Lines of Code
[root]/src/dr/evolution/datatype
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 110 (100.0%) | 2592 (100.0%) | 23.5 |
| alexei.drummond | 17 (15.5%) | 1134 (43.8%) | 66.7 |
| msuchard | 21 (19.1%) | 410 (15.8%) | 19.5 |
| alexander.alekseyenko | 4 (3.6%) | 371 (14.3%) | 92.7 |
| akaruiws | 3 (2.7%) | 266 (10.3%) | 88.6 |
| rambaut | 23 (20.9%) | 218 (8.4%) | 9.4 |
| dong.w.xie | 38 (34.5%) | 182 (7.0%) | 4.7 |
| jheled | 2 (1.8%) | 10 (0.4%) | 5.0 |
| dong.w.xie@gmail.com | 2 (1.8%) | 1 (0.0%) | 0.5 |
trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.
1 lines of code changed in 2 files:
Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.
2 lines of code changed in 2 files:
trunk:solve Issue 457: BEAST should raise an error if binary dataType set but data is not binary, and Issue 312: BEAST continues to run (inappropriately) when sequence contains invalid character
119 lines of code changed in 26 files:
Adding continuous traits in BEAUti
35 lines of code changed in 2 files:
Preliminary work on Markov modulated hidden class reporting
2 lines of code changed in 2 files:
Intermediate work on a Markov-modulated mixture model; returns equal (and correct) sequence likelihoods when mixing rates = 0.
54 lines of code changed in 3 files:
Missing data registry entry for co-evolution amino acid sites
2 lines of code changed in 1 file:
Updated compileNativeMacOSX.sh to work under 10.6 and added a parse class for paired-amino acid evolution
131 lines of code changed in 1 file:
Create set methods for max and min.
8 lines of code changed in 1 file:
Trunk: more work on micro-sat data in BEAUti.
14 lines of code changed in 1 file:
Trunk: big check-in to add micro-satellite in BEAUti.
1) Because it uses patterns not alignment, PartitionPattern is added, and PartitionData is still used for all previous data type.
2) getDataType is corrected to get actual data type, where traits are generalDataType, and trait name is getting from getDataDescription.
3) add MICRO_SAT data type.
9 lines of code changed in 3 files:
Created an HypermutantAlignment that flags hypermutation contexts for use in the APOBECErrorModel. It does this by replacing 'A's by an ambiguity code for A/G if it is in the correct context in the alignment. These can then be compressed into unique site patterns so that speed is not affected.
Extracted a common abstract base class with ConvertAlignment which wraps an alignment.
3 lines of code changed in 1 file:
TRUNK: sovle Issue 299: GeneralDataType should be registered for the purpose that DataType.getRegisteredDataTypeNames() returns the correct set of DataType
2 lines of code changed in 2 files:
TRUNK: BEAUti discrete traits prior and operator panels are working.
1 lines of code changed in 1 file:
TRUNK: BEAUti discrete traits site model panel is working.
3 lines of code changed in 1 file:
Trunk refactoring: organize Data Tpye parser (split parsers).
1 lines of code changed in 1 file:
Robust counting is working (as far as I can tell) and returns expected numbers of syn and non-syn changes on a tree, using just nucleotide models
39 lines of code changed in 1 file:
Added JUnitTest for counting synonymous jumps; also refactored a function in making codon models to avoid duplicating code
96 lines of code changed in 1 file:
Trunk refactoring: make evoxml parsers more organized.
1 lines of code changed in 1 file:
Trunk: incomplete correction of 2state coarion model, and leave to Alexei to complete.
3 lines of code changed in 1 file:
small code changes for binary covarion model
17 lines of code changed in 1 file:
added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.
7 lines of code changed in 1 file:
Changed getState method. When the raw length is not a multiple of the repeat unit length, the state is always rounded up.
13 lines of code changed in 1 file:
making stochastic Dollo compliant with the new DataType stuff...
7 lines of code changed in 1 file:
Microsatellite data type
245 lines of code changed in 1 file:
First step in development of a generic version of Parameter, called Variable for now. Parameter now implements Variable<Double> but eventually all dr.inference.* will be based on Variable rather than Parameter. At least that is the idea anyway...
217 lines of code changed in 1 file:
Update Big Change of BEAUTi: add PloidyType for BEAUTi.
29 lines of code changed in 1 file:
automatic idea changes, change type return type of getChild
3 lines of code changed in 1 file:
Added a default to GeneralDataType that '?' is treated as Unknown_State. Also when AncestralStateTreeLikelihood is logging states from GeneralDataType, it uses the full string codes rather than 1 letter chars.
15 lines of code changed in 2 files:
Made it easier to set up CTMC of locations by allowing GeneralDataTypeParser to take Identifyable objects as states (such as a set of Location objects). The AttributePatternsParser can then extract the states from attributes of the taxa.
95 lines of code changed in 2 files:
Added DuplicatedParameter for symmetric rates and assymetric indicators. Added ColtEigenSystem to compare numerical stability in beagle package.
12 lines of code changed in 3 files:
added an example of binary stochastic Dollo model, +some minor related bug fixes.
111 lines of code changed in 1 file:
Hidden codons run under GPU, substitution model is still a mess
4 lines of code changed in 2 files:
Hidden codon states are fun!
60 lines of code changed in 3 files:
64 state codon model for testing purposes
10 lines of code changed in 4 files:
Added classes necessary for MSSD a.k.a. Aquisition-Loss-Substitution (ALS) a.k.a. Immigration-Mutation-Death model functionality. Added prior and integrated immigration prior correction for alternative splicing creation and loss model.
AscertainedSitePatterns -- can handle ascertainment of two types
MutationDeathType -- extends a datatype with an additional state for the death state. Slightly differently (more clean?) structured than the other datatypes in the project. Let me know if you like it.
MutationDeathModel -- extends an arbitrary SubstitutionModel to include an additional absorbing death state.
ScaledTreeLengthRateModel -- Scales the sum of all edges to a specified value (like 1.0 in my case)
testBinary.xml -- a small example of who all of this stuff work
Changes:
BeastParser: added the parsers here
SitePatterns: made comparePatterns() protected instead of private
FrequencyModel: added a function to get the frequency parameter
246 lines of code changed in 1 file:
Moved NodeRateProvider and BranchRateProvider to dr.evolution.tree because dr.evolution.* should not depend on dr.evomodel.* (plus minor other tidying)
159 lines of code changed in 1 file:
fixed a couple of bugs in twoStateCovarionModel and wrote a JUnit test to ensure that normalization of the matrix works (I normalized the matrix so that the total number of substitutions (not including switching events) was on average 1.0 per unit time). Also added some pretty matrix toString code.
1 lines of code changed in 1 file:
still working on genrea dna covarion model -- the parameters seem to be in the wrong cells of the matrix...
2 lines of code changed in 1 file:
implemented general DNA covarion models - untested!
277 lines of code changed in 2 files:
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