Phenyx/format/pidresxml/indexing

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Getting peakist from pidres.xml

We have a indexMaker.pl (package into InSilicoSpectro on CPAN, don't ask why...) that builds xml index of xml files for faster data retrieval (in practice, we index this index with libraries like lucen in java for a real fast access). We can build more or less whatever index we want (the one we use for the java interface is slightly more complete, including peptmatches, DBMatches...)

Form the following example, you know that you can retrieve data for peaklist: sample_0%cmpd_2, you know that you can grab data from

• lineNumber="64774"
• columnNumber="10"
• startByte="3971438"
• lengthByte="2036"

<?xml version="1.0" encoding="ISO-8859-1"?>
<xmlIndex>
  <source>
    <file>/var/phenyx/results/203/pidres.xml</file>
    <MD5 type="base_64">B/ZW1V2bxcdgTKX7W/S9lQ</MD5>
    <indexMaker>/home/alex/tmp/pidres-peaklist.indexMaker.xml</indexMaker>
  </source>
  <processed>
    <date>2006-11-15</date>
    <time>11:16:12</time>
  </processed>
  <indexedElements>
    <oneIndexedElement path="/idr:IdentificationResult/anl:AnalysisList/ple:PeakListExport/ple:PeakLists/ple:MSMSRun/ple:peptide" id="0">
      <pos lineNumber="64624" columnNumber="10" startByte="3967480" lengthByte="2189"/>
      <attr name="key" value="sample_0%cmpd_0"/>
    </oneIndexedElement>
    <oneIndexedElement path="/idr:IdentificationResult/anl:AnalysisList/ple:PeakListExport/ple:PeakLists/ple:MSMSRun/ple:peptide" id="1">
      <pos lineNumber="64708" columnNumber="10" startByte="3969680" lengthByte="1747"/>
      <attr name="key" value="sample_0%cmpd_1"/>
    </oneIndexedElement>
    <oneIndexedElement path="/idr:IdentificationResult/anl:AnalysisList/ple:PeakListExport/ple:PeakLists/ple:MSMSRun/ple:peptide" id="2">
      <pos lineNumber="64774" columnNumber="10" startByte="3971438" lengthByte="2036"/>
      <attr name="key" value="sample_0%cmpd_2"/>
    </oneIndexedElement>
    <oneIndexedElement path="/idr:IdentificationResult/anl:AnalysisList/ple:PeakListExport/ple:PeakLists/ple:MSMSRun/ple:peptide" id="3">
      <pos lineNumber="64852" columnNumber="10" startByte="3973485" lengthByte="1849"/>
      <attr name="key" value="sample_0%cmpd_3"/>
    </oneIndexedElement>
    <oneIndexedElement path="/idr:IdentificationResult/anl:AnalysisList/ple:PeakListExport/ple:PeakLists/ple:MSMSRun/ple:peptide" id="4">
      <pos lineNumber="64922" columnNumber="10" startByte="3975345" lengthByte="610"/>
      <attr name="key" value="sample_0%cmpd_4"/>
    </oneIndexedElement>
...