), sync_colors.hlp (new), syncroots.hlp (+5 -5), syncscroll.hlp (+5 -5), tags.hlp (+10 -10), tbl_boot2len.hlp (new), tbl_justify.hlp (new), tbl_reset.hlp (new), tbl_scale.hlp (new), ted_boot.hlp (+5 -5), tkeep_mrkd.hlp (+7 -7), toggle_secinfo.hlp (new), topology_shader.hlp (+5 -5), tr_export.hlp (+6 -6), tr_import.hlp (new), tr_jump.hlp (+8 -8), tr_type_dendro.hlp (new 34), tr_type_irs.hlp (+16 -16), tr_type_list.hlp (del), tr_type_nds.hlp (new), tr_type_radial.hlp (+16 -21), track_ali_changes.hlp (+7 -7), trans_anal.hlp (new), transl_table.hlp (new), translate_dna_2_pro.hlp (+7 -7), tree2file.hlp (new), tree2prt.hlp (+6 -6), tree_group.hlp (+5 -5), tree_pseudo.hlp (new), tree_shading.hlp (new), treeadm.hlp (+7 -7), trees.hlp (new), trm_boot.hlp (new), trm_del.hlp (new), trm_mrkd.hlp (new), undo.hlp (+13 -13), unittest.hlp (+14 -14), universal_ift.hlp (new), unmark_list.hlp (new), user_matrix.hlp (+8 -8), version.hlp (+5 -5), viewdiff.hlp (+8 -8), visualizeSAI.hlp (+7 -7), vn_delete.hlp (+4 -4), vn_import.hlp (new), vn_search.hlp (new), vn_suggest.hlp (+8 -8), write_field_list.hlp (+5 -5), xferset.hlp (+5 -5), xterm.hlp (+7 -7)
westram 2025-08-07 18:50 Rev.: 19517


* fix typo.

1 lines of code changed in 1 file:

  • HELP_SOURCE/source: macro.hlp (+1 -1)
westram 2025-08-07 18:30 Rev.: 19516


* document automation using macros.

20 lines of code changed in 2 files:

  • HELP_SOURCE/source: arb_envar.hlp (+3 -3), macro.hlp (+17 -4)
westram 2025-08-07 18:27 Rev.: 19515


* allow to reduce the time-to-wait on error, by defining {{{ARB_SCRIPTED_SECS_WAIT_ON_ERROR}}}.

7 lines of code changed in 2 files:

  • HELP_SOURCE/source: arb_envar.hlp (+7)
westram 2024-10-01 18:45 Rev.: 19499


* implements #863
* add new ACI command "dupidx" (active in group search).
* update group-enumeration presets: use '~' instead of '_'. use new ACI command 'dupidx'.

9 lines of code changed in 2 files:

  • HELP_SOURCE/source: group_rename.hlp (new)
westram 2023-09-13 18:33 Rev.: 19489


* reintegrates 'macros' into 'trunk'
* implements #856
* adds: log:branches/macros@19482:19488

72 lines of code changed in 3 files:

  • HELP_SOURCE/source: macro.hlp (new), macro_interruption.hlp (new 58)
westram 2023-07-04 12:14 Rev.: 19425


* reintegrates 'ali' into 'trunk'
- refactorings + fixes related to SEQ_QUALITY + HELIX
* adds: log:branches/ali@19407:19424

15 lines of code changed in 3 files:

  • HELP_SOURCE/source: seq_quality.hlp (+3 -1), species_configs.hlp (new)
westram 2023-06-25 16:59 Rev.: 19411


* update documentation of SEQ_QUALITY:
- non-evaluated fields
- usage of default helix base pairings.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: seq_quality.hlp (new)
westram 2023-06-25 16:30 Rev.: 19407


* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406

19 lines of code changed in 3 files:

  • HELP_SOURCE/source: helixsym.hlp (+3 -1), sec_bonddef.hlp (+16 -8)
westram 2023-06-15 15:31 Rev.: 19393


* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392

2 lines of code changed in 2 files:

  • HELP_SOURCE/source: helixsym.hlp (+2 -2)
westram 2023-06-03 13:36 Rev.: 19376


* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375

17 lines of code changed in 1 file:

  • HELP_SOURCE/source: bad_alignment.hlp (+17 -1)
westram 2023-05-25 14:50 Rev.: 19363


* reintegrates 'ali' into 'trunk'
* basically implements #854
* adds: log:branches/ali@19357:19362

35 lines of code changed in 1 file:

  • HELP_SOURCE/source: bad_alignment.hlp (new 35)
westram 2022-11-30 20:16 Rev.: 19353


* added script to delete unlisted trees.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: treeadm.hlp (new)
westram 2022-11-30 20:12 Rev.: 19352


* added script to delete unlisted species selections.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: mg_species_configs.hlp (new)
westram 2022-11-30 20:00 Rev.: 19351


* added script to delete unlisted SAIs.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: ad_extended.hlp (changed)
westram 2022-11-17 12:29 Rev.: 19348


* emphasize reference- and ptserver-database have to be the same database!

18 lines of code changed in 1 file:

  • HELP_SOURCE/source: sina_main.hlp (+18 -6)
westram 2022-10-22 19:30 Rev.: 19283


* allow to define a separator used to generate clusternames
- old hardcoded default was '_' (which interferes with groupname conventions)
- new customisable default is '-'
- use custom separator
* in get_upgroup_info().
* for matchrate.
- correctly handle empty separator.
* change other hardcoded characters
- avoid '_' in {{{WHOLE_TREE}}} (now uses {{{<WHOLE TREE>}}}).
- neighter use '/' nor '-' when inserting relative notation (old: {{{3-4/7}}} new {{{3.4[7]}}}).
* part of #832

2 lines of code changed in 1 file:

  • HELP_SOURCE/source: cluster_group.hlp (+2)
westram 2022-10-22 19:17 Rev.: 19280


* document collaboration between 'create groups' with 'append original' and 'delete groups'.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: cluster_group.hlp (new)
westram 2022-09-08 13:45 Rev.: 19270


* document default of sina binary (was changed with [19240]).
* add warning.

2 lines of code changed in 1 file:

  • HELP_SOURCE/source: sina_main.hlp (+2 -1)
westram 2022-09-05 16:02 Rev.: 19262


* add 'View sysinfo' entry to arb 'Tools' menu.
- shows 'sys.info' generated by arb_launcher.
* document 'ARB session log archive'.

10 lines of code changed in 2 files:

  • HELP_SOURCE/source: console.hlp (new)
westram 2022-09-01 16:19 Rev.: 19245


* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

286 lines of code changed in 4 files:

  • HELP_SOURCE/source: markbyref.hlp (+3 -2), sina_main.hlp (+283 -53)
westram 2022-08-06 19:25 Rev.: 19222


* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221

4 lines of code changed in 1 file:

  • HELP_SOURCE/source: split.hlp (+4)
westram 2022-07-21 14:01 Rev.: 19167


* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

24 lines of code changed in 1 file:

  • HELP_SOURCE/source: split.hlp (+24 -5)
westram 2022-06-29 14:54 Rev.: 19100


* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099

51 lines of code changed in 5 files:

  • HELP_SOURCE/source: concatenate.hlp (new), merge_species.hlp (+1 -1), split.hlp (new 44)
westram 2022-05-06 10:44 Rev.: 19022


* add example macro for database maintainers
- allows to delete all fields except those listed in the script
- script needs to be edited (to allow execution and to maintain field list)
* mention script in "Delete Fields" help.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: spaf_delete.hlp (new)
westram 2022-03-30 11:48 Rev.: 18974


* {{{next_expand_mode}}} now also expands all groups containing unmarked species:
- can be applied to subtrees by key 'x'.
- update documentation.
- impl: also count **unmarked** species in {{{AWT_graphic_tree_group_state}}}.

4 lines of code changed in 2 files:

  • HELP_SOURCE/source: nt_keys.hlp (new)
westram 2022-03-30 11:44 Rev.: 18973


* implement 'expand unmarked'
- call from 'collapse' menu.
- document.

1 lines of code changed in 2 files:

  • HELP_SOURCE/source: tree_group.hlp (new)
westram 2022-02-28 14:58 Rev.: 18937


* mention various 'count species' menu entries.
* remove unused .hlp (count now refers to same helpfile as mark).

0 lines of code changed in 3 files:

  • HELP_SOURCE/source: sp_count_mrk.hlp (del), sp_mark.hlp (new)
westram 2021-12-20 18:44 Rev.: 18883


* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

33 lines of code changed in 4 files:

  • HELP_SOURCE/source: props_nds.hlp (new), tr_export.hlp (+31 -18)
westram 2021-12-17 16:32 Rev.: 18863


* document 'Import fields from calc-sheet'.
* link to 'Export fields (to calc-sheet using NDS)'.
* add another pointer, where to add helpfiles for GDE menus.

2 lines of code changed in 2 files:

  • HELP_SOURCE/source: arb_export_nds.hlp (+2)
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