maltcms.io.xml.mzXML

Class MZXMLStaxDataSource

java.lang.Object

maltcms.io.xml.mzXML.MZXMLStaxDataSource

All Implemented Interfaces:

IConfigurable, IDataSource, Serializable, org.apache.commons.configuration.event.ConfigurationListener

public class MZXMLStaxDataSource
extends Object
implements IDataSource

Implements IDataSource for mzXML Files.

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MZXMLStaxDataSource()

Method Summary

Methods

Modifier and Type	Method and Description
int	canRead(IFileFragment ff) Checks, if passed in file is valid mzXML, by trying to invoke the parser on it.
void	configurationChanged(org.apache.commons.configuration.event.ConfigurationEvent arg0)
void	configure(org.apache.commons.configuration.Configuration configuration)
String	getIntensityValuesVarName()
String	getMassRangeMax()
String	getMassRangeMin()
String	getMassValuesVarName()
String	getScanAcquisitionTimeVarName()
String	getScanIndexVarName()
String	getSourceFilesVarName()
String	getTotalIntensityVarName()
ArrayList<Array>	readAll(IFileFragment f)
ArrayList<Array>	readIndexed(IVariableFragment f)
Array	readSingle(IVariableFragment f) Reads a single array referenced by a IVariableFragment.
ArrayList<IVariableFragment>	readStructure(IFileFragment f)
IVariableFragment	readStructure(IVariableFragment f)
void	setIntensityValuesVarName(String intensity_values)
void	setMassRangeMax(String mass_range_max)
void	setMassRangeMin(String mass_range_min)
void	setMassValuesVarName(String mass_values)
void	setScanAcquisitionTimeVarName(String scan_acquisition_time)
void	setScanIndexVarName(String scan_index)
void	setSourceFilesVarName(String source_files)
void	setTotalIntensityVarName(String total_intensity)
boolean	structureWrite(IFileFragment f, ArrayList<IVariableFragment> a)
List<String>	supportedFormats()
boolean	write(IFileFragment f)

Methods inherited from class java.lang.Object

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

Constructor Detail

MZXMLStaxDataSource

public MZXMLStaxDataSource()

Method Detail

canRead

public int canRead(IFileFragment ff)

Checks, if passed in file is valid mzXML, by trying to invoke the parser on it.

Specified by:

canRead in interface IDataSource

configurationChanged

public void configurationChanged(org.apache.commons.configuration.event.ConfigurationEvent arg0)

Specified by:

configurationChanged in interface org.apache.commons.configuration.event.ConfigurationListener

configure

public void configure(org.apache.commons.configuration.Configuration configuration)

Specified by:

configure in interface IConfigurable

getIntensityValuesVarName

public String getIntensityValuesVarName()

Returns:

the intensity_values

getMassRangeMax

public String getMassRangeMax()

Returns:

the mass_range_max

getMassRangeMin

public String getMassRangeMin()

Returns:

the mass_range_min

getMassValuesVarName

public String getMassValuesVarName()

Returns:

the mass_values

getScanAcquisitionTimeVarName

public String getScanAcquisitionTimeVarName()

Returns:

the scan_acquisition_time

getScanIndexVarName

public String getScanIndexVarName()

Returns:

the scan_index

getSourceFilesVarName

public String getSourceFilesVarName()

Returns:

the source_files

getTotalIntensityVarName

public String getTotalIntensityVarName()

Returns:

the total_intensity

readAll

public ArrayList<Array> readAll(IFileFragment f)
                         throws IOException,
                                ResourceNotAvailableException

Specified by:

readAll in interface IDataSource

Throws:

IOException

ResourceNotAvailableException

readIndexed

public ArrayList<Array> readIndexed(IVariableFragment f)
                             throws IOException,
                                    ResourceNotAvailableException

Specified by:

readIndexed in interface IDataSource

Throws:

IOException

ResourceNotAvailableException

readSingle

public Array readSingle(IVariableFragment f)
                 throws IOException,
                        ResourceNotAvailableException

Reads a single array referenced by a IVariableFragment. This method mimics the semantics of NetcdfDataSource.

Specified by:

readSingle in interface IDataSource

Throws:

IOException

ResourceNotAvailableException

readStructure

public ArrayList<IVariableFragment> readStructure(IFileFragment f)
                                           throws IOException

Specified by:

readStructure in interface IDataSource

Throws:

IOException

readStructure

public IVariableFragment readStructure(IVariableFragment f)
                                throws IOException,
                                       ResourceNotAvailableException

Specified by:

readStructure in interface IDataSource

Throws:

IOException

ResourceNotAvailableException

setIntensityValuesVarName

public void setIntensityValuesVarName(String intensity_values)

Parameters:

intensity_values - the intensity_values to set

setMassRangeMax

public void setMassRangeMax(String mass_range_max)

Parameters:

mass_range_max - the mass_range_max to set

setMassRangeMin

public void setMassRangeMin(String mass_range_min)

Parameters:

mass_range_min - the mass_range_min to set

setMassValuesVarName

public void setMassValuesVarName(String mass_values)

Parameters:

mass_values - the mass_values to set

setScanAcquisitionTimeVarName

public void setScanAcquisitionTimeVarName(String scan_acquisition_time)

Parameters:

scan_acquisition_time - the scan_acquisition_time to set

setScanIndexVarName

public void setScanIndexVarName(String scan_index)

Parameters:

scan_index - the scan_index to set

setSourceFilesVarName

public void setSourceFilesVarName(String source_files)

Parameters:

source_files - the source_files to set

setTotalIntensityVarName

public void setTotalIntensityVarName(String total_intensity)

Parameters:

total_intensity - the total_intensity to set

structureWrite

public boolean structureWrite(IFileFragment f,
                     ArrayList<IVariableFragment> a)

supportedFormats

public List<String> supportedFormats()

Specified by:

supportedFormats in interface IDataSource

write

public boolean write(IFileFragment f)

Specified by:

write in interface IDataSource