org.proteios.io.mzdata
Class MzDataImpCommonDc

java.lang.Object
  org.proteios.io.mzdata.MzDataImpCommon
      org.proteios.io.mzdata.MzDataImpCommonDc

Direct Known Subclasses:

MzDataImpCommonAnnotation

public class MzDataImpCommonDc
extends MzDataImpCommon

This class supports import of mzData files into Proteios. It contains common attributes and methods, and is intended to be the parent class for other classes that process an XML block in an mzData file. An mzData file contains information on a mass spectrometry experiment. The mzData file is first vaildated against the XML Schema Definition file mzdata.xsd. If the file is valid, its content is parsed and selected information stored in Proteios. The mzData file is parsed using cursor-based XML stream parsing. The StAX (Stream API for XML) parser finds start and stop (end) tags, which are then processed. Element attributes are located in the start tag, and elements of simple types are stored directly after the start tag is read. For more complex elements, values of attributes and sub-elements are collected in temporary variables, until the end tag is reached, and the colelcted contents are stored. Example: XML tag tagData At start tag: Method thisTagElementStart() stores attribute values. Between tags: tagData is stored in temporary StringBuffer. At end tag: Method thisTagItem() processes collected data. Tag data may be exchanged for a start/end tag pair, etc.

Version:

2.0

Author:

Olle

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

protected Annotator	anna
protected DbControl	dc
protected ItemFactory	factory

Fields inherited from class org.proteios.io.mzdata.MzDataImpCommon

log

Constructor Summary

MzDataImpCommonDc(SessionControl sc)
Default constructor.

Method Summary

void	enableDbControl() Make sure that DbControl is running.
void	enableDbControl(BasicItem item) Make sure that DbControl is running, and that the item is attached to it.
DbControl	getDbControl() Get the DbControl.
SessionControl	getSessionControl()
void	setDbControl(DbControl dc) Set the DbControl.

Methods inherited from class org.proteios.io.mzdata.MzDataImpCommon

blockEnd, blockStart, getBlockTagName, getTempStrBuf, parse, processCData, processCharacters, processInternalEndElement, processInternalStartElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Field Detail

dc

protected DbControl dc

factory

protected ItemFactory factory

anna

protected Annotator anna

Constructor Detail

MzDataImpCommonDc

public MzDataImpCommonDc(SessionControl sc)

Default constructor.

Method Detail

getSessionControl

public SessionControl getSessionControl()

getDbControl

public DbControl getDbControl()

Get the DbControl.

Returns:

dc DbControl the current DbControl.

setDbControl

public void setDbControl(DbControl dc)

Set the DbControl.

Parameters:

dc - DbControl the DbControl to set.

enableDbControl

public void enableDbControl()

Make sure that DbControl is running.

enableDbControl

public void enableDbControl(BasicItem item)

Make sure that DbControl is running, and that the item is attached to it.

Parameters:

item - BasicItem item to reattach to DbController