Directory HELP_SOURCE/oldhelp/

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westram 2021-10-10 08:33 Rev.: 18781

* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

0 lines of code changed in 436 files:

• HELP_SOURCE/oldhelp: FAQS.hlp (del), FORM.hlp (del), Makefile (del), Protection.hlp (del), aaali.hlp (del), accessibility_sai.hlp (del), aci.hlp (del), acisrt.hlp (del), ad_align.hlp (del), ad_extended.hlp (del), advice.hlp (del), ae2_ift.hlp (del), agde_MAUS.hlp (del), agde_sativa.hlp (del), ale.hlp (del), align.hlp (del), alignment.hlp (del), ap_stack.hlp (del), arb.hlp (del), arb.pdf.gz (del), arb.ps.gz (del), arb_comm (del), arb_commands.hlp (del), arb_db.hlp (del), arb_edit.hlp (del), arb_edit4.hlp (del), arb_envar.hlp (del), arb_export.hlp (del), arb_export_nds.hlp (del), arb_gde.hlp (del), arb_import.hlp (del), arb_intro.hlp (del), arb_merge.hlp (del), arb_merge_into.hlp (del), arb_merge_outof.hlp (del), arb_merge_workflow.hlp (del), arb_ntree.hlp (del), arb_pars.hlp (del), arb_pars_init.hlp (del), arb_secedit.hlp (del), asciiprint.hlp (del), awt_csp.hlp (del), bonds.hlp (del), bootstrap.hlp (del), branch_analysis.hlp (del), change_security.hlp (del), check_quality.hlp (del), checkfield.hlp (del), checkgcg.hlp (del), chimera_check.hlp (del), cluster_group.hlp (del), color.hlp (del), color_loadsave.hlp (del), color_props.hlp (del), color_props_groups.hlp (del), color_ranges.hlp (del), colorize.hlp (del), commands.hlp (del), compare_taxonomy.hlp (del), compare_topo.hlp (del), concatenate.hlp (del), config_saveload.hlp (del), configuration.hlp (del), configurations.hlp (del), cons_params.hlp (del), consense_algo.hlp (del), consense_tree.hlp (del), consensus.hlp (del), consensus.ps.gz (del), consensus_def.hlp (del), console.hlp (del), copyNpaste.hlp (del), copyright.hlp (del), count_chars.hlp (del), csp_2_gnuplot.hlp (del), del_list.hlp (del), dewachter_ift.hlp (del), di_clusters.hlp (del), displayField.hlp (del), dist.hlp (del), dssp_ift.hlp (del), e4.hlp (del), e4_background_priority.hlp (del), e4_block.hlp (del), e4_consensus.hlp (del), e4_defaults.hlp (del), e4_get_species.hlp (del), e4_mode.hlp (del), e4_modsai.hlp (del), e4_options.hlp (del), e4_replace.hlp (del), e4_search.hlp (del), ebi_ift.hlp (del), ecoliref.hlp (del), ed4_flags.hlp (del), ed4_nds.hlp (del), edit_config.hlp (del), exec_bug.hlp (del), experiment_info.hlp (del), experiment_search.hlp (del), export_format.hlp (del), export_test.hlp (del), exportcursor.hlp (del), extended.hlp (del), faligner.hlp (del), fasta_ift.hlp (del), fastdnaml.hlp (del), field_sel_new.hlp (del), field_shader.hlp (del), galign_main.hlp (del), gde.hlp (del), gde_flat_ift.hlp (del), gde_ift.hlp (del), gde_menus.hlp (del), gen_create.hlp (del), gen_disp_style.hlp (del), gen_jump.hlp (del), gen_mode.hlp (del), gen_new_view.hlp (del), gen_options.hlp (del), gene_extract.hlp (del), gene_hide.hlp (del), gene_info.hlp (del), gene_map.hlp (del), gene_mark.hlp (del), gene_mode.hlp (del), gene_options.hlp (del), gene_pseudo.hlp (del), gene_search.hlp (del), gene_species.hlp (del), gene_species_field_transfer.hlp (del), gene_species_mark.hlp (del), genes.hlp (del), glossary.hlp (del), group_by_field.hlp (del), group_rename.hlp (del), group_search.hlp (del), group_trees.hlp (del), helix.hlp (del), helixsym.hlp (del), help.hlp (del), help.tar (del), import_test.hlp (del), importift.hlp (del), index (del), input_mask.hlp (del), input_mask_format.hlp (del), input_mask_new.hlp (del), insdel.hlp (del), insdel_sai.hlp (del), insdelchar.hlp (del), islandhopping.hlp (del), iupac-codes.hlp (del), join_species.hlp (del), keeled_groups.hlp (del), kernlin.hlp (del), macro.hlp (del), man_arb_edit4.hlp (del), manage_test.hlp (del), manual.hlp (del), mark.hlp (del), mark_configs.hlp (del), mark_duplicates.hlp (del), mark_genes.hlp (del), mark_list.hlp (del), mark_long_branches.hlp (del), markbyref.hlp (del), markcolor.hlp (del), matrix_settings.hlp (del), max_freq.hlp (del), merge_species.hlp (del), mergetaggedfield.hlp (del), mg_alignment.hlp (del), mg_configs.hlp (del), mg_extendeds.hlp (del), mg_names.hlp (del), mg_preserve.hlp (del), mg_spec_sel_field.hlp (del), mg_species.hlp (del), mg_species_configs.hlp (del), mg_trees.hlp (del), mg_xfer_field_of_listed.hlp (del), mg_xfer_field_of_sel.hlp (del), missbase.hlp (del), mod_field_list.hlp (del), mode.hlp (del), mode_angle.hlp (del), mode_group.hlp (del), mode_info.hlp (del), mode_kernlin.hlp (del), mode_length.hlp (del), mode_lzoom.hlp (del), mode_mark.hlp (del), mode_move.hlp (del), mode_nni.hlp (del), mode_optimize.hlp (del), mode_pzoom.hlp (del), mode_reset.hlp (del), mode_rotate.hlp (del), mode_select.hlp (del), mode_set_root.hlp (del), mode_setroot.hlp (del), mode_spread.hlp (del), mode_swap.hlp (del), mode_width.hlp (del), mode_www.hlp (del), move_groups.hlp (del), mp_params.hlp (del), multifurcate.hlp (del), multiprobe.hlp (del), multiproberesults.hlp (del), namesadmin.hlp (del), ne_align_seq.hlp (del), ne_compl.hlp (del), ne_copy_sequence.hlp (del), ne_new_sequence.hlp (del), ne_pretty.hlp (del), ne_replace.hlp (del), ne_search.hlp (del), nekey_map.hlp (del), neprops.hlp (del), neprops_data.hlp (del), newwindow.hlp (del), next_neighbours.hlp (del), next_neighbours_common.hlp (del), next_neighbours_listed.hlp (del), nni.hlp (del), no_tree.hlp (del), nt_align_select.hlp (del), nt_keys.hlp (del), nt_props_data.hlp (del), nt_tree_marker_settings.hlp (del), nt_tree_select.hlp (del), nt_tree_settings.hlp (del), nt_tree_settings_bootstrap.hlp (del), nt_tree_settings_expert.hlp (del), optimize.hlp (del), organism_mark.hlp (del), organisms.hlp (del), pa_add.hlp (del), pa_add_sel.hlp (del), pa_bootstrap.hlp (del), pa_branchlengths.hlp (del), pa_globopti.hlp (del), pa_kernlin.hlp (del), pa_locopti.hlp (del), pa_mixtree.hlp (del), pa_optimizer.hlp (del), pa_partial.hlp (del), pa_quick.hlp (del), pa_quick_sel.hlp (del), pa_ranchlengths.hlp (del), pa_reset.hlp (del), pa_value.hlp (del), pars.hlp (del), parser.hlp (del), partial_sequences.hlp (del), pd_match_iupac.hlp (del), pd_spec_param.hlp (del), pfold.hlp (del), pfold_props.hlp (del), pfold_sai.hlp (del), ph_export_markerline.hlp (del), phyl.hlp (del), phylo.hlp (del), pm_spec_param.hlp (del), pos_var_pars.hlp (del), pos_variability.ps.gz (del), primer.hlp (del), primer_new.hlp (del), primer_parameters.hlp (del), primer_result.hlp (del), probe_param.hlp (del), probeadmin.hlp (del), probedesign.hlp (del), probedesignresult.hlp (del), probematch.hlp (del), probespec.hlp (del), prop_configs.hlp (del), prop_configs_edit.hlp (del), props_frame.hlp (del), props_nds.hlp (del), props_www.hlp (del), proteinViewer.hlp (del), pt_server.hlp (del), questions.hlp (del), quit.hlp (del), rdp_ift.hlp (del), realign_dna.hlp (del), reg.hlp (del), regexpr.hlp (del), registration.hlp (del), rename.hlp (del), rerepair.hlp (del), reset_win_layout.hlp (del), resortbyother.hlp (del), resorttree.hlp (del), result.hlp (del), rl_dna_prot.hlp (del), rna3d_changeMolecule.hlp (del), rna3d_dispBases.hlp (del), rna3d_dispHelices.hlp (del), rna3d_dispMolecule.hlp (del), rna3d_general.hlp (del), rna3d_manual.pdf (del), rna3d_manual.pdf.gz (del), rna3d_manual.ps.gz (del), rna3d_mapSeqData.hlp (del), rst_log_zoom.hlp (del), rst_phys_zoom.hlp (del), saiProbe.hlp (del), saiProbeHelp.hlp (del), saicalc.hlp (del), save.hlp (del), save_def.hlp (del), save_matrix.hlp (del), saveas.hlp (del), savedef.hlp (del), scandb.hlp (del), search_duplicates.hlp (del), search_equal_fields.hlp (del), searching.hlp (del), sec_bonddef.hlp (del), sec_display.hlp (del), sec_imexport.hlp (del), sec_keys.hlp (del), sec_main.hlp (del), sec_mode.hlp (del), sec_props.hlp (del), secedit_imexport.hlp (del), security.hlp (del), sel_box.hlp (del), sel_fil.hlp (del), sel_spec.hlp (del), selected.hlp (del), selected_gene.hlp (del), seq_quality.hlp (del), sequence_colors.hlp (del), set_color_of_listed.hlp (del), set_meny_fields.hlp (del), set_protection.hlp (del), set_reference.hlp (del), sina_main.hlp (del), sp_IDs.hlp (del), sp_count_mrk.hlp (del), sp_del_mrkd.hlp (del), sp_info.hlp (del), sp_info_locked.hlp (del), sp_invert_mrk.hlp (del), sp_mark.hlp (del), sp_mrk_all.hlp (del), sp_mrk_tree.hlp (del), sp_rename.hlp (del), sp_search.hlp (del), sp_sort_fld.hlp (del), sp_sort_phyl.hlp (del), sp_sp_2_ext.hlp (del), sp_umrk_all.hlp (del), sp_umrk_tree.hlp (del), spa_copy.hlp (del), spa_create.hlp (del), spa_delete.hlp (del), spa_rename.hlp (del), spaf_convert.hlp (del), spaf_create.hlp (del), spaf_delete.hlp (del), spaf_reorder.hlp (del), spaf_scandb.hlp (del), species.hlp (del), species_configs.hlp (del), species_configs_highlight.hlp (del), species_configs_saveload.hlp (del), species_info.hlp (del), species_join.hlp (del), srt.hlp (del), st_ml.hlp (del), submission.hlp (del), sv_def.hlp (del), sync_colors.hlp (del), syncroots.hlp (del), syncscroll.hlp (del), tags.hlp (del), tbl_boot2len.hlp (del), tbl_justify.hlp (del), tbl_reset.hlp (del), tbl_scale.hlp (del), ted_boot.hlp (del), tgroupall.hlp (del), tgroupcolor.hlp (del), tgroupnmrkd.hlp (del), tkeep_mrkd.hlp (del), toggle_secinfo.hlp (del), topology_shader.hlp (del), tr_export.hlp (del), tr_import.hlp (del), tr_jump.hlp (del), tr_type_irs.hlp (del), tr_type_list.hlp (del), tr_type_nds.hlp (del), tr_type_radial.hlp (del), track_ali_changes.hlp (del), trans_anal.hlp (del), transl_table.hlp (del), translate_dna_2_pro.hlp (del), tree2file.hlp (del), tree2prt.hlp (del), tree_cmp.hlp (del), tree_diff.hlp (del), tree_group.hlp (del), tree_pseudo.hlp (del), tree_shading.hlp (del), treeadm.hlp (del), trees.hlp (del), trm_boot.hlp (del), trm_del.hlp (del), trm_mrkd.hlp (del), tungroupall.hlp (del), undo.hlp (del), unittest.hlp (del), universal_ift.hlp (del), unmark_list.hlp (del), user_matrix.hlp (del), version.hlp (del), viewdiff.hlp (del), visualizeSAI.hlp (del), vn_delete.hlp (del), vn_delete.hlp~ (del), vn_import.hlp (del), vn_import.hlp~ (del), vn_search.hlp (del), vn_search.hlp~ (del), vn_suggest.hlp (del), vn_suggest.hlp~ (del), write_field_list.hlp (del), xferset.hlp (del), xterm.hlp (del)

westram 2021-10-08 15:16 Rev.: 18762

* update documentation:
- reference most important SAI information from main SAI doc.
- add backlinks.

38 lines of code changed in 7 files:

• HELP_SOURCE/oldhelp: accessibility_sai.hlp (+1), e4_modsai.hlp (+1), extended.hlp (+32 -13), helix.hlp (+1), saiProbe.hlp (+1 -1), saicalc.hlp (+1), visualizeSAI.hlp (+1)

westram 2021-10-08 15:14 Rev.: 18761

* update documentation:
- link between accessibilty SAIs and SAI visualizers.
- shorten help titles (did not differ in first 38 characters (=part which is visible in help SUBTOPICS).
- uncapitalize + correct menu names etc.
- link from SAI visualizers to Probetools and editors.

46 lines of code changed in 5 files:

• HELP_SOURCE/oldhelp: accessibility_sai.hlp (+1), displayField.hlp (+1 -2), e4.hlp (+1), saiProbe.hlp (+12 -12), visualizeSAI.hlp (+31 -23)

westram 2021-10-08 15:07 Rev.: 18760

* change layout of 'Color Translation Table' properties window (make space for HELP button).
* add help button (fixes #326)
* change documentation of 'Define Color Translations'.

6 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: saiProbe.hlp (+6 -5)

westram 2021-10-06 09:46 Rev.: 18753

* list some useful character classes.
* show usage in double-brackets.
* {{{[:word:]}}} is not known in arb -> removed.

12 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: reg.hlp (+12 -2)

westram 2021-09-22 14:08 Rev.: 18742

* use terminal background color (=default, marked or colorized) also if SAI-translation isnt defined for a position.

3 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: e4_background_priority.hlp (+1 -1), visualizeSAI.hlp (+2 -2)

westram 2021-09-08 15:41 Rev.: 18713

* cleanup some helpfiles

3 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: ed4_nds.hlp (+1 -1), helixsym.hlp (+2 -5), pfold_props.hlp (-4)

westram 2021-09-08 15:38 Rev.: 18712

* delete obsolete help file (phyl.hlp)
- superseeded by dist.hlp and phylo.hlp.
- eliminate leftover links.

2 lines of code changed in 7 files:

• HELP_SOURCE/oldhelp: nt_tree_select.hlp (-1), pars.hlp (-1), sp_sort_phyl.hlp (+2 -2), tr_type_irs.hlp (-1), tr_type_list.hlp (-1), tr_type_nds.hlp (-1), tr_type_radial.hlp (-1)

westram 2021-09-08 15:35 Rev.: 18711

* translated help for sequencing primers (still very, very basic..).

17 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: primer.hlp (+17 -12)

westram 2021-09-08 15:28 Rev.: 18709

* insert homebrew url as {{{LINK}}}.

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_envar.hlp (+1 -1)

westram 2021-09-08 08:18 Rev.: 18707

* link to OSX-specific info on homebrew github.

3 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_envar.hlp (+3)

westram 2021-09-02 08:46 Rev.: 18697

* full update from child 'stable' into 'trunk'
- merge changes done to arb-7.0 release candidate
* adds: log:branches/stable@18690:18695

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_intro.hlp (+1 -1)

westram 2021-08-26 16:55 Rev.: 18686

* change references to (never released) arb-6.1 -> arb-7.0

4 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: keeled_groups.hlp (+2 -2), pa_optimizer.hlp (+1 -1), pa_quick.hlp (+1 -1)

westram 2021-07-08 13:12 Rev.: 18662

* add toggle to 'MODIFY DATABASE FIELD of listed ...' permitting to change the 'name' field.

10 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: mod_field_list.hlp (+10 -4)

westram 2021-06-25 15:01 Rev.: 18659

* update environment variable documentation (most changes OSX-specific). thx 2 Jan.

21 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_envar.hlp (+21 -3)

westram 2021-05-26 16:01 Rev.: 18652

* fix nameserver admin layout:
- status field now colored and resizeable
- change title
* change term 'name server' -> 'nameserver'.

3 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: namesadmin.hlp (+2 -2), sp_IDs.hlp (+1 -1)

westram 2021-05-26 15:50 Rev.: 18651

* add 'configure' button to 'synchronize ids'
- refactored AW_create_namesadmin_window -> AW_popup_namesadmin_window.
- document

4 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: rename.hlp (+4 -1)

westram 2021-05-26 11:53 Rev.: 18649

* link help (namesadmin -> merge check ids)

2 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: mg_names.hlp (+1 -1), namesadmin.hlp (+1 -1)

westram 2021-02-18 16:33 Rev.: 18643

* allow to 'edit bootstraps'
- document example.
- when a replacement results in an empty string => remove remark.

27 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: ted_boot.hlp (new 26), trm_boot.hlp (+1)

westram 2021-02-18 16:30 Rev.: 18642

* tweak replacement via regular expressions:
- allow replacement of whole line regexpr which matches empty source string.
- test to replace whole string by nothing.
- always fail BOL/EOL operator starting from second replace-operation. fixes some failing replacements.
* doc: describe other simpler, now working replacements.

7 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: reg.hlp (+7)

westram 2021-01-12 13:02 Rev.: 18639

* document accessibility SAIs as used in SILVA databases.
- link from related help.

77 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: accessibility_sai.hlp (new 71), saiProbe.hlp (+2 -1), visualizeSAI.hlp (+4 -4)

westram 2020-12-14 17:22 Rev.: 18637

* hide bootstrap values at zero-length branches.
- correct expected test results.
- document when bootstraps will be hidden automatically.

8 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: nt_tree_settings_bootstrap.hlp (+8 -1)

westram 2020-11-10 16:24 Rev.: 18634

* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633

56 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: keeled_groups.hlp (+1), mode_setroot.hlp (+1 -1), syncroots.hlp (new 54)

westram 2020-10-06 10:26 Rev.: 18602

* advice howto mark first occurrences (of found duplicates)

3 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: search_duplicates.hlp (+3)

westram 2020-09-23 12:46 Rev.: 18480

* mention problems with 'Space padded'-column-style in documentation.

8 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_export_nds.hlp (+8 -3)

westram 2020-09-04 09:31 Rev.: 18473

* support genebank entry "DBLINK"
- store in arb field 'db_xref'.

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: sp_info.hlp (+1 -1)

westram 2020-05-14 18:21 Rev.: 18463

* reintegrates 'top' into 'trunk'
* adds: log:branches/top@18453:18462

10 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: ad_extended.hlp (+5 -2), e4.hlp (+3), species_configs_saveload.hlp (+2 -1)

westram 2020-04-28 09:42 Rev.: 18446

* document key bindings for paging.
* show howto handle undefined result from remote_read_awar.

10 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: e4.hlp (+9), macro.hlp (+1)

westram 2020-03-04 10:08 Rev.: 18359

* add new FTS transfer mode to merge-tool (implements #825)
- allows to skip transport of sequence alignment data (i.e. allows plain metadata updates)
* update+fix documentation

27 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: mg_species.hlp (+27 -19)

westram 2020-02-21 13:07 Rev.: 18311

* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310

229 lines of code changed in 8 files:

• HELP_SOURCE/oldhelp: aci.hlp (+5 -1), ad_extended.hlp (+11 -1), e4_block.hlp (+17 -9), e4_get_species.hlp (+1 -1), e4_modsai.hlp (+11 -4), e4_replace.hlp (+4 -4), phyl.hlp (+5), saicalc.hlp (new 175)

westram 2019-12-30 11:55 Rev.: 18259

- document the scope upon which ARB_PHYLO will operate.

6 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: phylo.hlp (+6)

westram 2019-11-25 15:19 Rev.: 18222

* typo in documentation
* improve CLI help for arb_probe_match

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: pm_spec_param.hlp (+1 -1)

westram 2019-10-28 17:23 Rev.: 18186

* reintegrates 'fts' into 'trunk'
* adds: log:branches/fts@18177:18185

13 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: mg_species.hlp (+13 -1)

westram 2019-10-16 17:20 Rev.: 18176

* update outdated information in 'Synchronize IDs' window.
* some updates to related documentation.

9 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: rename.hlp (+2 -2), sp_IDs.hlp (+7 -3)

westram 2019-10-07 15:40 Rev.: 18149

* document howto "transport" IDs stored in fields to a new nameserver.

10 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: next_neighbours_listed.hlp (+10 -1)

westram 2019-10-07 13:56 Rev.: 18147

* add new ACI commands {{{findspec}}}, {{{findacc}}} + {{{findgene}}}
- allow to find species and genes by name (and species by acc)
- add tests (not for findgene)
- document

18 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: aci.hlp (+18)

westram 2019-09-17 14:46 Rev.: 18092

* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090

199 lines of code changed in 8 files:

• HELP_SOURCE/oldhelp: arb_export.hlp (+28 -10), arb_export_nds.hlp (+1 -1), arb_import.hlp (+7 -2), export_format.hlp (+1 -1), mg_species.hlp (+37 -14), mg_xfer_field_of_listed.hlp (+1 -1), mg_xfer_field_of_sel.hlp (+1 -1), xferset.hlp (new 123)

westram 2019-04-04 15:47 Rev.: 17742

* fix unnecessary typos.

2 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: arb_merge_workflow.hlp (+1 -1), consense_algo.hlp (+1 -1)

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)

(426 more)