org.fhcrc.cpl.viewer.amt
Class AmtXmlWriter

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

public class AmtXmlWriter
extends java.lang.Object

A restrictive wrapper for writing AmtXml files. We take advantage of XmlBeans to build the structure of the amtxmlxml file, and to build individual peptide_entries, but we stitch the XmlBeans XML output for features together by hand, writing out to a file as we go, so that we don't have to hold the whole structure in memory

Field Summary

protected java.lang.String	_documentPostscript
protected java.lang.String	_documentPrefix
protected org.apache.xmlbeans.XmlOptions	_optionsForPrinting
protected AmtDatabase	mAmtDatabase

Constructor Summary

AmtXmlWriter()
Constructor creates the XmlBeans representing the shell of a AmtXml document, and creates the "prefix" and "postscript" strings representing that shell

AmtXmlWriter(AmtDatabase amtDatabase)

Method Summary

protected void	generateStubs()
protected void	init()
void	setAmtDatabase(AmtDatabase database)
void	write(java.io.File file) Write out the full document, with all modifications and features, to a file
protected void	writeEntries(java.io.PrintWriter pw)
protected void	writeEntry(AmtPeptideEntry entry, java.io.PrintWriter pw) Write out a single peptide entry
protected void	writeModification(org.fhcrc.cpl.toolbox.proteomics.MS2Modification ms2Modification, java.io.PrintWriter pw)
protected void	writeModifications(java.io.PrintWriter pw)
protected void	writeRun(AmtRunEntry run, java.io.PrintWriter pw) Write out a single run
protected void	writeRuns(java.io.PrintWriter pw) Write out all the runs

Methods inherited from class java.lang.Object

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

Field Detail

mAmtDatabase

protected AmtDatabase mAmtDatabase

_documentPrefix

protected java.lang.String _documentPrefix

_documentPostscript

protected java.lang.String _documentPostscript

_optionsForPrinting

protected org.apache.xmlbeans.XmlOptions _optionsForPrinting

Constructor Detail

AmtXmlWriter

public AmtXmlWriter()

Constructor creates the XmlBeans representing the shell of a AmtXml document, and creates the "prefix" and "postscript" strings representing that shell

AmtXmlWriter

public AmtXmlWriter(AmtDatabase amtDatabase)

Method Detail

init

protected void init()

generateStubs

protected void generateStubs()

setAmtDatabase

public void setAmtDatabase(AmtDatabase database)

writeEntries

protected void writeEntries(java.io.PrintWriter pw)

writeEntry

protected void writeEntry(AmtPeptideEntry entry,
                          java.io.PrintWriter pw)

Write out a single peptide entry

Parameters:

entry -

pw -

writeModifications

protected void writeModifications(java.io.PrintWriter pw)

writeModification

protected void writeModification(org.fhcrc.cpl.toolbox.proteomics.MS2Modification ms2Modification,
                                 java.io.PrintWriter pw)

writeRuns

protected void writeRuns(java.io.PrintWriter pw)

Write out all the runs

Parameters:

pw -

writeRun

protected void writeRun(AmtRunEntry run,
                        java.io.PrintWriter pw)

Write out a single run

Parameters:

pw -

write

public void write(java.io.File file)
           throws java.io.IOException

Write out the full document, with all modifications and features, to a file

Parameters:

file -

Throws:

java.io.IOException