org.fhcrc.cpl.viewer.amt
Class AmtXmlReader

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AmtXmlReader

public class AmtXmlReader
extends java.lang.Object

A restrictive wrapper for reading AmtXml files. The method is a compromise between the elegance of DOM/XmlBeans and the efficiency of stax. We use Stax2DomBuilder to pull DOM subtrees out of the pepxml file for bits that we care about, namely modifications and features

Field Summary

protected AmtDatabase

mAmtDatabase

Constructor Summary

AmtXmlReader(java.io.File file)
Read in a amtxml file

Method Summary

protected void	extractEntries(java.io.File inputFile)
protected void	extractMetadataAndModifications(java.io.File inputFile) TODO: get hydrophobicity calculator and version
protected void	extractRuns(java.io.File inputFile) extracts interesting stuff at the amt_database level, and all runs
AmtDatabase	getDatabase() Accessor for loaded database
void	read(java.io.File file) Read in a file, extract modifications and features

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mAmtDatabase

protected AmtDatabase mAmtDatabase

Constructor Detail

AmtXmlReader

public AmtXmlReader(java.io.File file)
             throws java.io.FileNotFoundException,
                    javax.xml.stream.XMLStreamException

Read in a amtxml file

Parameters:

file -

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

Method Detail

read

public void read(java.io.File file)
          throws java.io.FileNotFoundException,
                 javax.xml.stream.XMLStreamException

Read in a file, extract modifications and features

Parameters:

file -

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

extractMetadataAndModifications

protected void extractMetadataAndModifications(java.io.File inputFile)
                                        throws java.io.FileNotFoundException,
                                               javax.xml.stream.XMLStreamException

TODO: get hydrophobicity calculator and version

Parameters:

inputFile -

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

extractRuns

protected void extractRuns(java.io.File inputFile)
                    throws java.io.FileNotFoundException,
                           javax.xml.stream.XMLStreamException

extracts interesting stuff at the amt_database level, and all runs

Parameters:

inputFile -

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

extractEntries

protected void extractEntries(java.io.File inputFile)
                       throws java.io.FileNotFoundException,
                              javax.xml.stream.XMLStreamException

Parameters:

inputFile -

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

getDatabase

public AmtDatabase getDatabase()

Accessor for loaded database

Returns: