Package de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper

Class Experiment

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

All Implemented Interfaces:

AttributeValuePairSupport, ExperimentInterface, MappingDataEntity, Cloneable, Iterable<SubstanceInterface>, Collection<SubstanceInterface>, List<SubstanceInterface>

public class Experiment
extends Object
implements ExperimentInterface

Author:

klukas

Field Summary

Fields inherited from interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

UNSPECIFIED_ATTRIBUTE_STRING, UNSPECIFIED_EXPERIMENTNAME, UNSPECIFIED_SUBSTANCE

Fields inherited from interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.MappingDataEntity

ANNO_DIV

Constructor Summary

Constructors

Constructor	Description
Experiment()
Experiment(ExperimentInterface data)
Experiment(SubstanceInterface data)
Experiment(List<SubstanceInterface> data)
Experiment(Document doc)

Method Summary

Modifier and Type	Method	Description
void	add(int index, SubstanceInterface element)
boolean	add(SubstanceInterface e)
boolean	addAll(int index, Collection<? extends SubstanceInterface> c)
void	addAll(ExperimentInterface m)
boolean	addAll(Collection<? extends SubstanceInterface> c)
void	addAndMerge(ExperimentInterface toBeAdded)
static void	addAndMerge(ExperimentInterface result, ExperimentInterface toBeAdded)	Deprecated.
void	clear()
Experiment	clone()
Experiment	cloneOldStyle()
boolean	contains(Object o)
boolean	containsAll(Collection<?> arg0)
void	ensureCapacity(int minCapacity)
void	fillAttributeMap(Map<String,Object> attributeValueMap)
Experiment	filter(Collection<String> validNames, Collection<String> validTimes)
SubstanceInterface	get(int index)
List<NumericMeasurementInterface>	getAllMeasurements()
static String[]	getConditionsAsString(ExperimentInterface experimentData)
String	getCoordinator()
static ArrayList<Document>	getDocuments(ExperimentInterface mappingDataList)	<experimentdata> <experiment experimentid="-1"> <experimentname>Gluthation</experimentname> <remark>SXD plants</remark> <coordinator>Mohammad Hajirezaei</coordinator> <excelfileid/> <importusername/> <importdate>Tue Mar 10 11:39:36 CET 2009</importdate> <startdate>Sun Jan 18 00:00:00 CET 2004</startdate> <measurements>92</measurements> <imagefiles>0</imagefiles> <sizekb>0</sizekb> </experiment> <measurements> <substance id="column 6" name="Cys"> ...
static ArrayList<Document>	getDocuments(ExperimentInterface mappingDataList, BackgroundTaskStatusProviderSupportingExternalCall status, boolean mergeExperimentsReturnOnlyOne)
static Document	getEmptyDocument(ExperimentHeaderInterface header)
static ExperimentInterface	getExperiment(List<org.jdom2.Document> documents)
static Experiment	getExperimentFromDOM(Document doc)
static Experiment	getExperimentFromJDOM(org.jdom2.Document doc)
ExperimentHeaderInterface	getHeader()
Collection<ExperimentHeaderInterface>	getHeaders()
Date	getImportDate()
double	getMeasurementValuesSum()
static double	getMeasurementValuesSum(ExperimentInterface md)	Deprecated.
String	getName()
int	getNumberOfMeasurementValues()
static int	getNumberOfMeasurementValues(ExperimentInterface md)	Deprecated.
String	getRemark()
String	getSequence()
Date	getStartDate()
static String	getString(ExperimentInterface mappingDataList)
void	getStringOfChildren(StringBuilder r)
static ArrayList<String>	getStrings(ExperimentInterface mappingDataList, BackgroundTaskStatusProviderSupportingExternalCall status, boolean mergeExperimentsReturnOnlyOne)
static String[]	getTimes(ExperimentInterface experimentData)
static DataMappingTypeManagerInterface	getTypeManager()
void	getXMLAttributeString(StringBuilder r)
int	indexOf(Object o)
static boolean	isBiologicalAndTechnicalReplicateDataAvailable(ExperimentInterface md)
boolean	isEmpty()
static boolean	isReplicateDataMissing(ExperimentInterface md)
Iterator<SubstanceInterface>	iterator()
int	lastIndexOf(Object o)
ListIterator<SubstanceInterface>	listIterator()
ListIterator<SubstanceInterface>	listIterator(int index)
void	mergeBiologicalReplicates(BackgroundTaskStatusProviderSupportingExternalCall status)
SubstanceInterface	remove(int index)
boolean	remove(Object o)
boolean	removeAll(Collection<?> arg0)
boolean	retainAll(Collection<?> arg0)
SubstanceInterface	set(int index, SubstanceInterface element)
void	setAttribute(org.jdom2.Attribute attr)
boolean	setData(org.jdom2.Element xmlElement)
void	setDataOfChildElement(org.jdom2.Element childElement)
void	setHeader(ExperimentHeaderInterface header)
static void	setTypeManager(DataMappingTypeManagerInterface m)
int	size()
Collection<ExperimentInterface>	split()
Collection<ExperimentInterface>	splitOldStyle()
List<SubstanceInterface>	subList(int fromIndex, int toIndex)
Object[]	toArray()
<T> T[]	toArray(T[] a)
String	toString()
String	toStringWithErrorThrowing()
void	trimToSize()
void	writeToFile(File targetDir, boolean asDocument)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Constructor Details

Experiment

public Experiment()

Experiment

public Experiment(SubstanceInterface data)

Experiment

public Experiment(List<SubstanceInterface> data)

Experiment

public Experiment(ExperimentInterface data)

Experiment

public Experiment(Document doc)

Method Details

addAll

public void addAll(ExperimentInterface m)

Specified by:

addAll in interface ExperimentInterface

filter

public Experiment filter(Collection<String> validNames,
Collection<String> validTimes)

Specified by:

filter in interface ExperimentInterface

getName

public String getName()

Specified by:

getName in interface ExperimentInterface

getRemark

public String getRemark()

Specified by:

getRemark in interface ExperimentInterface

getCoordinator

public String getCoordinator()

Specified by:

getCoordinator in interface ExperimentInterface

getImportDate

public Date getImportDate()

Specified by:

getImportDate in interface ExperimentInterface

getStartDate

public Date getStartDate()

Specified by:

getStartDate in interface ExperimentInterface

splitOldStyle

public Collection<ExperimentInterface> splitOldStyle()

split

public Collection<ExperimentInterface> split()

Specified by:

split in interface ExperimentInterface

getAllMeasurements

public List<NumericMeasurementInterface> getAllMeasurements()

setHeader

public void setHeader(ExperimentHeaderInterface header)

Specified by:

setHeader in interface ExperimentInterface

getHeader

public ExperimentHeaderInterface getHeader()

Specified by:

getHeader in interface ExperimentInterface

getHeaders

public Collection<ExperimentHeaderInterface> getHeaders()

Specified by:

getHeaders in interface ExperimentInterface

getEmptyDocument

public static Document getEmptyDocument(ExperimentHeaderInterface header)

getDocuments

public static ArrayList<Document> getDocuments(ExperimentInterface mappingDataList,
BackgroundTaskStatusProviderSupportingExternalCall status,
boolean mergeExperimentsReturnOnlyOne)

getStrings

public static ArrayList<String> getStrings(ExperimentInterface mappingDataList,
BackgroundTaskStatusProviderSupportingExternalCall status,
boolean mergeExperimentsReturnOnlyOne)

getDocuments

public static ArrayList<Document> getDocuments(ExperimentInterface mappingDataList)

<experimentdata> <experiment experimentid="-1"> <experimentname>Gluthation</experimentname> <remark>SXD plants</remark> <coordinator>Mohammad Hajirezaei</coordinator> <excelfileid/> <importusername/> <importdate>Tue Mar 10 11:39:36 CET 2009</importdate> <startdate>Sun Jan 18 00:00:00 CET 2004</startdate> <measurements>92</measurements> <imagefiles>0</imagefiles> <sizekb>0</sizekb> </experiment> <measurements> <substance id="column 6" name="Cys"> ...

Parameters:

mappingDataList -

status -

getString

public static String getString(ExperimentInterface mappingDataList)

setTypeManager

public static void setTypeManager(DataMappingTypeManagerInterface m)

getTypeManager

public static DataMappingTypeManagerInterface getTypeManager()

getExperimentFromDOM

public static Experiment getExperimentFromDOM(Document doc)

getExperiment

public static ExperimentInterface getExperiment(List<org.jdom2.Document> documents)

getExperimentFromJDOM

public static Experiment getExperimentFromJDOM(org.jdom2.Document doc)

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<SubstanceInterface>

Specified by:

isEmpty in interface ExperimentInterface

Specified by:

isEmpty in interface List<SubstanceInterface>

add

public void add(int index,
SubstanceInterface element)

Specified by:

add in interface ExperimentInterface

Specified by:

add in interface List<SubstanceInterface>

add

public boolean add(SubstanceInterface e)

Specified by:

add in interface Collection<SubstanceInterface>

Specified by:

add in interface ExperimentInterface

Specified by:

add in interface List<SubstanceInterface>

addAll

public boolean addAll(Collection<? extends SubstanceInterface> c)

Specified by:

addAll in interface Collection<SubstanceInterface>

Specified by:

addAll in interface ExperimentInterface

Specified by:

addAll in interface List<SubstanceInterface>

addAll

public boolean addAll(int index,
Collection<? extends SubstanceInterface> c)

Specified by:

addAll in interface ExperimentInterface

Specified by:

addAll in interface List<SubstanceInterface>

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<SubstanceInterface>

Specified by:

contains in interface ExperimentInterface

Specified by:

contains in interface List<SubstanceInterface>

containsAll

public boolean containsAll(Collection<?> arg0)

Specified by:

containsAll in interface Collection<SubstanceInterface>

Specified by:

containsAll in interface ExperimentInterface

Specified by:

containsAll in interface List<SubstanceInterface>

ensureCapacity

public void ensureCapacity(int minCapacity)

Specified by:

ensureCapacity in interface ExperimentInterface

indexOf

public int indexOf(Object o)

Specified by:

indexOf in interface ExperimentInterface

Specified by:

indexOf in interface List<SubstanceInterface>

lastIndexOf

public int lastIndexOf(Object o)

Specified by:

lastIndexOf in interface ExperimentInterface

Specified by:

lastIndexOf in interface List<SubstanceInterface>

listIterator

public ListIterator<SubstanceInterface> listIterator()

Specified by:

listIterator in interface ExperimentInterface

Specified by:

listIterator in interface List<SubstanceInterface>

listIterator

public ListIterator<SubstanceInterface> listIterator(int index)

Specified by:

listIterator in interface ExperimentInterface

Specified by:

listIterator in interface List<SubstanceInterface>

remove

public SubstanceInterface remove(int index)

Specified by:

remove in interface ExperimentInterface

Specified by:

remove in interface List<SubstanceInterface>

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<SubstanceInterface>

Specified by:

remove in interface ExperimentInterface

Specified by:

remove in interface List<SubstanceInterface>

removeAll

public boolean removeAll(Collection<?> arg0)

Specified by:

removeAll in interface Collection<SubstanceInterface>

Specified by:

removeAll in interface ExperimentInterface

Specified by:

removeAll in interface List<SubstanceInterface>

retainAll

public boolean retainAll(Collection<?> arg0)

Specified by:

retainAll in interface Collection<SubstanceInterface>

Specified by:

retainAll in interface ExperimentInterface

Specified by:

retainAll in interface List<SubstanceInterface>

set

public SubstanceInterface set(int index,
SubstanceInterface element)

Specified by:

set in interface ExperimentInterface

Specified by:

set in interface List<SubstanceInterface>

subList

public List<SubstanceInterface> subList(int fromIndex,
int toIndex)

Specified by:

subList in interface ExperimentInterface

Specified by:

subList in interface List<SubstanceInterface>

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<SubstanceInterface>

Specified by:

toArray in interface ExperimentInterface

Specified by:

toArray in interface List<SubstanceInterface>

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<SubstanceInterface>

Specified by:

toArray in interface ExperimentInterface

Specified by:

toArray in interface List<SubstanceInterface>

toString

public String toString()

Specified by:

toString in interface ExperimentInterface

Overrides:

toString in class Object

toStringWithErrorThrowing

public String toStringWithErrorThrowing()
                                 throws IOException,
TransformerException,
org.jdom2.JDOMException

Specified by:

toStringWithErrorThrowing in interface ExperimentInterface

Throws:

IOException

TransformerException

org.jdom2.JDOMException

trimToSize

public void trimToSize()

Specified by:

trimToSize in interface ExperimentInterface

size

public int size()

Specified by:

size in interface Collection<SubstanceInterface>

Specified by:

size in interface ExperimentInterface

Specified by:

size in interface List<SubstanceInterface>

get

public SubstanceInterface get(int index)

Specified by:

get in interface ExperimentInterface

Specified by:

get in interface List<SubstanceInterface>

iterator

public Iterator<SubstanceInterface> iterator()

Specified by:

iterator in interface Collection<SubstanceInterface>

Specified by:

iterator in interface ExperimentInterface

Specified by:

iterator in interface Iterable<SubstanceInterface>

Specified by:

iterator in interface List<SubstanceInterface>

clear

public void clear()

Specified by:

clear in interface Collection<SubstanceInterface>

Specified by:

clear in interface ExperimentInterface

Specified by:

clear in interface List<SubstanceInterface>

getSequence

public String getSequence()

Specified by:

getSequence in interface ExperimentInterface

fillAttributeMap

public void fillAttributeMap(Map<String,Object> attributeValueMap)

Specified by:

fillAttributeMap in interface AttributeValuePairSupport

Specified by:

fillAttributeMap in interface ExperimentInterface

getStringOfChildren

public void getStringOfChildren(StringBuilder r)

Specified by:

getStringOfChildren in interface MappingDataEntity

getXMLAttributeString

public void getXMLAttributeString(StringBuilder r)

Specified by:

getXMLAttributeString in interface MappingDataEntity

setAttribute

public void setAttribute(org.jdom2.Attribute attr)

Specified by:

setAttribute in interface MappingDataEntity

setData

public boolean setData(org.jdom2.Element xmlElement)

Specified by:

setData in interface MappingDataEntity

setDataOfChildElement

public void setDataOfChildElement(org.jdom2.Element childElement)

Specified by:

setDataOfChildElement in interface MappingDataEntity

writeToFile

public void writeToFile(File targetDir,
boolean asDocument)

cloneOldStyle

public Experiment cloneOldStyle()

clone

public Experiment clone()

Specified by:

clone in interface ExperimentInterface

addAndMerge

@Deprecated
public static void addAndMerge(ExperimentInterface result,
ExperimentInterface toBeAdded)

Deprecated.

Use experiment.addAndMerge instead.

addAndMerge

public void addAndMerge(ExperimentInterface toBeAdded)

Specified by:

addAndMerge in interface ExperimentInterface

getTimes

public static String[] getTimes(ExperimentInterface experimentData)

getConditionsAsString

public static String[] getConditionsAsString(ExperimentInterface experimentData)

isReplicateDataMissing

public static boolean isReplicateDataMissing(ExperimentInterface md)

isBiologicalAndTechnicalReplicateDataAvailable

public static boolean isBiologicalAndTechnicalReplicateDataAvailable(ExperimentInterface md)

getNumberOfMeasurementValues

@Deprecated
public static int getNumberOfMeasurementValues(ExperimentInterface md)

Deprecated.

Use experiment.getNumberOfMeasurementValues() instead.

getNumberOfMeasurementValues

public int getNumberOfMeasurementValues()

Specified by:

getNumberOfMeasurementValues in interface ExperimentInterface

getMeasurementValuesSum

@Deprecated
public static double getMeasurementValuesSum(ExperimentInterface md)

Deprecated.

Use experiment.getMeasurementValuesSum() instead.

getMeasurementValuesSum

public double getMeasurementValuesSum()

Specified by:

getMeasurementValuesSum in interface ExperimentInterface

mergeBiologicalReplicates

public void mergeBiologicalReplicates(BackgroundTaskStatusProviderSupportingExternalCall status)

Specified by:

mergeBiologicalReplicates in interface ExperimentInterface