May 2017 Commit Log

Number of Commits:

7

Number of Active Developers:

1

westram 2017-05-29 10:15 #7 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

47 lines of code changed in 3 files:

• EDIT4: ED4_root.cxx (+16 -16)
• HELP_SOURCE/oldhelp: e4_block.hlp (+29 -30), group_by_field.hlp (+2 -2)

westram 2017-05-24 13:26 #6 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 #5 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 #4 Rev.: 15971

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

29 lines of code changed in 4 files:

• HELP_SOURCE/oldhelp: arb_merge_workflow.hlp (+5 -2), glossary.hlp (+1 -10), selected.hlp (+22 -6), sp_search.hlp (+1 -1)

westram 2017-05-21 16:59 #3 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

1780 lines of code changed in 62 files:

• Makefile (+3), arb_CHANGES.txt (+2 -1), demo.arb (changed)
• ARBDB: adtree.cxx (+1 -1)
• AWT: awt_canvas.hxx (+2)
• GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)
• 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)
• NTREE: Makefile (+57), NT_extern.cxx (+12 -3), NT_group_search.cxx (new 1041), NT_group_search.h (new 23), needs_libs (+1)
• SL: README (+5 -1)
• SL/AP_TREE: AP_Tree.cxx (+4 -1)
• SL/CB: needs_libs (new)
• SL/DB_QUERY: db_query.cxx (+3 -4)
• SL/QUERY: query_expr.cxx (new), query_expr.h (+18 -3)
• SL/TREEDISP: TreeCallbacks.cxx (+12 -1), TreeDisplay.cxx (+9 -6)
• SOURCE_TOOLS: dep.4dummy (+2 -1), dep.alltargets (+1), dep.libtargets (+1), generate_all_links.sh (+1)
• TEMPLATES: arbtools.h (+2)
• UNIT_TESTER/run/display: dendro_CH.fig (+1 -1), dendro_CH_centered.fig (+1 -1), dendro_CH_centered_diagonal.fig (+1 -1), dendro_CH_diagonal.fig (+1 -1), dendro_CN.fig (+1 -1), dendro_CN_diagonal.fig (+1 -1), dendro_CN_shortSmall.fig (+1 -1), dendro_MH.fig (+1 -1), dendro_MH_diagonal.fig (+1 -1), dendro_MH_long.fig (+1 -1), dendro_MN.fig (+1 -1), dendro_MN_diagonal.fig (+1 -1), irs_CH.fig (+1 -1), irs_CN.fig (+1 -1), irs_MH.fig (+1 -1), irs_MN.fig (+1 -1), nds_CH.fig (+29 -29), nds_CN.fig (+29 -29), nds_MH.fig (+29 -29), nds_MN.fig (+29 -29), radial_CH.fig (+1 -1), radial_CN.fig (+1 -1), radial_MH.fig (+1 -1), radial_MN.fig (+1 -1)
• WINDOW: AW_help.cxx (+1 -1), AW_window.cxx (+4 -3), aw_window.hxx (+4 -3)
• lib/pictures: group_search.fig (new 83), group_trees.fig (new 23)

westram 2017-05-03 14:31 #2 Rev.: 15876

* reintegrates 'fix' into 'trunk'
- automatically deletes field 'group_name' at root of tree
- done while loading tree
- provides workaround for #753
* adds: log:branches/fix@15870:15875

34 lines of code changed in 5 files:

• ARBDB: TreeNode.h (+1 -2), adquery.cxx (+1 -1), adtree.cxx (+31)
• TOOLS: arb_test.cxx (+1 -1)
• UNIT_TESTER/run: TEST_nuc_seqcompr_exp.arb (changed)

westram 2017-05-03 08:47 #1 Rev.: 15869

* gcc 7.1.0
- add to list of known compilers
- refuse to compile (see #752 for details)

10 lines of code changed in 1 file:

• Makefile (+10)

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