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Package-private fields #327

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Anaphory opened this issue Apr 24, 2015 · 1 comment
Open

Package-private fields #327

Anaphory opened this issue Apr 24, 2015 · 1 comment
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@Anaphory
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What is the reason that there are quite a few package-private (i.e. not marked as “private”, “protected” or “public”) fields in Beast2 classes?

I am now looking into writing a data type with appropriate substitution model, but all of DataType.Base.stateCount, .mapCodeToStateSet, … are package-private. Is there a good reason that they are, and I should leave them like that? Or is this just because “protected” is more to type than “ ”, and is has not come up yet, so can I change them to beprotected (with a pull request here etc.) without it leading to any problems?
rbouckaert added a commit that referenced this issue May 3, 2015
@rbouckaert
issue #327 make fields in DataType.Bare protected
39a2ba4
@rbouckaert
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Please feel free to create pull requests, or simply list fields you want to have access to. I made all DataType.Bare field protected.

@Anaphory Anaphory mentioned this issue May 7, 2015
Merged
tgvaughan added a commit that referenced this issue May 8, 2015
@tgvaughan
Merge pull request #336 from Anaphory/master
5d78a80 
Make package-private properties of substitutionmodels protected instead, as per #327
rbouckaert added a commit that referenced this issue May 26, 2015
@rbouckaert
issue #327 make fields protected instead of package private
9981e8b
rbouckaert added a commit that referenced this issue Aug 16, 2015
@rbouckaert
issue #327 access to Tree.postCache
b3ecc6f
rbouckaert added a commit that referenced this issue Jun 20, 2016
@rbouckaert
make BeautiSubTemplate.removeSubnet public #327
637c443
rbouckaert added a commit that referenced this issue Mar 7, 2017
@rbouckaert
make TreeSet and friends in TreeAnnotator public for use in package a…
fb43454 
…pps. #327
tgvaughan pushed a commit to tgvaughan/beast2 that referenced this issue Mar 22, 2017
@rbouckaert @tgvaughan
make TreeSet and friends in TreeAnnotator public for use in package a…
b212e2c 
…pps. CompEvol#327
@rbouckaert rbouckaert mentioned this issue May 10, 2017
Closed
walterxie added a commit that referenced this issue Oct 10, 2017
@walterxie
issue #327 change Alignment usingTipLikelihoods to protected
c9ac577
walterxie added a commit that referenced this issue Oct 30, 2017
@walterxie
#327 Frequencies update() and needsUpdate to protected
7e672ce
@walterxie walterxie mentioned this issue Apr 4, 2018
Closed
walterxie added a commit that referenced this issue Jun 21, 2018
@walterxie
make TraitSet members accessible to subclasses #327
5c1f7a2
rbouckaert added a commit that referenced this issue Jan 28, 2019
@rbouckaert
relax access to Logger, MCMC #327
f5ac20d
rbouckaert added a commit that referenced this issue Jun 4, 2019
@rbouckaert
access issues for packages #327
ec1ecec
rbouckaert added a commit that referenced this issue Jun 10, 2019
@rbouckaert
comment BEASTClassLoader #834 and access PackageManager #327
bacd951
rbouckaert added a commit that referenced this issue Aug 7, 2019
@rbouckaert
make Frequencies.estimateFrequencies() protected #327 found during re…
8e5bad2 
…lease testing #869
rbouckaert added a commit that referenced this issue Aug 7, 2019
@rbouckaert
make SiteModel members protected #327 found to be problematic during …
91592f6 
…release testing #869
jordandouglas added a commit that referenced this issue Nov 18, 2019
@jordandouglas
Logger getFileName() method #327
6c87d8d
NicoNeureiter added a commit to NicoNeureiter/beast2 that referenced this issue Apr 23, 2020
@NicoNeureiter
make Node members protected CompEvol#327
6d585a8
rbouckaert added a commit that referenced this issue Apr 23, 2020
@rbouckaert
Merge pull request #897 from NicoNeureiter/master
69dd9b6 
make Node members protected #327
rbouckaert added a commit that referenced this issue Aug 5, 2020
@rbouckaert
tree likelihood access #327 to facilitate modularisation #834
28bc01a
rbouckaert added a commit that referenced this issue Aug 9, 2020
@rbouckaert
getter/setter access #327 to facilitate modularisation #834
a0bde23
rbouckaert added a commit that referenced this issue Jul 27, 2022
@rbouckaert
make methods public in substitution model #327, fix typose #683
fbf92f9
walterxie added a commit that referenced this issue Nov 20, 2022
@walterxie
add protected to times and indices in TreeIntervals #327
6f0eeb1
walterxie added a commit that referenced this issue Dec 13, 2022
@walterxie
Make InverseGamma dist accessible #327
f26710c
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@Anaphory @rbouckaert