org.sigpath.bioimport.reaction2
Class Concentration_measurement

java.lang.Object
  org.sigpath.bioimport.reaction2.Concentration_measurement

All Implemented Interfaces:

Serializable

public class Concentration_measurement
extends Object
implements Serializable

Used to describe concentration measurements for molecules in SigPath

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

Concentration_measurement()

Method Summary

void	deleteValue() Method deleteValue
String	getComments() Returns the value of field 'comments'.
String	getId() Returns the value of field 'id'.
String	getMeasurement_method() Returns the value of field 'measurement_method'.
Molecule	getMolecule() Returns the value of field 'molecule'.
Ref	getRef() Returns the value of field 'ref'.
String	getSample_prep() Returns the value of field 'sample_prep'.
String	getSpid() Returns the value of field 'spid'.
String	getTissue() Returns the value of field 'tissue'.
UnitType	getUnit() Returns the value of field 'unit'.
double	getValue() Returns the value of field 'value'.
boolean	hasValue() Method hasValue
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
void	setComments(String comments) Sets the value of field 'comments'.
void	setId(String id) Sets the value of field 'id'.
void	setMeasurement_method(String measurement_method) Sets the value of field 'measurement_method'.
void	setMolecule(Molecule molecule) Sets the value of field 'molecule'.
void	setRef(Ref ref) Sets the value of field 'ref'.
void	setSample_prep(String sample_prep) Sets the value of field 'sample_prep'.
void	setSpid(String spid) Sets the value of field 'spid'.
void	setTissue(String tissue) Sets the value of field 'tissue'.
void	setUnit(UnitType unit) Sets the value of field 'unit'.
void	setValue(double value) Sets the value of field 'value'.
static Concentration_measurement	unmarshal(Reader reader) Method unmarshal
void	validate() Method validate

Methods inherited from class java.lang.Object

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

Constructor Detail

Concentration_measurement

public Concentration_measurement()

Method Detail

deleteValue

public void deleteValue()

Method deleteValue

getComments

public String getComments()

Returns the value of field 'comments'. The field 'comments' has the following description: Allows you to include comments

Returns:

String

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

getMeasurement_method

public String getMeasurement_method()

Returns the value of field 'measurement_method'. The field 'measurement_method' has the following description: Used to annotate the concentration measurement method

Returns:

String

getMolecule

public Molecule getMolecule()

Returns the value of field 'molecule'. The field 'molecule' has the following description: Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac. (accession number; this attribute has the second highest precedence) or spid (unique SigPath identifier; this identifier has the lowest precedence)

Returns:

Molecule

getRef

public Ref getRef()

Returns the value of field 'ref'. The field 'ref' has the following description: annotates a reference which has a PubMed ID

Returns:

Ref

getSample_prep

public String getSample_prep()

Returns the value of field 'sample_prep'. The field 'sample_prep' has the following description: Used to annotate sample preparation methods

Returns:

String

getSpid

public String getSpid()

Returns the value of field 'spid'.

Returns:

String

getTissue

public String getTissue()

Returns the value of field 'tissue'. The field 'tissue' has the following description: Tissue in which the concentration was measured

Returns:

String

getUnit

public UnitType getUnit()

Returns the value of field 'unit'. The field 'unit' has the following description: Selects units for the reaction parameter

Returns:

UnitType

getValue

public double getValue()

Returns the value of field 'value'. The field 'value' has the following description: Defines the value of a reaction parameter

Returns:

double

hasValue

public boolean hasValue()

Method hasValue

Returns:

boolean

isValid

public boolean isValid()

Method isValid

Returns:

boolean

marshal

public void marshal(Writer out)
             throws MarshalException,
                    ValidationException

Method marshal

Parameters:

out -

Throws:

MarshalException

ValidationException

marshal

public void marshal(ContentHandler handler)
             throws IOException,
                    MarshalException,
                    ValidationException

Method marshal

Parameters:

handler -

Throws:

IOException

MarshalException

ValidationException

setComments

public void setComments(String comments)

Sets the value of field 'comments'. The field 'comments' has the following description: Allows you to include comments

Parameters:

comments - the value of field 'comments'.

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

setMeasurement_method

public void setMeasurement_method(String measurement_method)

Sets the value of field 'measurement_method'. The field 'measurement_method' has the following description: Used to annotate the concentration measurement method

Parameters:

measurement_method - the value of field 'measurement_method'.

setMolecule

public void setMolecule(Molecule molecule)

Sets the value of field 'molecule'. The field 'molecule' has the following description: Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac. (accession number; this attribute has the second highest precedence) or spid (unique SigPath identifier; this identifier has the lowest precedence)

Parameters:

molecule - the value of field 'molecule'.

setRef

public void setRef(Ref ref)

Sets the value of field 'ref'. The field 'ref' has the following description: annotates a reference which has a PubMed ID

Parameters:

ref - the value of field 'ref'.

setSample_prep

public void setSample_prep(String sample_prep)

Sets the value of field 'sample_prep'. The field 'sample_prep' has the following description: Used to annotate sample preparation methods

Parameters:

sample_prep - the value of field 'sample_prep'.

setSpid

public void setSpid(String spid)

Sets the value of field 'spid'.

Parameters:

spid - the value of field 'spid'.

setTissue

public void setTissue(String tissue)

Sets the value of field 'tissue'. The field 'tissue' has the following description: Tissue in which the concentration was measured

Parameters:

tissue - the value of field 'tissue'.

setUnit

public void setUnit(UnitType unit)

Sets the value of field 'unit'. The field 'unit' has the following description: Selects units for the reaction parameter

Parameters:

unit - the value of field 'unit'.

setValue

public void setValue(double value)

Sets the value of field 'value'. The field 'value' has the following description: Defines the value of a reaction parameter

Parameters:

value - the value of field 'value'.

unmarshal

public static Concentration_measurement unmarshal(Reader reader)
                                           throws MarshalException,
                                                  ValidationException

Method unmarshal

Parameters:

reader -

Returns:

Concentration_measurement

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException