Lines of Code
[root]/src/dr/app/beauti/modelsPanel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 46 (100.0%) | 1518 (100.0%) | 33.0 |
| alexei.drummond | 8 (17.4%) | 909 (59.9%) | 113.6 |
| dong.w.xie | 25 (54.3%) | 415 (27.3%) | 16.6 |
| rambaut | 13 (28.3%) | 194 (12.8%) | 14.9 |
BEAUTi: Resolved issue #99: spearate models panel into Site Models and Clock Models two panels.
0 lines of code changed in 4 files:
A few final tweaks: added a few names to the credits. Fixed issue 107 (credits appearing twice) and 101 (fixed rate box small on Mac).
4 lines of code changed in 2 files:
Fixed issue 105: http://code.google.com/p/beast-mcmc/issues/detail?id=105
and addressed 106 (made the dialog box say it is a 'Warning') rather than an error.
4 lines of code changed in 1 file:
BEAUTi: add message for choose Fix mean rate and comments in FixRateType.
6 lines of code changed in 1 file:
Big Change of BEAUTI:
1) implement FixRateType containing estimate, fix mean, fix 1st partition to replace fixSubstitionRate;
2) comment out "mu" for no condon model;
3) correct *BEAST xml by adding updown operators;
4) fix bug to import NEXUS file when it contains subsititution model.
43 lines of code changed in 1 file:
Update Big Change of BEAUTi:
1) correct branch rate generator and its parameters idref;
2) move Ploidy type for PartitionData into PartitionTreeModel, and add Ploidy type in Tree Model panel when EBSP prior is selected;
3) replace "value" by Parameters.Paser.Value;
4) correct XML for EBSP prior.
31 lines of code changed in 3 files:
Update Big Change of BEAUTi:
1) fix the bug of Operator generator;
2) remove all rates into PartitionClockModelTreeModelLink;
3) comment out autocorrelated and random clock model before the release.
But there will be bugs in generator waiting regarding these changes.
4 lines of code changed in 1 file:
intellij tidy
105 lines of code changed in 6 files:
Update Big Change of BEAUTi: add clock model table in Model panel
48 lines of code changed in 2 files:
Update Big Change of BEAUTi: store the links between PD, PSM, PCM, PTM, PTP in the class using their class references, List<> of them in BeautiOption is not used anymore. And use getPartition...() in BeautiOption to get the current list of PD or PSM or PCM or PTM.
2 lines of code changed in 1 file:
BEAUTi: replace all dataType with getter.
3 lines of code changed in 2 files:
Renew Big Change of BEAUTi: update the structure containing multi-substitution models, multi-clock models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionClockModel; and PartitionData <=> PartitionTreeModel <=> PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PCM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also
PD~(PSM,PCM,PTM) and PTM~(PTP).
But updown operator does not init properly.
206 lines of code changed in 1 file:
Big Change of BEAUTi: finish the structure in GUI only, containing multi-substitution
models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionTreeModel <=>
PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also
PD~(PSM,PTM) and PTM~(PTP).
Function and generator not completed.
29 lines of code changed in 1 file:
Big Change of BEAUTi: to create a structure containing multi-substitution models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionTreeModel <=> PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also PD~(PSM,PTM) and PTM~(PTP).
Not completed.
6 lines of code changed in 1 file:
BEAUTi: rename partition series classes, and final relation is PartitionData => PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior.
20 lines of code changed in 2 files:
BEAUTi: Rename DataPartition into PartitionData, and add PartitionPopulation, to create the structure of PartitionData => PartitionModel => PartitionTree => PartitionPopulation.
1 lines of code changed in 1 file:
Fix BEAUTi bug: combo Number of Gamma Categories should be disable when the initial value of combo Site Heterogeneity is None.
9 lines of code changed in 1 file:
Refactory BEAUTI package structure, add few panel packages and util package.
2 lines of code changed in 2 files:
Fix bug that cannot start Beauti because of null point exception in setOption.
5 lines of code changed in 1 file:
This may seem like a rather large load of edits but it is just to get the 'plugin' model generator working better. All the Generators are now created in BeastGenerator's constructor. I am going to implement a factory system for the plug in modules but thought I would submit my changes now before things move on too much. I updated before committing so hopefully no painful merges for anyone.
4 lines of code changed in 1 file:
Extended linking/unlinking to include trees by mirroring the setup we use for substitution models. Not complete yet so have included a static switch in DataPanel.ALLOW_UNLINKED_TREES which when false, reverts to the old GUI.
8 lines of code changed in 1 file:
Further work on BEAUti. Added options to allow sampling of tip dates.
10 lines of code changed in 2 files:
Lots of work on BEAUti
Started work on a modularization of BEAST generation (look in beauti.components). Lots of insertion points are defined throughout the BEAST file (relative to all the standard content) and a component can offer to write content to each or any of these. Instances of each component are created in BeautiFrame constructor. Started converting some of the monolithic generation into components (see SequenceErrorModel for an example).
Implemented the ability to import an existing BEAST file but at the moment the taxa, dates and sequences are all that are picked up.
Started work on a 'locations' tab but am currently uncertain whether this shouldn't just be a general traits tab.
Save/Apply templates menu options are hidden as we don't have an implementation yet.
8 lines of code changed in 1 file:
Have tried to make the connections between the different panels a bit more robust. GetOptions/SetOptions is now called when a new tab is selected. Have fixed a problem with delta exchange on allMus having a weight of 0 and thus not being put into the mix.
4 lines of code changed in 1 file:
Alex and I have been experimenting with a path sampling approach to estimating marginal likelihoods. See eXML in examples/testPathSampling.xml. Not sure it works.
21 lines of code changed in 1 file:
Added the sequencing error/DNA damage model options to BEAUti.
19 lines of code changed in 1 file:
More work on Trees panel
112 lines of code changed in 2 files:
refactoring model panel in BEAUti
804 lines of code changed in 2 files: