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Eric Rynes writes:

Today, for the first time, I fed Tracer data which contained some numbers in 
scientific notation:  1e
+06, 1.00002e+06, etc.  Version 1.3 raised an exception when it encountered the 
first number 
expressed in this notation in my input file.  I downloaded v1.4, and observed 
identical behavior. 
("Problem with trace file: State 0:Expected real value in column 40000")

Loading a trace file that contains NaN in a column causes Tracer to hang (no UI 
response, requires 
the JVM to be killed) when that column is processed. Probably an infinite loop 
in the ESS 
calculations?

TreeAnnotator (and presumably other command line programs) get confused when 
specified file 
names have '-' in them:

hros001-nrg4:beast hros001$ 
/Users/hros001/Software/BEAST/UNIXversion/BEAST.v1.4.6/bin/treeannotator 
-target Akodon-
target.tree Akodon.trees Akodon_out.txt

              TreeAnnotator v1.4.6, 2002-2007
                    MCMC Output analysis
                             by
           Andrew Rambaut and Alexei J. Drummond

             Institute of Evolutionary Biology
                  University of Edinburgh
                     [email protected]

               Department of Computer Science
                   University of Auckland
                  [email protected]


Reading trees...
Total trees read: 10001
No user target tree specified.

What steps will reproduce the problem?
1. Create a taxon set and enforce monophyly
2. Create a second taxon set, with different taxa
3. Try to enforce monophyly

What is the expected output? What do you see instead?
Should work but instead claims that taxon sets are not compatible. Entirely 
nested taxon sets are 
allowed.

Work around: Enforce monophyly on taxon sets before adding taxa (this exposes 
another aspect to 
this bug which is that it should check compatibility when taxa are added.

It would be a useful feature to be able to specify lognormal priors' parameters 
in real rather than 
log space (similarly to the UCLN).

What steps will reproduce the problem?
1. include a 
<log id="logTree1" logEvery="100" fileName="trees.log">
            <treeModel idref="treeModel"/>
</log>
 <treeTraceAnalysis fileName="trees.log"> 

elements in beast xml file
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.

 Error reading tree for state 0
25/02/2008 14:11:16 dr.app.beastdev.BeastMain <init>
SEVERE: Fatal exception (email the authors)
Fatal exception (email the authors)
java.lang.RuntimeException: dr.evolution.io.Importer$ImportException:
Number format error: For input string: "#"
    at
dr.evomodel.tree.TreeTraceAnalysis.analyzeLogFile(TreeTraceAnalysis.java:389)
    at
dr.evomodel.tree.TreeTraceAnalysisParser.parseXMLObject(TreeTraceAnalysisParser.
java:83)
    at
dr.xml.AbstractXMLObjectParser.parseXMLObject(AbstractXMLObjectParser.java:72)
    at dr.xml.XMLParser.convert(XMLParser.java:177)
    at dr.xml.XMLParser.convert(XMLParser.java:155)
    at dr.xml.XMLParser.parse(XMLParser.java:107)
    at dr.app.beastdev.BeastMain.<init>(BeastMain.java:106)
    at dr.app.beastdev.BeastMain.main(BeastMain.java:323)

What steps will reproduce the problem?
1. Run the attached file on an x86 platform (Opteron, P4?)
2. Wait until after preBurnin
3. Marvel as the errors start to appear.

Speculation: Given the errors appear on x86 processors and not G5, this may be
due to some difference in numerics of the respective compilers. May be an issue
with the native library.

The attached file is affected.

Reports that selection of forwards or backwards option for dates is being 
lost/changed in BEAUti. At 
present we have no recipe for replicating this. Investigations are underway

1. Import Nexus file into BEAUti with taxa names finishing in \.[0-9]+ or 
\_[0-9]+ where the final 
digits represent the date of the sequence 
2. Use Guess dates option to guess dates by prefix (either '.' or '_')
3. No dates are guessed and the dates column remains full of zeros.

The expected output is for the dates column to be populated with the correct 
numbers.

If you accidentally enter a large number (in the thousands) into the lognormal 
mean box (I was 
doing this for tmrca(taxongroup), the entire programme locks up.

What steps will reproduce the problem?
1. Initialize a tree with UPGMA
2. Calculate initial density of the coalescent

This bug was introduced in revision 811 in Coalescent.java lines 101-106.  I 
believe the changes 
were made to fix something in the EBSP, but the fix causes a new break.  Doh!

Joseph, would you mind messing around with this?   

In the meantime, I have gone back to an older version.

What steps will reproduce the problem?
1. run a beast file with -seed 0
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.


            BEAST v1.5 developmental, 2002-2006
       Bayesian Evolutionary Analysis Sampling Trees
                             by
           Alexei J. Drummond and Andrew Rambaut

               Department of Computer Science
                   University of Auckland
                  [email protected]

             Institute of Evolutionary Biology
                  University of Edinburgh
                     [email protected]

Downloads, Help & Resources:
        http://evolve.zoo.ox.ac.uk/beast/

Source code distributed under the GNU Lesser General Public License:
        http://code.google.com/p/beast-mcmc/

Additional programming & components created by:
        Roald Forsberg
        Gerton Lunter
        Sidney Markowitz
        Oliver Pybus

Thanks to (for use of their code):
        Korbinian Strimmer

Random number seed: 0

UTF8
Parsing XML file: xrun042.xml
Read alignment, 'alignment000':
  Sequences = 24
      Sites = 1600
   Datatype = nucleotide
Site patterns 'patterns000' created from positions 1-1600 of alignment
'alignment000'
  pattern count = 20
Read alignment, 'alignment001':
  Sequences = 24
      Sites = 1600
   Datatype = nucleotide
Site patterns 'patterns001' created from positions 1-1600 of alignment
'alignment001'
  pattern count = 8
Read alignment, 'alignment002':
  Sequences = 24
      Sites = 1600
   Datatype = nucleotide
Site patterns 'patterns002' created from positions 1-1600 of alignment
'alignment002'
  pattern count = 13
Read alignment, 'alignment003':
  Sequences = 12
      Sites = 1600
   Datatype = nucleotide
Site patterns 'patterns003' created from positions 1-1600 of alignment
'alignment003'
  pattern count = 26
Creating the tree model, 'truetreeModel000'
  initial tree topology =
((((((((l00_tip_003,l00_tip_019),l00_tip_017),l00_tip_011),l00_tip_007),(((l00_t
ip_006,l00_tip_009),(l00_tip_008,l00_tip_016)),(l00_tip_013,l00_tip_020))),(l00_
tip_005,l00_tip_012)),(((l00_tip_001,l00_tip_004),(l00_tip_010,l00_tip_021)),l00
_tip_022)),((((l00_tip_000,l00_tip_015),l00_tip_014),l00_tip_002),(l00_tip_018,l
00_tip_023)))
21/11/2007 17:42:12 dr.app.beastdev.BeastMain <init>
SEVERE: Fatal exception (email the authors)
Fatal exception (email the authors)
java.lang.RuntimeException: failed to merge trees after 1000 tries!
        at
dr.evolution.coalescent.CoalescentSimulator.simulateCoalescent(Unknown Source)
        at dr.evolution.coalescent.CoalescentSimulator.simulateTree(Unknown
Source)
        at dr.evomodel.coalescent.CoalescentSimulator.simulateTree(Unknown
Source)
        at
dr.evomodel.coalescent.CoalescentSimulator$1.parseXMLObject(Unknown Source)
        at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
        at dr.xml.XMLParser.convert(Unknown Source)
        at dr.xml.XMLParser.convert(Unknown Source)
        at dr.xml.XMLParser.parse(Unknown Source)
        at dr.app.beastdev.BeastMain.<init>(Unknown Source)
        at dr.app.beastdev.BeastMain.main(Unknown Source)

The Dialog in Tracer exists, but code is commented out. There is no Beauti
support. The model has now 5 parameters.

Either the dialog has to go or the correct code re-instated.

I somehow messed up the initial check in so that when I ran svn update an
extra copy of all source files were in the bin directory tree, but when I
deleted the files from the bin tree they were also removed from the src
directory. Some kind of symbolic link? I'm filing this as a bug report to
note what is going on and to test the Tracker system.

/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/bin/java -Xmx1000m -Xss512k -ea
-Djava.library.path=/home/joseph/phd/beast/beast-mcmc/native -Xdebug
-Xrunjdwp:transport=dt_socket,address=127.0.0.1:56431,suspend=y,server=n
-Dfile.encoding=UTF-8 -classpath
/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/javaws.jar:/usr/lib/jvm/java-1.5.0-
sun-1.5.0.13/jre/lib/plugin.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/rt.
jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/deploy.jar:/usr/lib/jvm/java-1.
5.0-sun-1.5.0.13/jre/lib/jce.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/ch
arsets.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/jsse.jar:/usr/lib/jvm/ja
va-1.5.0-sun-1.5.0.13/jre/lib/ext/sunjce_provider.jar:/usr/lib/jvm/java-1.5.0-su
n-1.5.0.13/jre/lib/ext/localedata.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/l
ib/ext/dnsns.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/ext/sunpkcs11.jar:
/home/joseph/phd/beast/beast-mcmc/classes:/home/joseph/phd/beast/beast-mcmc/lib/
commons-math-1.1.jar:/home/joseph/phd/beast/beast-mcmc/lib/jdom.jar:/home/joseph
/phd/beast/beast-mcmc/lib/mtj.jar:/home/joseph/phd/beast/beast-mcmc/lib/colt.jar
:/home/joseph/phd/beast/beast-mcmc/lib/junit-4.4.jar:/home/joseph/phd/beast/beas
t-mcmc/lib/itext-1.4.5.jar:/home/joseph/phd/beast/beast-mcmc/lib/jebl.jar:/home/
joseph/phd/beast/beast-mcmc/lib/commons-math-1.2.jar:/home/joseph/bin/idea-7364/
lib/idea_rt.jar
dr.app.tools.TreeLogAnalyser cg1673.fasta.trees
Connected to the target VM, address: '127.0.0.1:56431', transport: 'socket'
+-----------------------------------------------\
|           TreeLogAnalyser v1.3 2005           |\
|              MCMC Output analysis             ||
|             BEAST Library: v1.5a1             ||
|       Alexei Drummond and Andrew Rambaut      ||
|              University of Oxford             ||
|           http://beast.bio.ed.ac.uk/          ||
\-----------------------------------------------\|
 \-----------------------------------------------\

Analysing tree file: cg1673.fasta.trees
WARNING: Burn-in larger than total number of states - using 10% of smallest
trace
Analyzing 9001 trees...
0              25             50             75            100
|--------------|--------------|--------------|--------------|
Exception in thread "main" java.lang.NullPointerException
    at dr.evomodel.tree.TreeTraceAnalysis.analyze(TreeTraceAnalysis.java:123)
    at dr.evomodel.tree.TreeTraceAnalysis.<init>(TreeTraceAnalysis.java:69)
    at
dr.evomodel.tree.TreeTraceAnalysis.analyzeLogFile(TreeTraceAnalysis.java:430)
    at dr.app.tools.TreeLogAnalyser.analyze(TreeLogAnalyser.java:107)
    at dr.app.tools.TreeLogAnalyser.<init>(TreeLogAnalyser.java:82)
    at dr.app.tools.TreeLogAnalyser.main(TreeLogAnalyser.java:229)
Disconnected from the target VM, address: '127.0.0.1:56431', transport:
'socket'

All we need is a nicer error message than this:

SEVERE: Fatal exception (email the authors)
Fatal exception (email the authors)
java.lang.NullPointerException
    at dr.evoxml.NewickParser.parseXMLObject(Unknown Source)
    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.parse(Unknown Source)
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:324)
    at apple.launcher.LaunchRunner.run(LaunchRunner.java:88)
    at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
    at
apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

What steps will reproduce the problem?
1. Create taxon sets in BEAUti
2. Save a template file
3. Attempt to reload the template file

What is the expected output? What do you see instead?
The table in the Data panel is not drawn correctly - an exception is thrown.

What steps will reproduce the problem?
1. open BSP reconstruction in Tracer
2. mark check-box "Solid Interval"
3.

What steps will reproduce the problem?
1. Open BEAUti
2. Select Skyline as Tree Prior
3. Attempt to change default value

What is the expected output? What do you see instead?
Simply reverts to default value

Please use labels and text to provide additional information.

Select BSP. Select other tree prior. Number of groups etc. remains visible.

Introduced in v1.4.1

BEAUti added a constraint for *every* taxon set that is specified in
the taxa tab, even if monophyletic is not selected. This is a problem because
sometimes the user just wants to specify some tMRCA to specify a prior on and
the taxa groups might be overlapping.

What steps will reproduce the problem?
1. Start Tracer
2. Click the '+' button
3. Select a large trace file.

What steps will reproduce the problem?
1. Select a continuous parameter and press the Prior button.
2. Choose a normal prior
3. Set mean to 6.0 and stdev to 0.5

What is the expected output? What do you see instead?
Should see the resulting distribution - but it is missing. 

BEAST defaults to a value of zero for the offset of the exponential prior. It 
is not clear at this point 
whether this is a parser issue (because <exponentialPrior> is essentially just 
a parser) or some 
problem in the underlying classes.

The problem: LogCombiner assumes that the order of sequence names in the two 
tree files are 
the same (the list of taxa occurs at the start of each tree file and the trees 
refer to them by 
number). The list of taxa get copied from the first tree file and then used by 
all the subsequent 
ones. If the order is not the same in the two (or more) tree files then the 
trees will have 
mislabelled taxon names for some trees in the combined tree file. 

Running multiple runs of BEAST with random starting trees will result in 
different taxon orders 
and will be affected by this problem. Using a user starting tree (or UPGMA 
tree) should give the 
same taxon order and not be affected.

The consequences: Using the combined tree file to make a consensus tree or to 
annotate a tree 
using TreeAnnotator will produce incorrect results. Using the combined tree 
files to construct a 
Bayesian Skyline graphic in tracer will not be affected as the taxon labelling 
is not used.

The solution: Don't combine tree files using LogCombiner unless the taxon 
orders are the same 
(the taxon and translate sections of the nexus file should be identical). 
Alternatively, combine the 
trees using a program such as PAUP.

What steps will reproduce the problem?
1. run the attached file in beast


What is the expected output? 
run starts 

Line 209 in DistributionLikelihood is:

            DistributionLikelihood likelihood = new DistributionLikelihood(new ExponentialDistribution
(mean), offset);

it *should* be this:

            DistributionLikelihood likelihood = new DistributionLikelihood(new ExponentialDistribution
(1.0/mean), offset);

As a result all BEAST analyses using <exponentialPrior> elements with a mean 
other than 1.0 are 
incorrect! ALERT ALERT.

It would be nice to have a simple check-box in BEAUTi so that a second BEAST 
XML that samples the 
prior with no data is also generated.

What steps will reproduce the problem?
1. make a BEAST run a with a BSP reconstruction 
2. open Tracer
3. Analysis/Bayesian Skyline Reconstruction
4. File/Print

Tracer hangs for a long time. Java error messages

/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/bin/java -Xmx1000m -Xss512k -ea
-Didea.launcher.port=7533
-Didea.launcher.bin.path=/home/joseph/bin/idea-7364/bin
-Dfile.encoding=UTF-8 -classpath
/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/javaws.jar:/usr/lib/jvm/java-1.5.0-
sun-1.5.0.13/jre/lib/plugin.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/rt.
jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/deploy.jar:/usr/lib/jvm/java-1.
5.0-sun-1.5.0.13/jre/lib/jce.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/ch
arsets.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/jsse.jar:/usr/lib/jvm/ja
va-1.5.0-sun-1.5.0.13/jre/lib/ext/sunjce_provider.jar:/usr/lib/jvm/java-1.5.0-su
n-1.5.0.13/jre/lib/ext/localedata.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/l
ib/ext/dnsns.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.13/jre/lib/ext/sunpkcs11.jar:
/home/joseph/phd/beast/beast-mcmc/classes:/home/joseph/phd/beast/beast-mcmc/lib/
commons-math-1.1.jar:/home/joseph/phd/beast/beast-mcmc/lib/jdom.jar:/home/joseph
/phd/beast/beast-mcmc/lib/mtj.jar:/home/joseph/phd/beast/beast-mcmc/lib/colt.jar
:/home/joseph/phd/beast/beast-mcmc/lib/junit-4.4.jar:/home/joseph/phd/beast/beas
t-mcmc/lib/itext-1.4.5.jar:/home/joseph/phd/beast/beast-mcmc/lib/jebl.jar:/home/
joseph/phd/beast/beast-mcmc/lib/commons-math-1.2.jar:/home/joseph/bin/idea-7364/
lib/idea_rt.jar
com.intellij.rt.execution.application.AppMain
dr.app.tracer.application.TracerApp
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: null
attribute
    at
sun.print.IPPPrintService.isAttributeValueSupported(IPPPrintService.java:1100)
    at
sun.print.ServiceDialog$OrientationPanel.updateInfo(ServiceDialog.java:2092)
    at sun.print.ServiceDialog$PageSetupPanel.updateInfo(ServiceDialog.java:1234)
    at sun.print.ServiceDialog.updatePanels(ServiceDialog.java:428)
    at sun.print.ServiceDialog.initPrintDialog(ServiceDialog.java:193)
    at sun.print.ServiceDialog.<init>(ServiceDialog.java:141)
    at javax.print.ServiceUI.printDialog(ServiceUI.java:180)
    at sun.print.RasterPrinterJob.printDialog(RasterPrinterJob.java:852)
    at sun.print.PSPrinterJob.printDialog(PSPrinterJob.java:418)
    at org.virion.jam.framework.AbstractFrame.doPrint(AbstractFrame.java:77)
    at org.virion.jam.framework.AbstractFrame.doPrint(AbstractFrame.java:62)
    at
org.virion.jam.framework.AbstractFrame$3.actionPerformed(AbstractFrame.java:270)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
    at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
    at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuIt
emUI.java:1155)
    at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:578)
    at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:475)
    at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:422)
    at
javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:283
)
    at
javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupM
enuUI.java:783)
    at
java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2206)
    at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2100)
    at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2099)
    at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2058)
    at java.awt.Component.dispatchEventImpl(Component.java:3883)
    at java.awt.Container.dispatchEventImpl(Container.java:2024)
    at java.awt.Component.dispatchEvent(Component.java:3819)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
    at java.awt.Container.dispatchEventImpl(Container.java:2010)
    at java.awt.Window.dispatchEventImpl(Window.java:1791)
    at java.awt.Component.dispatchEvent(Component.java:3819)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
    at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:2
42)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163
)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

What steps will reproduce the problem?
1. Navigate to Priors panel in BEAUti
2. Change tree prior using drop-down menu
3. tree prior parameters in prior table are not updated

When changing to, for example, "Coalescent: Exponential Growth" we expect to 
see the two 
exponential growth parameters appear in the priors table (replacing the 
constant.popSize 
parameter). In BEAST 1.4.3 and earlier, the table is not updated...

Workaround: change the clock model in the model panel (and then change it back)

What steps will reproduce the problem?
1. check out the source
2. type 'ant'

I can build OK if I delete the maconly directory, but it gets replaced
every time I update.

What steps will reproduce the problem?
1. Load some data into BEAUTi.
2. Create a taxon set in the Taxa tab
2. Create a uniform prior with bounds of 10 and 100 on the tMRCA of the taxon 
set
3. Run BEAST on the generated BEAST XML file.

The expected output is that an MCMC analysis will begin. However what actually 
happens is an error 
occurs because the starting tree has zero likelihood.

What steps will reproduce the problem?
Accessing a datatype instance such as Nucleotides.INSTANCE

What is the expected output? What do you see instead?
Null pointer in static initialization code:
Caused by: java.lang.NullPointerException
    at java.util.Hashtable.put(Hashtable.java:396)
    at dr.evolution.datatype.DataType.registerDataType(DataType.java:88)
    at dr.evolution.datatype.DataType.<clinit>(DataType.java:60)

Please use labels and text to provide additional information.
The static initialization of Nucleotide.INSTANCE has not occurred by the time 
the line:
        registerDataType(Nucleotides.DESCRIPTION, Nucleotides.INSTANCE);
is called in the static block of DataType

Was returning: 

return popSize1 * (width-t) + (popSize2 * t) / width;

Should have been returning:

return (popSize1 * (width-t) + (popSize2 * t)) / width;

What steps will reproduce the problem?
1. set X axis in tracer  to (say) -1 to 3
2.
3.

Seems the major tick count (axis.getMajorTickCount()) is set to something
like 10M while it was 5-9 when automatic

In a number of cases, the constructor of a class throws an exception like 
'IllegalArgumentException' 
when provided with wrongly setup values. This results in a stack trace and ugly 
error messsages. All 
such exceptions should be caught by the calling parser and re-thrown as a 
XMLParserException 
with an appropriately descriptive error message. Alternatively, the parser 
could check for these 
conditions prior to constructing the object.

Example: DiscretizedBranchRatesModel throws an IllegalArgumentException if the 
rate indices 
parameter is not of dimension internal_node_count - 1.

BEAUti sorts the names of the taxon sets, but does not similarly move the 
monophyly checkbox.  
So, if my first two sets in my list are "Ants" and "Bees" and both are 
constrained to monophyly, and I 
add a new set that alphabetizes between these two, the new one gets the 
tick-mark that belongs to 
"Bees", and "Bees" is sorted down the list without a tick-mark.

We should have a standard of building with no warning messages, as a policy
that makes it easier to notice some bugs introduced by new code. I'm
opening this ticket to track the task of removing the 910 warnings that
Eclipse notes in the initial code checkin.

The posterior probability limit box in TreeAnnotator does not seem to work. 
Regardless the figure 
you type in the result seems to be always the same.

What steps will reproduce the problem?
1. Define an exponential prior on a tMRCA
2. Run chain
3. age of node does not obey prior, e.g. is younger than the offset.

What is the expected output? What do you see instead?
Expect to see ages older than offset, but don't..

What version of the product are you using? On what operating system?
It occurs in v1.4.2 on Mac OS X, and in version v1.3 on linux (Rocks
distribution v4.2.1).

Please provide any additional information below.
sorry I haven't got an example file - i've already copied over them with
fixed ones. The work around (thanks to ArchDev) is to use a gammaPrior with
shape=1, which is exponential.

svn commit 773 commented out a line 181 in BeautiFrame.

As a result the priors for model parameters panel does not update anymore
when changing the Tree prior.

If the user selects a zero posterior limit, it is possible for TreeAnnotator to 
try and calculate a 
median node height or HPDs from a sample of only 1 height. This produces 
obviously erroneous 
results. 

HPDs should probably have a fixed lower limit for number of samples.

Is the median of 1 sample the value of that sample? Or undefined?

What steps will reproduce the problem?
1. Create a general data type
2. Try to use it in an alignment

Description:

In order to model the indel data I have followed the example XML code in the 
tutorial on
the BEAST website that demonstrates how to create a general data type.
However, when the XML file is run in BEAST the following error message is
returned:

SEVERE: Parsing error - poorly formed BEAST file, mixedmodfile_glenn.txt:
Error parsing '<alignment>' element with id, 'alignmentindels':
Multiple dataTypes defined for alignment element

What steps will reproduce the problem?

When trying to remove the last plot

/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/bin/java -Xmx1000m -Xss512k -ea
-Didea.launcher.port=7532
-Didea.launcher.bin.path=/home/joseph/bin/idea-6107/bin
-Dfile.encoding=UTF-8 -classpath
/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/javaws.jar:/usr/lib/jvm/java-1.5.0-
sun-1.5.0.11/jre/lib/plugin.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/rt.
jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/deploy.jar:/usr/lib/jvm/java-1.
5.0-sun-1.5.0.11/jre/lib/jce.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/ch
arsets.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/jsse.jar:/usr/lib/jvm/ja
va-1.5.0-sun-1.5.0.11/jre/lib/ext/sunjce_provider.jar:/usr/lib/jvm/java-1.5.0-su
n-1.5.0.11/jre/lib/ext/localedata.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/l
ib/ext/dnsns.jar:/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/ext/sunpkcs11.jar:
/home/joseph/phd/beast/beast-mcmc/classes:/home/joseph/phd/beast/beast-mcmc/lib/
commons-math-1.1.jar:/home/joseph/phd/beast/beast-mcmc/lib/jdom.jar:/home/joseph
/phd/beast/beast-mcmc/lib/jebl-0.4.jar:/home/joseph/bin/idea-6107/lib/idea_rt.ja
r
com.intellij.rt.execution.application.AppMain
dr.app.tracer.application.TracerApp
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 0
    at java.util.Vector.get(Vector.java:710)
    at dr.gui.chart.JChart.getPlot(JChart.java:158)
    at dr.app.tracer.traces.JTraceChart.paintContents(JTraceChart.java:149)
    at dr.gui.chart.JChart.paintComponent(JChart.java:349)
    at javax.swing.JComponent.paint(JComponent.java:1006)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4972)
    at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4925)
    at javax.swing.JComponent._paintImmediately(JComponent.java:4868)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4675)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:451)
    at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueU
tilities.java:114)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
    at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:2
42)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163
)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 0
    at java.util.Vector.get(Vector.java:710)
    at dr.gui.chart.JChart.getPlot(JChart.java:158)
    at dr.app.tracer.traces.JTraceChart.paintContents(JTraceChart.java:149)
    at dr.gui.chart.JChart.paintComponent(JChart.java:349)
    at javax.swing.JComponent.paint(JComponent.java:1006)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintChildren(JComponent.java:843)
    at javax.swing.JComponent.paint(JComponent.java:1015)
    at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4972)
    at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4925)
    at javax.swing.JComponent._paintImmediately(JComponent.java:4868)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4675)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:451)
    at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueU
tilities.java:114)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
    at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:2
42)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163
)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

What steps will reproduce the problem?
1. Choose the codon-partitioned model and unlink the substitution model in 
BEAUti
2. Generate a BEAST file

What is the expected output? What do you see instead?

The hky1.frequencies and hky2.frequencies should be different values but they 
are the same (when 
the BEAST XML is run). They should be calculated from the individual partitions 
rather than from the 
overall alignment.

Edit the burnin cell in LogCombiner/TreeAnnotator and then press Run without 
finishing the editing 
(by pressing return / tab or selecting another cell. The new burnin is ignored. 

Beauti always output a gamma prior distribution with offset of 0.0 regardless 
of user settings.

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

Attached file should run properly.

Please use labels and text to provide additional information.

User report 

> From: Siobain Duffy <[email protected]>
> Date: 17 September 2007 10:17:35 PM
> To: [email protected]
> Cc: [email protected]
> Subject: Beast 1.4.4 severe error, too many iterations in
getNumericalIntegral
>
> Hello,
>
> Thank you so much for creating and maintaining BEAST!
>
> A run this morning failed and told me to inform you, so here's the log
file, the xml file, and the text of the log file also follows this email.
>
> It is a relaxed (exponential) molecular clock/expansion demographic model
.xml file, which was created with BEAUTI 1.4.4.
>
> Thank you, and please contact me if you need any additional information,
> Siobain Duffy
>
> NSF Postdoctoral Fellow
> Center for Infectious Disease Dynamics
> The Pennsylvania State University
>
>
>
>
>                   BEAST v1.4.4, 2002-2007
>        Bayesian Evolutionary Analysis Sampling Trees
>                              by
>            Alexei J. Drummond and Andrew Rambaut
>
>                Department of Computer Science
>                    University of Auckland
>                   [email protected]
>
>              Institute of Evolutionary Biology
>                   University of Edinburgh
>                      [email protected]
>
> Downloads, Help & Resources:
> http://beast.bio.ed.ac.uk/
>
> Source code distributed under the GNU Lesser General Public License:
> http://code.google.com/p/beast-mcmc/
>
> Additional programming & components created by:
> Roald Forsberg
> Gerton Lunter
> Sidney Markowitz
> Oliver Pybus
>
> Thanks to (for use of their code):
> Korbinian Strimmer
>
> Random number seed: 1190022893839
>
> MacRoman
> Parsing XML file: Bv1EXPexpand
> Read alignment, 'alignment':
>   Sequences = 43
>       Sites = 798
>    Datatype = nucleotide
> Site patterns 'patterns' created from positions 1-798 of alignment
'alignment'
>   pattern count = 177
> Creating the tree model, 'treeModel'
>   initial tree topology =
((((((((((EACMV-K35,EACMV-UGK140),EACMZV-K10),EACMV-UG3Svr),(EACMV-K29,EACMV-UG3
Mld)),((EACMV-K211,EACMV-UG1),EACMV-UGK115)),(((EACMV-K24,EACMZV-K270),(EACMV-KE
2K25,EACMV-UGK282)),EACMKV-K300)),((((EACMV-UGK81,EACMZV-K212),EACMKV-K228),EACM
ZV-K272),((EACMKV-K230,EACMKV-K261),EACMV-UGK223))),(((EACMZV-K18,EACMZV-K275),E
ACMV-KE2K208),EACMZV-K19)),(((((((EACMV-UGK137,EACMV-UGK66),(EACMV-UGK72,EACMZV-
K3)),EACMV-UGK23),EACMV-KE2K27),EACMKV-K238),EACMV-KE2K48),(EACMKV-K229,EACMV-K3
25))),(((((EACMV-KEK197,EACMV-UGK262),EACMV-UGK90),EACMV-UGK79),EACMV-K268),((EA
CMV-KE2K201,EACMZV-KE:Kil),EACMZV-K337)))
> Using discretized relaxed clock model.
>   parametric model = exponentialDistributionModel
>    rate categories = 84
> Creating site model:
>   4 category discrete gamma with initial shape = 0.5
>   initial proportion of invariant sites = 0.5
> TreeLikelihood using native nucleotide likelihood core
>   Ignoring ambiguities in tree likelihood.
>   Partial likelihood scaling off.
> Branch rate model used: discretizedBranchRates
> Creating swap operator for parameter branchRates.categories (weight=30)
> Creating the MCMC chain:
>   chainLength=10000000
>   autoOptimize=true
>   fullEvaluation=2000
> Sep 17, 2007 6:07:35 AM dr.app.beast.BeastMain <init>
> SEVERE: Error running file: Bv1EXPexpand
> Sep 17, 2007 6:07:35 AM dr.app.beast.BeastMain <init>
> SEVERE: Fatal exception (email the authors)
> Fatal exception (email the authors)
> java.lang.RuntimeException: Too many iterations in getNumericalIntegral
> at
dr.evolution.coalescent.DemographicFunction$Abstract.getNumericalIntegral(Unknow
n
Source)
> at dr.evolution.coalescent.Expansion.getIntegral(Unknown Source)
> at dr.evolution.coalescent.Coalescent.calculateLogLikelihood(Unknown Source)
> at
dr.evomodel.coalescent.NewCoalescentLikelihood.calculateLogLikelihood(Unknown
Source)
> at
dr.evomodel.coalescent.NewCoalescentLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.markovchain.MarkovChain.evaluate(Unknown Source)
> at dr.inference.markovchain.MarkovChain.<init>(Unknown Source)
> at dr.inference.mcmc.MCMC.init(Unknown Source)
> at dr.inference.mcmc.MCMC$2.parseXMLObject(Unknown Source)
> at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
> at dr.xml.XMLParser.convert(Unknown Source)
> at dr.xml.XMLParser.convert(Unknown Source)
> at dr.xml.XMLParser.parse(Unknown Source)
> at dr.app.beast.BeastMain.<init>(Unknown Source)
> at dr.app.beast.BeastMain.main(Unknown Source)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
> at java.lang.reflect.Method.invoke(Method.java:585)
> at apple.launcher.LaunchRunner.run(LaunchRunner.java:88)
> at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
> at
apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)
>
>
>
>
>

Would be nice to have an exponential change skyline model.

The code to calculate the Auto-Correlation-Time and the
Effective-Sample-Size is duplicated in two files.

1. LogAnalyzer uses "src/dr/inference/trace/TraceAnalysis.java"
2. Tracer uses "src/dr/app/tracer/TraceCorrelation.java"

Hopefully this will eventually be in one place.