Directory HELP_SOURCE/oldhelp/

Directory Created:
2001-11-26 14:00
Total Files:
343
Deleted Files:
88
Lines of Code:
25879

[root]/HELP_SOURCE/oldhelp
            directory in repo prompt (1 files, 31 lines)
            Folder removed from repo seer (0 files, 0 lines)

Lines of Code

HELP_SOURCE/oldhelp/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 1851 (100.0%) 36870 (100.0%) 19.9
westram 1813 (97.9%) 35848 (97.2%) 19.7
yadhu 15 (0.8%) 440 (1.2%) 29.3
murban 10 (0.5%) 406 (1.1%) 40.6
richter 9 (0.5%) 121 (0.3%) 13.4
huberj 1 (0.1%) 49 (0.1%) 49.0
epruesse 3 (0.2%) 6 (0.0%) 2.0

Most Recent Commits

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

43 lines of code changed in 3 files:

  • HELP_SOURCE/oldhelp: proteinViewer.hlp (+2), transl_table.hlp (new 37), translate_dna_2_pro.hlp (+4 -4)
westram 2018-10-17 10:00 Rev.: 17478


* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

30 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: nt_tree_settings_bootstrap.hlp (+27 -5), trm_boot.hlp (+3 -9)
westram 2018-09-20 18:17 Rev.: 17398


* adds a help page describing intended way to work with AA alignments in ARB

53 lines of code changed in 4 files:

  • HELP_SOURCE/oldhelp: aaali.hlp (new 49), faligner.hlp (+1 -1), realign_dna.hlp (+1 -1), translate_dna_2_pro.hlp (+2)
westram 2018-09-14 11:37 Rev.: 17370


* checked quality calculation (probe design):
- document more details
- added comments
- debug code to dump quality calculation

15 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: probedesignresult.hlp (+15 -6)
westram 2018-09-12 09:54 Rev.: 17361


* fix {{{GB_xcmd}}} for OSX with SIP

1 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: arb_envar.hlp (+1)
westram 2018-09-04 13:15 Rev.: 17353


* more details for example

10 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: move_groups.hlp (+10 -2)
westram 2018-09-03 12:57 Rev.: 17349


* add + document configs for
- reporting transfer quality
- restoring original name (after quality has been reviewed)

11 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: move_groups.hlp (+11 -1)
westram 2018-08-30 16:24 Rev.: 17342


* reintegrates 'group' into 'trunk'
- implements #780
* adds: log:branches/group@17162:17190,17261:17341

121 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: move_groups.hlp (+121 -28)
westram 2018-08-30 09:58 Rev.: 17336


* typos
- some had ''two'' good language skills ;-)
- fix some plural forms

3 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: help.hlp (+2 -2), prop_configs_edit.hlp (+1 -1)
westram 2018-07-06 15:02 Rev.: 17160


* reintegrates 'group' into 'trunk'
- misc. cleanup:
* group related functions now all accessible via menu of 1st ntree window
* DRY selection of 2 trees
* warn if annotated tree isnt visible
* fix mnemonics
* fix error handling (compare taxonomy)
* unittest comments added to tree remarks
* names
* adds: log:branches/group@17139:17159

89 lines of code changed in 7 files:

  • HELP_SOURCE/oldhelp: compare_taxonomy.hlp (+5 -1), compare_topo.hlp (new 37), move_groups.hlp (new 46), tree_cmp.hlp (del), tree_diff.hlp (del), treeadm.hlp (-10), trm_boot.hlp (+1 -1)
westram 2018-06-15 12:08 Rev.: 17110


* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

131 lines of code changed in 6 files:

  • HELP_SOURCE/oldhelp: group_search.hlp (+3), keeled_groups.hlp (new 83), mode_group.hlp (+12 -3), mode_move.hlp (+23 -1), mode_setroot.hlp (+3 -1), tr_export.hlp (+7)
westram 2018-06-14 09:41 Rev.: 17100


* document valid characters for PVP

2 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: pos_var_pars.hlp (+2)
westram 2018-05-30 13:59 Rev.: 17078


* DRY duplicated description of primer search parameters
* tested unclear behavior
* document bugs + problems in #784

13 lines of code changed in 3 files:

  • HELP_SOURCE/oldhelp: iupac-codes.hlp (-1), primer_new.hlp (+13 -3), primer_parameters.hlp (del)
westram 2018-04-30 17:27 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:

  • HELP_SOURCE/oldhelp: copyNpaste.hlp (-2)
westram 2018-04-05 11:09 Rev.: 16873


* fix typos ("neither")

1 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: realign_dna.hlp (+1 -1)
westram 2018-03-27 08:41 Rev.: 16869


* ACI/SRT selection button in NDS
- always edited the same NDS entry (that one it was 1st used for). Now correctly follows different entries.
- when selecting an entry that contains a predefined expression => select the predefined expression in the selection list

2 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: acisrt.hlp (+2 -2)
westram 2018-03-26 16:18 Rev.: 16868


* updated NDS help. document behavior
- in case of missing field
- at groups
- if {{{<no field>}}} selected

38 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: props_nds.hlp (+38 -22)
westram 2018-02-05 12:03 Rev.: 16835


* updated primer design documentation
- done according to Wolframs IDP paper from 2001

56 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: primer_new.hlp (+56)
westram 2017-12-08 13:30 Rev.: 16799


* reintegrates 'fix' into 'trunk'
- implements #773
- tested with asan + fixed harmless undefined behavior
* adds: log:branches/fix@16793:16798

57 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: searching.hlp (+57 -8)
westram 2017-11-28 10:55 Rev.: 16760


* document details of pairwise excluded columns in matrix calculation

15 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: dist.hlp (+15 -6)
westram 2017-11-16 13:36 Rev.: 16658


* PVP documentation
- bit more details about method
- list explicit mutation rates of PVP categories
- explain possible systematic error (PVP <-> topology)

76 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: pos_var_pars.hlp (+76 -11)
westram 2017-10-21 12:40 Rev.: 16564


* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

141 lines of code changed in 11 files:

  • HELP_SOURCE/oldhelp: arb_export.hlp (+3), arb_import.hlp (+14 -6), ebi_ift.hlp (del), export_format.hlp (+2), export_test.hlp (new 43), fasta_ift.hlp (del), import_test.hlp (new 37), importift.hlp (+9 -7), manage_test.hlp (new 32), rdp_ift.hlp (del), sec_display.hlp (+1 -1)
westram 2017-10-08 14:54 Rev.: 16508


* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

3 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: spa_create.hlp (+3 -2)
westram 2017-10-03 17:26 Rev.: 16469


* reintegrates 'textedit' into 'trunk'
- fixes #586
* editor now always started asynchronously
* uses inotify to track file changes
- ~~also use inotify to track directory updates (in order to update file selections when needed)~~\\(./) by [16515] ff.; merged by [16551]
* adds: log:branches/textedit@16448:16468

3 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: arb_envar.hlp (+3 -2)
westram 2017-09-23 13:03 Rev.: 16425


* reintegrates 'aci' into 'trunk'
- extends ACI language (implementing #707)
* boolean operators: {{{And}}},{{{Or}}},{{{Not}}}
* numeric comparison: {{{isAbove}}},{{{isBelow}}},{{{isEqual}}}
* floating point arithmetic: {{{fplus}}},{{{fminus}}},{{{fmult}}},{{{fdiv}}}
* misc: {{{round}}},{{{inRange}}},{{{isEmpty}}}
- enforce parameter checks in ACI function code
- case of commands completely ignored
* adds: log:branches/aci@16385,16391:16424

115 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: aci.hlp (+115 -67)
westram 2017-09-19 13:40 Rev.: 16391


* full update from child 'aci' into 'trunk'
- allow to view console from inside ARB
- slightly tweaked ACI trace
* adds: log:branches/aci@16386:16390

90 lines of code changed in 5 files:

  • HELP_SOURCE/oldhelp: aci.hlp (+5 -1), console.hlp (new 38), probeadmin.hlp (+6 -1), searching.hlp (+2 -3), xterm.hlp (new 39)
westram 2017-09-18 14:23 Rev.: 16374


* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

66 lines of code changed in 6 files:

  • HELP_SOURCE/oldhelp: aci.hlp (+6 -2), group_rename.hlp (+29), props_www.hlp (+8), reg.hlp (+11), searching.hlp (+3 -2), srt.hlp (+9 -9)
westram 2017-09-03 16:51 Rev.: 16261


* add new sort-criteria to 'search&query' (sort numerically; fixes #203)

2 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: searching.hlp (+2)
westram 2017-08-28 12:31 Rev.: 16243


* fix typos ("successfull")

1 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: realign_dna.hlp (+1 -1)
westram 2017-08-23 12:42 Rev.: 16237


* fix spelling for 'occurrence'

1 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: aci.hlp (+1 -1)
westram 2017-08-21 13:37 Rev.: 16233


* improve ACI documentation

54 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: aci.hlp (+54 -37)
westram 2017-07-19 12:25 Rev.: 16164


* reintegrates 'group' into 'trunk'
- implements #653
* adds: log:branches/group@16147:16163

11 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: group_search.hlp (+11)
westram 2017-06-02 10:17 Rev.: 15982


* full update from child 'fix' into 'trunk'
- fixes #478
* adds: log:branches/fix@15976:15981

12 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: sp_info.hlp (+4 -5), sp_info_locked.hlp (+8 -3)
westram 2017-05-29 10:15 Rev.: 15974


* solve remaining confusion in terminology (concerning "selected species"):
- sequence-range-blocks in EDIT4 are now called "highlighted species" or "highlighted block"
- Note: code still talks about selected species

31 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: e4_block.hlp (+29 -30), group_by_field.hlp (+2 -2)
westram 2017-05-24 13:26 Rev.: 15973


* minor changes

7 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: nt_keys.hlp (+3 -3), species_configs.hlp (+4 -1)
westram 2017-05-24 13:22 Rev.: 15972


* link term {{{selected species}}} to explaining helpfile

21 lines of code changed in 16 files:

  • HELP_SOURCE/oldhelp: arb_pars.hlp (+1 -1), di_clusters.hlp (+1 -1), e4_get_species.hlp (+3 -3), ecoliref.hlp (+1 -1), macro.hlp (+1 -1), markbyref.hlp (+1 -1), mg_xfer_field_of_sel.hlp (+1 -1), next_neighbours.hlp (+1 -1), nt_tree_settings.hlp (+1 -1), pa_quick.hlp (+1 -1), pfold_sai.hlp (+1 -1), sec_display.hlp (+2 -2), sp_info.hlp (+1 -1), sp_info_locked.hlp (+1 -1), tr_jump.hlp (+3 -3), vn_search.hlp (+1 -1)
westram 2017-05-24 13:15 Rev.: 15971


* update documentation concerning the "selected species"
- remove duplicate helpfile
- remove help from glossary (link instead)

29 lines of code changed in 5 files:

  • HELP_SOURCE/oldhelp: arb_merge_workflow.hlp (+5 -2), glossary.hlp (+1 -10), sel_spec.hlp (del), selected.hlp (+22 -6), sp_search.hlp (+1 -1)
westram 2017-05-21 16:59 Rev.: 15966


* reintegrates 'group' into 'trunk'
- implements #652 (group search)
* adds: log:branches/group@15733:15740,15743:15748,15750:15752,15754,15756,15758:15777,15781:15793,15796,15798:15806,15808:15817,15819:15965

319 lines of code changed in 5 files:

  • HELP_SOURCE/oldhelp: group_rename.hlp (new 55), group_search.hlp (new 216), group_trees.hlp (new 25), prop_configs.hlp (+4), searching.hlp (+19 -8)
westram 2017-04-03 14:00 Rev.: 15731


* reintegrates 'keys' into 'trunk'
- completes #687
* adds: log:branches/keys@15706:15730

22 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: nt_keys.hlp (+22 -3)
westram 2017-03-26 16:00 Rev.: 15691


* reintegrates 'keys' into 'trunk'
- implements part of #687 (species traversal via keys)
- adds temp. unfolding of selected species
- several fixes to [15665] (PARSIMONY)
* adds: log:branches/keys@15591:15690

38 lines of code changed in 2 files:

  • HELP_SOURCE/oldhelp: nt_keys.hlp (+34 -14), nt_tree_settings.hlp (+4)

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