same pattern id given to two different partitions

[GoogleCodeExporter]

What steps will reproduce the problem?
1. add two files for a *beast analysis
2. use essentially the default settings
3. export xml file

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

from beauti 1.6.2, npatterns= are correct, patterns id are unique

    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=335                                                           -->
    <patterns id="gpcytb.patterns" from="1">
        <alignment idref="alignment2"/>
    </patterns>

    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=284                                                           -->
    <patterns id="gp.s7.patterns" from="1">
        <alignment idref="alignment1"/>
    </patterns>

from beauti 1.7.0 Prerelease r4563, npatterns= for second loci is equal to 
total number of bp (if I change the order of the loci the second one is always 
incorrect), patterns id are identical

    <!-- The unique patterns from 1 to end                                       -->
    <!-- npatterns=335                                                           -->
    <patterns id="patterns" from="1">
        <alignment idref="alignment1"/>
    </patterns>

    <!-- The patterns from 1 to end                                              -->
    <!-- npatterns=899                                                           -->
    <patterns id="patterns" from="1" unique="false">
        <alignment idref="alignment2"/>
    </patterns>

When I make the patterns statement unique and change the values below as well, 
ie,

    <!-- Likelihood for tree given sequence data                                 -->
    <treeLikelihood id="treeLikelihood" useAmbiguities="false">
        <patterns idref="gp.s7.patterns"/>

beast will run, but gives an error.

Fatal exception: dr.evolution.util.TaxonList$MissingTaxonException: Taxon, 
GN0949.2.a, in tree, gp.s7.treeModel, is not found in patternList, 
gp.s7.patterns

java.lang.RuntimeException: dr.evolution.util.TaxonList$MissingTaxonException: 
Taxon, GN0949.2.a, in tree, gp.s7.treeModel, is not found in patternList, 
gp.s7.patterns

I've attached the full output from beast.

What version of the product are you using? On what operating system?

beauti 1.7.0 Prerelease r4563

Please provide any additional information below.

Original issue reported on code.google.com by peter.un...@gmail.com on 9 Jan 2012 at 7:03

Attachments:

• beast.output.txt

[GoogleCodeExporter]

Note too, that when beast starts, it reports the site patterns incorrectly as 
well.  Whatever locus is added second gets the pattern count equal to the total 
number of bp in the alignment.

Site patterns 'gp.s7.patterns' created from positions 1-899 of alignment 
'alignment2'
  pattern count = 899

Original comment by peter.un...@gmail.com on 9 Jan 2012 at 10:10

[GoogleCodeExporter]

Original comment by ramb...@gmail.com on 2 Feb 2012 at 3:16

• Changed state: Fixed