org.proteios.io
Class XTandemParameterFileUtil

java.lang.Object
  org.proteios.io.XTandemParameterFileUtil

All Implemented Interfaces:

FileValidationInterface, XTandemParameterFileUtilInterface

public class XTandemParameterFileUtil
extends Object
implements XTandemParameterFileUtilInterface, FileValidationInterface

This class implements the XTandemParameterFileUtilInterface that defines methods to access input data from an XTandem input file.

Author:

olle

Constructor Summary

XTandemParameterFileUtil()
Default constructor.

XTandemParameterFileUtil(File xTandemParameterFile)
Constructor that takes an XTandem parameter file item as parameter.

XTandemParameterFileUtil(InputStream xmlInputStream)
Constructor that takes an XTandem input XML input stream as parameter.

Method Summary

void	exportXTandemParameterSet(XTandemParameterSet xTandemParameterSet) Export XTandemParameterSet item to output stream.
XTandemParameterSet	fetchXTandemParameterSet() Fetch XTandemParameterSet item from input stream.
String	getXMLFilePath() Get XTandem input XML file path.
InputStream	getXMLInputStream() Get XTandem input XML input stream.
OutputStream	getXMLOutputStream() Get XTandem input XML output stream.
String	getXsdFilePath() Get XSD schema file to validate against.
File	getXTandemParameterFile() Get the XTandem parameter file item.
XTandemParameterSet	getXTandemParameterSet() Get the XTandem parameter set item.
boolean	importable() Validates first element of input stream.
void	saveXTandemParameterSet() Save XTandem parameter set from XTandemParameterSet item instance variable to XML output stream.
void	saveXTandemParameterSet(XTandemParameterSet xTandemParameterSetArg) Save XTandem parameter set from XTandemParameterSet item to XML output stream.
void	setXMLFilePath(String xmlFilePath) Set XTandem input XML file path.
void	setXMLInputStream(InputStream xmlInputStream) Set XTandem input XML input stream.
void	setXMLOutputStream(OutputStream xmlOutputStream) Set XTandem input XML output stream.
void	setXsdFilePath(String xsdFilePath) Set XSD schema file to validate against.
void	setXTandemParameterFile(File xTandemParameterFile) Set the XTandem parameter file item.
void	setXTandemParameterSet(XTandemParameterSet xTandemParameterSet) Set the XTandem parameter set item.
boolean	valid() Validates XTandem input XML input stream against current XTandem input XSD file.
void	writeBlankLine() Writes a blank line.
void	writeEndTag(String tagName) Writes XML end tag for an XML block.
void	writeHeaderNoteTag(String value) Writes an XTandem input header note XML tag.
void	writeHeaderNoteTag(String attrName, String attrValue, String value) Writes an XTandem input header note XML tag.
void	writeIndentedText(String text, int extraIndentation) Writes indented text with optional extra indentation.
void	writeNoteTag(String label, String value) Writes an XTandem input "note" XML tag.
void	writeStartTag(String tagName) Writes XML start tag for an XML block.

Methods inherited from class java.lang.Object

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

Constructor Detail

XTandemParameterFileUtil

public XTandemParameterFileUtil()

Default constructor.

XTandemParameterFileUtil

public XTandemParameterFileUtil(File xTandemParameterFile)

Constructor that takes an XTandem parameter file item as parameter.

Parameters:

xTandemParameterFile - File xTandemParameterFile XTandem parameter file item.

XTandemParameterFileUtil

public XTandemParameterFileUtil(InputStream xmlInputStream)

Constructor that takes an XTandem input XML input stream as parameter.

Parameters:

xmlInputStream - InputStream XTandem input XML input stream.

Method Detail

getXsdFilePath

public String getXsdFilePath()

Get XSD schema file to validate against.

Returns:

xsdFilePath String with path for XSD schema file.

setXsdFilePath

public void setXsdFilePath(String xsdFilePath)

Set XSD schema file to validate against.

Parameters:

xsdFilePath - String with path for XSD schema file.

getXMLFilePath

public String getXMLFilePath()

Get XTandem input XML file path.

Returns:

xmlFilePath String with path for XTandem input XML file.

setXMLFilePath

public void setXMLFilePath(String xmlFilePath)

Set XTandem input XML file path.

Parameters:

xmlFilePath - String with path for XTandem input XML file.

getXMLInputStream

public InputStream getXMLInputStream()

Get XTandem input XML input stream.

Returns:

xmlFilePath InputStream XTandem input XML input stream.

setXMLInputStream

public void setXMLInputStream(InputStream xmlInputStream)

Set XTandem input XML input stream.

Parameters:

xmlInputStream - InputStream XTandem input XML input stream.

getXMLOutputStream

public OutputStream getXMLOutputStream()

Get XTandem input XML output stream.

Returns:

xmlFilePath OutputStream XTandem input XML output stream.

setXMLOutputStream

public void setXMLOutputStream(OutputStream xmlOutputStream)

Set XTandem input XML output stream.

Parameters:

xmlOutputStream - OutputStream XTandem input XML output stream.

getXTandemParameterFile

public File getXTandemParameterFile()

Get the XTandem parameter file item.

Returns:

File XTandem parameter file item.

setXTandemParameterFile

public void setXTandemParameterFile(File xTandemParameterFile)

Set the XTandem parameter file item.

Parameters:

xTandemParameterFile - File XTandem parameter file item.

getXTandemParameterSet

public XTandemParameterSet getXTandemParameterSet()

Get the XTandem parameter set item.

Specified by:

getXTandemParameterSet in interface XTandemParameterFileUtilInterface

Returns:

XTandemParameterSet XTandem parameter set item.

setXTandemParameterSet

public void setXTandemParameterSet(XTandemParameterSet xTandemParameterSet)

Set the XTandem parameter set item.

Parameters:

xTandemParameterSet - XTandemParameterSet XTandem parameter set item.

valid

public boolean valid()
              throws javax.xml.stream.XMLStreamException,
                     SAXException

Validates XTandem input XML input stream against current XTandem input XSD file.

Specified by:

valid in interface FileValidationInterface

Returns:

True if the XTandem input XML input stream is valid, else false

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

SAXException

importable

public boolean importable()

Validates first element of input stream.

Specified by:

importable in interface FileValidationInterface

Returns:

True if the input stream is valid, else false

fetchXTandemParameterSet

public XTandemParameterSet fetchXTandemParameterSet()

Fetch XTandemParameterSet item from input stream.

Returns:

item with settings data.

saveXTandemParameterSet

public void saveXTandemParameterSet()

Save XTandem parameter set from XTandemParameterSet item instance variable to XML output stream.

saveXTandemParameterSet

public void saveXTandemParameterSet(XTandemParameterSet xTandemParameterSetArg)

Save XTandem parameter set from XTandemParameterSet item to XML output stream.

Parameters:

xTandemParameterSetArg - item with settings data.

exportXTandemParameterSet

public void exportXTandemParameterSet(XTandemParameterSet xTandemParameterSet)

Export XTandemParameterSet item to output stream.

Parameters:

xTandemParameterSet - XTandemParameterSet item with settings data.

writeStartTag

public void writeStartTag(String tagName)
                   throws javax.xml.stream.XMLStreamException

Writes XML start tag for an XML block.

Parameters:

tagName - String tag name

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeEndTag

public void writeEndTag(String tagName)
                 throws javax.xml.stream.XMLStreamException

Writes XML end tag for an XML block.

Parameters:

tagName - String tag name

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeBlankLine

public void writeBlankLine()
                    throws javax.xml.stream.XMLStreamException

Writes a blank line.

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeNoteTag

public void writeNoteTag(String label,
                         String value)
                  throws javax.xml.stream.XMLStreamException

Writes an XTandem input "note" XML tag.

Parameters:

label - String label

value - String value

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeHeaderNoteTag

public void writeHeaderNoteTag(String value)
                        throws javax.xml.stream.XMLStreamException

Writes an XTandem input header note XML tag.

Parameters:

value - String value

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeHeaderNoteTag

public void writeHeaderNoteTag(String attrName,
                               String attrValue,
                               String value)
                        throws javax.xml.stream.XMLStreamException

Writes an XTandem input header note XML tag.

Parameters:

attrName - String attrName

attrValue - String attrValue

value - String value

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

writeIndentedText

public void writeIndentedText(String text,
                              int extraIndentation)
                       throws javax.xml.stream.XMLStreamException

Writes indented text with optional extra indentation. The indentation level counter is not updated.

Parameters:

text - String with text.

extraIndentation - int optional extra indentation.

Throws:

javax.xml.stream.XMLStreamException - If there is an error