* fix {{{ARB_edge::iteration_count()}}}:
- did report ''negative'' counts for broken trees (see previous commit)
- added tests; fixed behavior: now returns zero in these cases.
* accept zero as increment amount to {{{arb_progress::inc_by()}}}.
14 lines of code changed in 4 files:
* warn when invalid trees exist (e.g. relicts from old bug, caused by deleting all species).
6 lines of code changed in 1 file:
* fixes display of 'no tree' message:
- adds 2nd horizontal line.
- adds space between line(s) and text.
* the above changes somehow fixed the display in dendrogram and IRS mode
- assumption is, the bug was caused by zero X-size.
13 lines of code changed in 1 file:
* update documentation of SEQ_QUALITY:
- non-evaluated fields
- usage of default helix base pairings.
0 lines of code changed in 2 files:
* automatically add changekeys for keys generated by calculating sequence quality.
- add 'evaluation' (=result) as last field.
53 lines of code changed in 1 file:
* mostly cosmetic changes to SEQ_QUALITY:
- compact else-if cascades.
* avoid using {{{abs()}}} repeatedly in cascades
- unwrap lines.
- use {{{GB_end_transaction}}}.
- whitespace fixes.
106 lines of code changed in 8 files:
* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406
468 lines of code changed in 22 files:
* 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
190 lines of code changed in 18 files:
* fix build w/o unittests
2 lines of code changed in 1 file:
* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375
316 lines of code changed in 8 files:
May 2023 »