Directory EDIT4/

Directory Created:
2000-11-23 11:41
Total Files:
52
Deleted Files:
13
Lines of Code:
28725

[root]/EDIT4

Lines of Code

EDIT4/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 2545 (100.0%) 74888 (100.0%) 29.4
westram 2292 (90.1%) 42459 (56.7%) 18.5
oldcode 31 (1.2%) 22406 (29.9%) 722.7
yadhu 158 (6.2%) 5944 (7.9%) 37.6
murban 23 (0.9%) 2127 (2.8%) 92.4
urban 4 (0.2%) 1160 (1.5%) 290.0
meierh 2 (0.1%) 521 (0.7%) 260.5
epruesse 18 (0.7%) 179 (0.2%) 9.9
jobb 3 (0.1%) 49 (0.1%) 16.3
baderk 5 (0.2%) 22 (0.0%) 4.4
boehnel 7 (0.3%) 20 (0.0%) 2.8
foerster 1 (0.0%) 1 (0.0%) 1.0
artemov 1 (0.0%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-04-05 19:32 Rev.: 17748


* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

  • EDIT4: ED4_no_class.cxx (+1 -1)
westram 2019-04-01 17:41 Rev.: 17724


* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

12 lines of code changed in 1 file:

  • EDIT4: Makefile (+12)
westram 2019-03-07 18:30 Rev.: 17651


* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@17627:17650

4 lines of code changed in 1 file:

  • EDIT4: ed4_visualizeSAI.hxx (+4 -4)
westram 2018-10-31 10:52 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

11 lines of code changed in 2 files:

  • EDIT4: ED4_ProteinViewer.cxx (+10 -18), Makefile (+1)
westram 2018-10-24 15:58 Rev.: 17534


* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

11 lines of code changed in 5 files:

  • EDIT4: ED4_main.cxx (+1 -1), ED4_search.cxx (+5 -4), ED4_seq_colors.cxx (+2 -1), Makefile (+2), ed4_edit_string.hxx (+1 -1)
westram 2018-10-23 10:36 Rev.: 17510


* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]

2 lines of code changed in 1 file:

  • EDIT4: ED4_ProteinViewer.cxx (+2 -2)
westram 2018-10-04 15:17 Rev.: 17445


* use {{{SmartPtr::content()}}}

1 lines of code changed in 1 file:

  • EDIT4: ED4_root.cxx (+1 -1)
westram 2018-09-20 18:43 Rev.: 17396


* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

7 lines of code changed in 2 files:

  • EDIT4: ED4_cursor.cxx (+7 -7), ed4_class.hxx (-2)
westram 2018-09-12 10:54 Rev.: 17361


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

1 lines of code changed in 1 file:

  • EDIT4: ED4_naligner.cxx (+1)
westram 2018-07-23 16:52 Rev.: 17262


* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

3 lines of code changed in 2 files:

  • EDIT4: ED4_cursor.cxx (+2 -2), ED4_no_class.cxx (+1 -1)
westram 2018-05-02 11:32 Rev.: 16961


* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960

68 lines of code changed in 6 files:

  • EDIT4: ED4_cursor.cxx (+1 -1), ED4_flags.cxx (+2 -2), ED4_terminal.cxx (+4 -4), ED4_text_terminals.cxx (+33 -48), EDB_root_bact.cxx (+1 -1), Makefile (+27)
westram 2018-04-30 18:27 Rev.: 16936


* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

5 lines of code changed in 3 files:

  • EDIT4: ED4_root.cxx (+3 -16), ed4_class.hxx (+2 -7), ed4_defs.hxx (-4)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

212 lines of code changed in 20 files:

  • EDIT4: ED4_ProteinViewer.cxx (+40 -45), ED4_base.cxx (+25 -50), ED4_container.cxx (+11 -13), ED4_cursor.cxx (+10 -18), ED4_edit_string.cxx (+8 -16), ED4_main.cxx (+1 -2), ED4_manager.cxx (+17 -22), ED4_naligner.cxx (+3 -3), ED4_nds.cxx (+2 -3), ED4_no_class.cxx (+3 -4), ED4_protein_2nd_structure.cxx (+1 -1), ED4_root.cxx (+15 -23), ED4_search.cxx (+33 -63), ED4_terminal.cxx (+16 -29), ED4_text_terminals.cxx (+4 -5), ED4_visualizeSAI.cxx (+1 -1), ED4_window.cxx (+13 -16), EDB_root_bact.cxx (+2 -4), ed4_defs.hxx (+5 -10), ed4_search.hxx (+2 -4)
westram 2017-11-28 18:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

585 lines of code changed in 32 files:

  • EDIT4: ED4_ProteinViewer.cxx (+12 -12), ED4_base.cxx (+33 -33), ED4_block.cxx (+35 -35), ED4_colStat.cxx (+4 -4), ED4_consensus.cxx (+3 -3), ED4_container.cxx (+6 -6), ED4_cursor.cxx (+28 -28), ED4_dots.cxx (+7 -7), ED4_dump.cxx (+2 -2), ED4_edit_string.cxx (+35 -36), ED4_flags.cxx (+12 -12), ED4_main.cxx (+13 -13), ED4_manager.cxx (+30 -30), ED4_nds.cxx (+4 -4), ED4_no_class.cxx (+55 -55), ED4_objspec.cxx (+1 -1), ED4_plugins.cxx (+8 -8), ED4_protein_2nd_structure.cxx (+17 -17), ED4_root.cxx (+89 -89), ED4_search.cxx (+51 -51), ED4_seq_colors.cxx (+11 -11), ED4_terminal.cxx (+30 -30), ED4_text_terminals.cxx (+8 -8), ED4_visualizeSAI.cxx (+14 -14), ED4_window.cxx (+3 -3), EDB_root_bact.cxx (+7 -7), ed4_block.hxx (+1 -1), ed4_class.hxx (+38 -38), ed4_flags.hxx (+1 -1), ed4_list.hxx (+6 -6), ed4_protein_2nd_structure.hxx (+1 -1), graph_aligner_gui.cxx (+20 -20)
westram 2017-11-19 16:19 Rev.: 16683


* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

17 lines of code changed in 2 files:

  • EDIT4: ED4_main.cxx (+16 -14), ED4_manager.cxx (+1 -1)
westram 2017-11-17 13:54 Rev.: 16668


* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

13 lines of code changed in 1 file:

  • EDIT4: ED4_edit_string.cxx (+13 -13)
westram 2017-10-08 15:54 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

49 lines of code changed in 2 files:

  • EDIT4: ED4_visualizeSAI.cxx (+48 -90), Makefile (+1)
westram 2017-09-23 14:03 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

2 lines of code changed in 1 file:

  • EDIT4: Makefile (+2)
westram 2017-09-18 15:23 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

20 lines of code changed in 3 files:

  • EDIT4: ED4_block.cxx (+12 -10), ED4_nds.cxx (+6 -4), Makefile (+2)
westram 2017-07-08 11:55 Rev.: 16112


* reintegrates 'fix' into 'trunk'
- fixes #267
- adds new default color translation table 'PVP'
* adds: log:branches/fix@16107:16111

14 lines of code changed in 1 file:

  • EDIT4: ED4_visualizeSAI.cxx (+14 -19)
westram 2017-05-29 11:15 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

16 lines of code changed in 1 file:

  • EDIT4: ED4_root.cxx (+16 -16)
westram 2017-04-05 11:06 Rev.: 15738


* rename only

1 lines of code changed in 1 file:

  • EDIT4: ED4_root.cxx (+1 -1)
westram 2017-03-31 14:13 Rev.: 15715


* fix click on species flags
- did not work when display was scrolled vertically

1 lines of code changed in 1 file:

  • EDIT4: ED4_terminal.cxx (+1 -1)
westram 2017-01-09 16:10 Rev.: 15529


* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

1 lines of code changed in 1 file:

  • EDIT4: ed4_class.hxx (+1 -1)
westram 2017-01-04 18:06 Rev.: 15513


* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

36 lines of code changed in 4 files:

  • EDIT4: ED4_base.cxx (-6), ED4_manager.cxx (+3 -3), ED4_terminal.cxx (-14), ed4_class.hxx (+33 -27)
westram 2017-01-04 11:51 Rev.: 15506


* partial merge from 'warnings' into 'trunk'
- remove some useless virtuality (mostly functions only usable with ED4_manager)
- other design fixes (get_parent returns ED4_manager, ...)
* adds: log:branches/warnings@15502:15505

44 lines of code changed in 7 files:

  • EDIT4: ED4_base.cxx (+6 -26), ED4_colStat.cxx (+1 -1), ED4_cursor.cxx (+1 -1), ED4_manager.cxx (+12 -23), ED4_no_class.cxx (+2 -2), ED4_terminal.cxx (+1 -33), ed4_class.hxx (+21 -25)
westram 2016-12-17 13:12 Rev.: 15425


* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424

1 lines of code changed in 1 file:

  • EDIT4: EDB_root_bact.cxx (+1 -1)
westram 2016-10-19 13:04 Rev.: 15346


* remove outdated link

1 lines of code changed in 1 file:

  • EDIT4: graph_aligner_gui.cxx (+1 -2)
westram 2016-10-02 15:02 Rev.: 15290


* add some predefined settings for editor flags

9 lines of code changed in 1 file:

  • EDIT4: ED4_flags.cxx (+9 -1)
westram 2016-09-30 16:16 Rev.: 15288


* reintegrates 'flags' into 'trunk'
- implements #261
* adds: log:branches/flags@15225:15230,15232:15238,15240:15241,15243:15246,15248,15250:15287

825 lines of code changed in 17 files:

  • EDIT4: ED4_base.cxx (+9), ED4_dump.cxx (+2), ED4_flags.cxx (new 266), ED4_main.cxx (+2 -1), ED4_manager.cxx (+13 -16), ED4_no_class.cxx (+27 -3), ED4_root.cxx (+32 -19), ED4_seq_colors.cxx (+6 -1), ED4_terminal.cxx (+172 -82), ED4_text_terminals.cxx (+28 -40), ED4_window.cxx (+1 -1), EDB_root_bact.cxx (+7), Makefile (+54), ed4_class.hxx (+62 -25), ed4_defs.hxx (+3), ed4_extern.hxx (+11 -9), ed4_flags.hxx (new 130)
westram 2016-09-27 16:23 Rev.: 15279


* reintegrates 'errhandle' into 'trunk'
* adds: log:branches/errhandle@15275:15278

3 lines of code changed in 1 file:

  • EDIT4: ED4_no_class.cxx (+3 -4)
westram 2016-09-24 08:08 Rev.: 15268


* {{{GB_xcmd}}}
- remove from perl interface
- replace bool-flag-couple by enum
- guard unused case {{{XCMD_SYNC_WAITKEY}}}

1 lines of code changed in 1 file:

  • EDIT4: graph_aligner_gui.cxx (+1 -1)
westram 2016-09-23 08:53 Rev.: 15265


* document used references from display-elements to database-entries

12 lines of code changed in 1 file:

  • EDIT4: ed4_class.hxx (+12)
westram 2016-09-23 08:25 Rev.: 15264


* {{{EDB_root_bact::search_sequence_data_rek}}} now always called with alignment-container (or one of its subcontainers)
* rename some variables

26 lines of code changed in 3 files:

  • EDIT4: EDB_root_bact.cxx (+24 -33), ed4_class.hxx (+2 -3), ed4_defs.hxx (-5)
westram 2016-08-30 14:26 Rev.: 15256


* replace redundant data {{{AW_font_limits::height}}} with {{{get_height()}}}

1 lines of code changed in 1 file:

  • EDIT4: ED4_no_class.cxx (+1 -1)
westram 2016-08-30 12:30 Rev.: 15254


* depends for [15253]

26 lines of code changed in 1 file:

  • EDIT4: Makefile (+26)
westram 2016-08-24 12:42 Rev.: 15230


* remove undocumented feature (build IUPAC string from block selected in detailed column stat and write it to probe-match IUPAC input)
- code was unstable
- if multiple detailed column stat terminals were visible/selected, awar was modified multiple times
- more or less just a hack (should be implemented differently, e.g. optionally sync probe-match-target with single selected block)

5 lines of code changed in 4 files:

  • EDIT4: ED4_block.cxx (+5 -20), ED4_main.cxx (-2), ED4_terminal.cxx (-35), ed4_class.hxx (-2)
westram 2016-08-22 15:34 Rev.: 15223


* reintegrates 'flags' into 'trunk'
- DRYed
* group generation code
* ref-terminal access
- layout done by managers (removed manual coordinate calculation)
- dynamic size calculated by terminals themselves
- fix design issues
* brackets were used where groups should have been used. fixed
* fix many bad/spammy names
- fix broken member-code (only worked with a NULL sentinel present)
- dynamic indentation (according to visible group-nesting)
* adds: log:branches/flags@15098:15222

1803 lines of code changed in 28 files:

  • EDIT4: ED4_ProteinViewer.cxx (+37 -38), ED4_base.cxx (+242 -251), ED4_colStat.cxx (+23 -22), ED4_consensus.cxx (+4 -7), ED4_container.cxx (new 377), ED4_cursor.cxx (+32 -46), ED4_dots.cxx (+1 -1), ED4_dump.cxx (+15 -11), ED4_edit_string.cxx (+5 -7), ED4_main.cxx (+8 -8), ED4_manager.cxx (+263 -308), ED4_members.cxx (del), ED4_nds.cxx (+6 -12), ED4_no_class.cxx (+138 -79), ED4_objspec.cxx (+31 -31), ED4_plugins.cxx (+1 -1), ED4_root.cxx (+88 -98), ED4_search.cxx (+1 -1), ED4_seq_colors.cxx (+6 -6), ED4_terminal.cxx (+139 -121), ED4_text_terminals.cxx (+5 -5), ED4_window.cxx (+4 -5), EDB_root_bact.cxx (+90 -246), Makefile (+38 -38), ed4_awars.hxx (-1), ed4_class.hxx (+186 -160), ed4_defs.hxx (+62 -50), ed4_nds.hxx (+1 -1)
westram 2016-08-17 20:39 Rev.: 15198


* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

79 lines of code changed in 2 files:

  • EDIT4: ED4_plugins.cxx (+1 -1), ed4_class.hxx (+78 -78)
westram 2016-08-11 11:05 Rev.: 15176


* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

170 lines of code changed in 20 files:

  • EDIT4: ED4_base.cxx (+2 -2), ED4_block.cxx (+13 -9), ED4_cursor.cxx (+3 -7), ED4_dots.cxx (+1 -1), ED4_edit_string.cxx (+4 -5), ED4_main.cxx (+14 -18), ED4_members.cxx (+21 -56), ED4_no_class.cxx (+7 -7), ED4_plugins.cxx (+2 -2), ED4_protein_2nd_structure.cxx (+17 -17), ED4_root.cxx (+2 -2), ED4_search.cxx (+27 -39), ED4_seq_colors.cxx (+2 -2), ED4_terminal.cxx (+3 -3), ED4_text_terminals.cxx (+7 -11), ED4_visualizeSAI.cxx (+11 -15), EDB_root_bact.cxx (+3 -4), Makefile (+24), ed4_class.hxx (+7 -7), ed4_defs.hxx (-1)

(865 more)

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