Directory lib/pictures/faligner/

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westram 2019-10-10 18:16 Rev.: 18168

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18159:18167

77 lines of code changed in 3 files:

• lib/pictures/faligner: faligner.fig (+38 -40), family_settings.fig (+6 -6), islandhopping.fig (+33 -41)

westram 2015-04-15 16:37 Rev.: 13725

* add config manager to integrated aligners

1 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+1)

westram 2015-04-15 14:25 Rev.: 13722

* minor layout fixes for fast-aligner window (avoids some overlapping elements in gtk)

6 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+6 -6)

westram 2012-05-02 19:21 Rev.: 8696

* merge from saiali log:branches/saiali@8635-8695
- unalign center (blockop)
- modify SAI range (using ACI/SRT)
- align ranges defined by SAI
- refactorings
* block ops
* selection lists

41 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+41 -48)

westram 2012-04-19 08:13 Rev.: 8607

merge from e4fix [8135] [8136] [8137] [8138] [8139] [8140] [8141] [8142] [8143] [8144] [8222]
(this revives the reverted patches [8129] [8130] [8131] [8132]; see [8133])

* fixes
- some free/delete mismatches
- wrong definition of ORF objects (Level was no bit value)
- amino consensus (failed for columns only containing 'C')
* rename
- AA_sequence_term -> orf_term
- ED4_sequence_terminal_basic -> ED4_abstract_sequence_terminal
* cleaned up hierarchy dumps
* tweaked is_terminal()/to_terminal()

0 lines of code changed in 3 files:

• lib/pictures/faligner: faligner.fig (changed), family_settings.fig (changed), islandhopping.fig (changed)

westram 2012-03-28 16:32 Rev.: 8535

* scaling of relative scores in 'Next neighbour search' can be configured now
- scale vs source or target POC (or min/max of both)
- added toggles to 'Search next neighbours of ...'
- added tests
* help (score/scaling)
- describe new options
- fix wrong facts

15 lines of code changed in 1 file:

• lib/pictures/faligner: family_settings.fig (+15 -16)

westram 2011-03-24 18:42 Rev.: 7316

merged from dev [7283] [7285] [7297] [7298] [7299] [7305] [7306] [7307] [7308] [7311] [7312] [7313]
* fast aligner
- relative search optionally uses only data from aligned range
- fixed 2 RUIs
- added / changed tests
* !TargetRange
- made independent from target(sequence) to which it is applied
- added copy_corresponding_part() + tests
- added is_restricted() and op == !=
* fixes a bug in next relative search (when no upper limit was given, nothing was found)
* restricts oligo counting to !TargetRange of !FakeFamilyFinder (adapt PT server bahavior)
* !CompactedSubSequence
- fixed expdLength (was wrong if last position contained a base; failed assertion when !CompactedSequence did not contain bases - case seems not to occur during alignment)
- added tests for expdPosition() and compPosition() (documenting new behavior)
- test !CompactedSubSequence to be self-reflexive
- fixed bug in binary search (had no effect on aligner results for examples used in unittests)
* !CompactedSequence
- deny to construct from empty sequence

36 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+36 -35)

westram 2010-08-13 17:43 Rev.: 6691

* allow failures in fast_aligner
- added 'Continue on error' toggle and action-selector to aligner window
- if checked, aligner allows single alignments to fail and continues (instead of undoing all work done)
- optionally failed or succeeded species can be marked by aligner
* no longer touch progress bar from AlignBuffer
* fixed assertions in PT_FamilyFinder

5 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+5 -8)

westram 2010-08-12 10:10 Rev.: 6688

* added unit tests for aligner (covering selection of targets and references)
- implemented a FakeFamilyFinder (to simulate search of relatives (as done by PTserver) in unit tests)
* refactored aligner() -> class Aligner ["break out method object"]
- moved selection of reference to classes derived from AlignmentReference -> selection of aligned species is no longer duplicated
* bugfixes
- when aligning to relatives and only one relative found or used, that releative was never logged to field 'used_rels'
* changed behavior
- FamilyList dtor deletes whole list
- added awar FA_AWAR_CONTINUE_ON_ERROR and new GUI element (disabled because has no effect yet)
* wrapped DEBUG prints (triggered by defines now)

34 lines of code changed in 1 file:

• lib/pictures/faligner: faligner.fig (+34 -30)

westram 2010-02-12 20:49 Rev.: 6426

- ... and filenames

154 lines of code changed in 3 files:

• lib/pictures/faligner: faligner.fig (new 59), family_settings.fig (new 27), islandhopping.fig (new 68)