Directory src/dr/evomodelxml/tree/

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rambaut 2013-05-13 04:17 Rev.: 5648

Auto sets the size of the MarkovJump count register

1 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (new)

rambaut 2013-03-26 05:04 Rev.: 5541

<trait> element in Tree Logger can now take a filter="XXX" attribute instead of specifying a particular name to log all traits that starts with a particular string. Also if the <trait> element has neither a name or a filter attribute then all traits are logged.

67 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+67 -31)

rambaut 2013-02-02 05:17 Rev.: 5376

Porting changes from 1.7

15 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+15 -2)

rambaut 2013-01-10 05:31 Rev.: 5303

Drifting

56 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: TreeModelParser.java (+56 -19)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

16 lines of code changed in 3 files:

• src/dr/evomodelxml/tree: AncestralTraitParser.java (+1 -1), TreeLoggerParser.java (+15)

rambaut 2012-07-31 03:25 Rev.: 5078

Fixed issue with precision bounds for dates of leaf nodes

1 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeModelParser.java (+1 -1)

rambaut 2012-07-19 04:52 Rev.: 5074

Added an option to define a precision level for a date which automatically creates appropriate bounds for a leaf-height parameter. Then you can sample from those bounds using a uniform or randomwalk operator. The attribute: precision="1.0" means the date has been specified to the precision of 1 unit (missing or 0.0 means exact precision).

12 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeModelParser.java (+12)

rambaut 2012-07-19 04:41 Rev.: 5073

Overhauled the date system so that the 'height' timescale is now universal to all taxa. Previously there was an issue if you create independent trees on different taxon sets, they would have their own 'zero' point depending on their most recently sampled taxon. Now, when you call 'setDate' for a taxon (as done by the TaxonParser) it keeps track of the globally most recent sample (in a static variable) and can give the global height from a given date object using a static function. Taxon objects also have a 'getHeight' methods that uses this system. The two main sources of trees (CoalescentSimulator and NewickParser) now use these heights (simplifying their own code). Runs benchmarks correctly but keep an eye out for issues.

16 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeModelParser.java (+16 -1)

rambaut 2012-06-06 21:07 Rev.: 5014

Changing the 'traitFilter' behaviour of TreeLoggerParser so it only matches prefixes (previously it used contains() so this made it difficult to filter).

1 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+1 -1)

msuchard 2012-05-15 01:24 Rev.: 4955

Introduced a trial TreeParameterModel that excludes external branches; created a new branch-specific Pagel estimator

5 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: TransformedTreeModelParser.java (+5 -1)

msuchard 2012-05-11 16:02 Rev.: 4952

Trying a tree transform

10 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TransformedTreeModelParser.java (+10 -5)

msuchard 2012-05-11 15:19 Rev.: 4951

Refactoring TransformedTree to make generalizations easier

7 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TransformedTreeModelParser.java (+7 -3)

msuchard 2012-03-27 07:45 Rev.: 4895

Implementing transformed trees and Pagel's lambda estimator

89 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TransformedTreeModelParser.java (+89)

msuchard 2012-03-27 06:41 Rev.: 4894

Improved ability to co-opt an existing root height in StarTreeModel

12 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: StarTreeModelParser.java (new)

msuchard 2012-03-26 15:04 Rev.: 4888

Added ability to co-opt an existing root height in StarTreeModel

8 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: StarTreeModelParser.java (+8 -8)

rambaut 2011-12-04 10:41 Rev.: 4500

Fixed an issue where once a 'substitutions' TreeLogger was created all subsequent TreeLoggers were also using the same BranchRates model to do substitution trees. This was an issue in the parser. The issue would not manifest itself if the substitutions tree log was the last in the XML (as generated by BEAUti).

4 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+4 -1)

rambaut 2011-11-24 19:18 Rev.: 4483

Started to implement ancestral state reconstruction at a node.

7 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: AncestralTraitParser.java (+7 -4)

rambaut 2011-11-16 03:18 Rev.: 4431

Added ability to log a specific tree trait using a different tag. XML looks like this (will log the second branch rates as 'trait.rate' whereas the first one will use its default 'rate'):

<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="untitled.trees" sortTranslationTable="true">
<treeModel idref="treeModel"/>
<posterior idref="posterior"/>

<branchRates idref="branchRates"/>
<trait name="rate" tag="trait.rate">
<branchRates idref="trait.diffusionRates"/>
</trait>
</logTree>

31 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+31 -4)

rambaut 2011-11-16 03:13 Rev.: 4430

Loggers weren't logging if they overrode the base class log(int state) - because it had been changed to log(long state). Put a final int version in the base class to prevent overriding.

40 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+40 -13)

rambaut 2011-11-16 00:45 Rev.: 4429

Made BranchRateModel a TreeTraitProvider so it can be logged more easily. Also added feature to TreeLoggerParser where a tree trait can be specified (with a special tag).

39 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+39 -17)

msuchard 2011-10-18 08:34 Rev.: 4365

Better way to handle star trees via a derived TreeModel

280 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: StarTreeModelParser.java (+280)

msuchard 2011-05-09 09:29 Rev.: 3972

Re-implemented logging of random local clock indicators in tree log files; this ability was lost when we converted over to tree traits.

43 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: RLTVLoggerOnTreeParser.java (new 43)

rambaut 2011-04-29 01:36 Rev.: 3967

Allow treelogger to have more than one trait filter (comma or space delimited).

10 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+10 -8)

dong.w.xie 2011-03-03 17:13 Rev.: 3854

Trunk: test calibration yule model more with non disjoint trees error

2 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: TMRCAStatisticParser.java (+2 -5)

rambaut 2010-10-08 11:17 Rev.: 3614

examples/benchmark1.xml used to take 160 seconds - it now takes 35. This is because it is a very large tree (1442 tips). The likelihood calculation was taking 22 seconds of the 160, most of the rest was spent checking the bounds of the node heights. It turned out that TreeModel.endTreeEdit() was checking the bounds of every node after every tree move. This check is simply to ensure that the tree move was behaving correctly (program stops with a RuntimeException if it doesn't). So, commented out this check and 3 fold speed up.

Actually it turned out all the nodes had their bounds added twice so this check was even more costly.

We could include this check in the initial phase of the run or as an assert.

2 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeModelParser.java (+2 -1)

dong.w.xie 2010-10-04 10:56 Rev.: 3596

Trunk: @Override is JDK1.6 code.

6 lines of code changed in 2 files:

• src/dr/evomodelxml/tree: HiddenLinkageModelParser.java (new)

aaron.darling 2010-10-02 15:18 Rev.: 3593

Several small changes to TreeLoggerParser that structure it in a way that allows subclasses to use much of its functionality without reimplementing or copying code.
---------------
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

33 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+33 -17)

aaron.darling 2010-10-02 15:11 Rev.: 3588

Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.

167 lines of code changed in 3 files:

• src/dr/evomodelxml/tree: HiddenLinkageLoggerParser.java (new 58), HiddenLinkageModelParser.java (+55), HiddenLinkageTreeLoggerParser.java (new 54)

msuchard 2010-09-27 09:25 Rev.: 3573

TreeLoggerParser can now filter which tree traits to report.

23 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+23 -5)

dong.w.xie 2010-09-15 10:45 Rev.: 3541

Trunk: solve Issue 396: make alias "forParent" of "includeStem" in TMRCAPasrer

19 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TMRCAStatisticParser.java (+19 -4)

rambaut 2010-08-19 21:31 Rev.: 3411

LoggerParser uses a special function to get the log file which may set different paths (for example to a working directory). Thus just checking that fileName exists may not work. So moved the check for existing file into XMLParser.getFilePrintWriter(). This has the added benefit that all loggers use this function and thus all have the overwriting behaviour.

Also added a check box to the BEAST options dialog box.

2 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+2)

msuchard 2010-06-17 10:45 Rev.: 3273

Critical fix: branch rates now print out in tree log under new TreeTrait framework. Also starting to remove duplicated code from classes needing to output different combinations of TreeTrait summaries

17 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+17 -2)

rambaut 2010-06-03 01:10 Rev.: 3218

I have abandoned dr.app.beagle.evomodel.branchratemodel.MarkovJumpsBranchRateModel and integrated that functionality into DiscreteTraitRateModel. This latter class now takes a TreeTrait which is either of the Integer type in which case it is assumed to be a node reconstruction of the state or a 'double[]' type in which case it is assumed to be a vector of dwell times for each state for each branch. I have also left the option of a parsimony reconstruction. I have also restructured things so that everything is done as dwell times - the node reconstruction variants (both likelihood and parsimony) just assume a state transition mid point on the branch. I have tried to average the parsimony variant across ambiguous state reconstructions at the nodes but I am not sure that this is a good idea (but then probably the same could be said for the whole parsimony approximation).

3 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: AncestralTraitParser.java (+3 -3)

rambaut 2010-06-02 23:10 Rev.: 3216

In the interests of generalization, AncestralState has been improved to optionally take a trait name, renamed AncestralTrait, moved to dr.evomodel.tree. It has a parser synonym of AncestralState and defaults to getting the 'state' trait so it is backwards compatible with existing XML (namely testAncestralSequenceReconstuction.xml).

77 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: AncestralTraitParser.java (+77)

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

42 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+42 -45)

jheled 2010-06-02 07:04 Rev.: 3211

code police

4 lines of code changed in 8 files:

• src/dr/evomodelxml/tree: MonophylyStatisticParser.java (new), NodeHeightsStatisticParser.java (+1 -1), SpeciesTreeStatisticParser.java (new), TreeLengthStatisticParser.java (new)

jheled 2010-06-02 07:02 Rev.: 3209

Make tree height statistic available

48 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeHeightStatisticParser.java (new 48)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

215 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (+215)

dong.w.xie 2010-03-02 10:24 Rev.: 3002

Trunk refactoring: finish Logger (split parsers).

0 lines of code changed in 1 file:

• src/dr/evomodelxml/tree: TreeLoggerParser.java (del)

dong.w.xie 2010-02-22 14:29 Rev.: 2957

Trunk refactoring: finish tree model (split parsers)..

596 lines of code changed in 9 files:

• src/dr/evomodelxml/tree: CompatibilityStatisticParser.java (new 60), ExternalLengthStatisticParser.java (new 57), MonophylyStatisticParser.java (+99), ParsimonyStateStatisticParser.java (new 67), ParsimonyStatisticParser.java (new 60), RateCovarianceStatisticParser.java (new 51), RateStatisticParser.java (new 67), SpeciesTreeStatisticParser.java (+47), UniformNodeHeightPriorParser.java (new 88)

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