Re: [Fastphylo-users] FNJ: XML parsing bug

[Mehmood K. <mal...@kt...>]

Fixed... I was making mistake in writing xml to file.


<?xml version="1.0"?>
 <root>
  <runs>
   <run id="run1" dim="3">
    <identities>
     <identity name="Alpha"/>
     <identity name="Beta"/>
     <identity name="Gamma"/>
    </identities>
    <tree>
     <count>1</count>
     <newick-xml><branch><leaf>Gamma</leaf><leaf>Beta</leaf><leaf>Alpha</leaf></branch></newick-xml>
     <newick>(Gamma,Beta,Alpha);</newick>
    </tree>
   </run>
   <run id="run2" dim="3">
    <identities>
     <identity name="Alpha"/>
     <identity name="Beta"/>
     <identity name="Gamma"/>
    </identities>
    <tree>
     <count>1</count>
     <newick-xml><branch><leaf>Gamma</leaf><leaf>Beta</leaf><leaf>Alpha</leaf></branch></newick-xml>
     <newick>(Gamma,Beta,Alpha);</newick>
    </tree>
   </run>
  </runs>
 </root>


On Jul 30, 2012, at 3:46 PM, Mehmood Khan wrote:

Hi,

It seems like the XML functionality for FNJ is not working, getting this error with the input file attached here...

error:
malagori@nitrogen:/tmp/install/bin$ ./fnj -I xml ~/svn/fastphylo/fdist_xml_xml.out
<?xml version="1.0"?>
 <root>
  <runs>
/afs/pdc.kth.se/home/m/malagori/svn/fastphylo/fdist_xml_xml.out:16: element dm: Relax-NG validity error : Did not expect element dm there

-----------------
Exception
File:      /afs/pdc.kth.se/home/m/malagori/svn/fastphylo/trunk/src/c++/programs/fnj/XmlInputStream.cpp
Function:  readDM
Line:      71
Message:   xml input does not validate
-----------------


Cheers,
Mehmood


<fdist_xml_xml.out>------------------------------------------------------------------------------
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