XML Handling

[Beynon, Rob]

Hello all,

I'm experimenting with moving to XML for some of my data files, a typical example is placed at the bottom of this message. It is attractive since there are lots of XML editors out there which means that users can make minor changes to the data file without running the programme. The programme reads in some experimental data and generates an SVG file for presentation quality graphics - I have not bothered to write the same graphic within Rev. If you want to see the program it is at http://www.liv.ac.uk/pfg/Downloads/PeptideMapper.zip but you'd probably need to be a bit of a biochemist to make sense of it! It is my first real Rev program.

 

What I'm not clear about is how I use Rev's XML functions to read in such a file, and populate my program's variables with the various values. It seems as though I would need to still write lots of nested loops, which suggests I'm missing a trick. Can anyone point me at some demonstration material that would help me generate an XML parser.

 

BTW, the XML file below was created in a text editor. I will also need to learn how to write this file within my programme!

 

Thanks in advance

Rob

 

p.s. The file has been truncated because the total posting was too large..sigh L

 

<?xml version="1.0" encoding="utf-8"?>

<PEPMAP>

  <HEADERS>

    <HEADER name="Head" value="QconCAT_LS1" />

    <HEADER name="Note" value="Test of XML format for pmap" />

    <HEADER name="Operator" value="Rob Beynon" />

    <HEADER name="Date" value="7th June 2008" />

  </HEADERS>

  <SEQUENCE>

    <SEQ name="protein" Value="SEQSAMEALILQLHEIGAVKVTNWSNVVIAYEPVWAIGTGKNDEWLNGEFISTVQQREITAELPIYLANSLNSLRDAPALVDLATGQEILATGIKVLPTAQSGAEPLPEGLLWLLLTGKANADIIQISGYDGGTGASPISSIKALDWGPGGGPDLIVDDGGDATLLIHEGVKGQMEPWDGPALVLFSDGKVLVVANPANTNALILKGMTGLLWETSLLDPEEGIRSGETEDTFIADLAVGLSTGQIKTTTGDEEQVSSTLAEKTPEESLMILVPEAYK" />

  </SEQUENCE>

  <MAPPROPS>

    <PROP name="Annotation" value="YES" />

    <PROP name="UseLines" value="YES" />

    <PROP name="Protease" value="trypsin" />

    <PROP name="Height" value="15" />

    <PROP name="LabelLimit" value="600" />

    <PROP name="LabelMasses" value="M2H" />

    <PROP name="Scale" value="2" />

    <PROP name="FragmentNumbers" value="YES" />

    <PROP name="LabelCMCys" value="NO" />

    <PROP name="Labels" type="YES" />

    <PROP name="Annotation" value="YES" />

    <PROP name="FlagRK" value="YES" />

  </MAPPROPS>

  <PEPLABELS>

    <PEPLABEL name="1" value="PYR5_ARATH_UMP_Synthase" />

    

  </PEPLABELS>

  <BOXCOLOURS>

    <COLOR name="0" value="255,255,255" />

    <COLOR name="1" value="128,128,255" />

    <COLOR name="2" value="255,128,0" />

    <COLOR name="3" value="64,128,64" />

  </BOXCOLOURS>

  <BLOCKCOLOURS>

    <BLOCKCOLOUR name="1" value="1,2,5,6,7,8,9,10,12,13,14" />

    <BLOCKCOLOUR name="2" value="3,4,11" />

    <BLOCKCOLOUR name="3" value="1,13,14" />

  </BLOCKCOLOURS>

</PEPMAP>

 

This email was sent on 14/06/08 at 4:03 PM.