Class Substance
java.lang.Object
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
- All Implemented Interfaces:
AttributeValuePairSupport
,MappingDataEntity
,SubstanceInterface
,Cloneable
,Comparable<SubstanceInterface>
,Iterable<ConditionInterface>
,Collection<ConditionInterface>
,HelperClass
public class Substance extends Object implements SubstanceInterface, Cloneable
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Field Summary
Fields Modifier and Type Field Description static boolean
includeEmptyAttributes
Fields inherited from interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.MappingDataEntity
ANNO_DIV
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Constructor Summary
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Method Summary
Modifier and Type Method Description boolean
add(ConditionInterface e)
boolean
addAll(Collection<? extends ConditionInterface> c)
static void
addAndMerge(ExperimentInterface result, SubstanceInterface tobeMerged)
ConditionInterface
addAndMergeData(ConditionInterface seriesnew)
void
clear()
int
clearSynonyms()
SubstanceInterface
clone()
int
compareTo(SubstanceInterface o)
boolean
contains(Object o)
boolean
containsAll(Collection<?> c)
boolean
equals(Object obj)
void
fillAttributeMap(Map<String,Object> attributeValueMap)
String
getAffyHit()
static void
getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues)
static void
getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues, boolean asElements)
double
getAverage()
String
getClusterId()
Collection<ConditionInterface>
getConditions(Collection<String> validConditons)
int
getDataPointCount(boolean returnAvgValues)
Collection<MyComparableDataPoint>
getDataPoints(boolean returnAvgValues, boolean removeEmptyConditions)
String
getFormula()
String
getFuncat()
String
getInfo()
int
getMaximumSynonymeIndex(int returnIfNoSynonymes)
String
getName()
String
getNewBlast()
String
getNewBlastEval()
String
getNewBlastScore()
int
getNumberOfDifferentTimePoints()
String
getRowId()
String
getScore()
String
getSecure()
String
getSpot()
void
getStringOfChildren(StringBuilder s)
String
getSubstancegroup()
void
getSubstanceString(StringBuilder r)
double
getSum()
String
getSynonyme(int idx)
HashMap<Integer,String>
getSynonymMap()
Collection<String>
getSynonyms()
void
getXMLAttributeString(StringBuilder s)
String
getXMLstring()
int
hashCode()
boolean
isEmpty()
Iterator<ConditionInterface>
iterator()
boolean
remove(Object o)
boolean
removeAll(Collection<?> c)
boolean
retainAll(Collection<?> c)
void
setAffyHit(String affy_hit)
void
setAttribute(org.jdom2.Attribute attr)
void
setClusterId(String cluster_id)
boolean
setData(org.jdom2.Element experimentElement)
void
setDataOfChildElement(org.jdom2.Element childElement)
void
setDataOfChildElement(org.jdom2.Element childElement, org.jdom2.Element experimentChildElement)
void
setFormula(String formula)
void
setFuncat(String funcat)
void
setInfo(String info)
boolean
setMappedData(org.jdom2.Element e, org.jdom2.Element experimentChildElement)
Dataset, transformed for data mapping: <substance id="" name=""> <line experimentname="" genotype="WT" growthconditions="" id="1" name= "Unknown 1" treatment="" variety=""> <sample id="" measurementtool="" time="26" unit="day"> <average max="" min="" replicates="1" stddev="0.0" unit= "units">48.5313748658488</average> <data replicates="" unit="">48.5313748658488</data> </sample> ...void
setName(String name)
void
setNewBlast(String new_blast)
void
setNewBlastEval(String new_blast_e_val)
void
setNewBlastScore(String new_blast_score)
void
setRowId(String rowId)
void
setScore(String score)
void
setSecure(String secure)
void
setSpot(String spot)
void
setSubstancegroup(String substancegroup)
void
setSynonyme(int idx, String value)
void
setSynonyme(HashMap<Integer,String> hashMap)
int
size()
Object[]
toArray()
<T> T[]
toArray(T[] a)
String
toString()
static void
validate(Document doc)
Methods inherited from interface java.util.Collection
parallelStream, removeIf, spliterator, stream, toArray
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Field Details
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includeEmptyAttributes
public static boolean includeEmptyAttributes
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Constructor Details
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Substance
public Substance() -
Substance
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Method Details
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setMappedData
public boolean setMappedData(org.jdom2.Element e, org.jdom2.Element experimentChildElement)Dataset, transformed for data mapping: <substance id="" name=""> <line experimentname="" genotype="WT" growthconditions="" id="1" name= "Unknown 1" treatment="" variety=""> <sample id="" measurementtool="" time="26" unit="day"> <average max="" min="" replicates="1" stddev="0.0" unit= "units">48.5313748658488</average> <data replicates="" unit="">48.5313748658488</data> </sample> ...- Specified by:
setMappedData
in interfaceSubstanceInterface
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addAndMerge
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addAndMergeData
- Specified by:
addAndMergeData
in interfaceSubstanceInterface
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getXMLstring
- Specified by:
getXMLstring
in interfaceSubstanceInterface
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toString
- Specified by:
toString
in interfaceSubstanceInterface
- Overrides:
toString
in classObject
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getXMLAttributeString
- Specified by:
getXMLAttributeString
in interfaceMappingDataEntity
- Specified by:
getXMLAttributeString
in interfaceSubstanceInterface
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getStringOfChildren
- Specified by:
getStringOfChildren
in interfaceMappingDataEntity
- Specified by:
getStringOfChildren
in interfaceSubstanceInterface
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getAttributeString
public static void getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues) -
getAttributeString
public static void getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues, boolean asElements)- Parameters:
asElements
- indicates, that the attribute shall be written as single element, eg
<attrname>attrvalue</attrname>
insteadattrname='attrvalue'
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getDataPoints
public Collection<MyComparableDataPoint> getDataPoints(boolean returnAvgValues, boolean removeEmptyConditions)- Specified by:
getDataPoints
in interfaceSubstanceInterface
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getSynonyms
- Specified by:
getSynonyms
in interfaceSubstanceInterface
- Returns:
- Null or eventually empty list of synonyms.
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getSynonymMap
- Specified by:
getSynonymMap
in interfaceSubstanceInterface
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getNumberOfDifferentTimePoints
public int getNumberOfDifferentTimePoints()- Specified by:
getNumberOfDifferentTimePoints
in interfaceSubstanceInterface
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clearSynonyms
public int clearSynonyms()- Specified by:
clearSynonyms
in interfaceSubstanceInterface
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setSynonyme
- Specified by:
setSynonyme
in interfaceSubstanceInterface
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setSynonyme
- Specified by:
setSynonyme
in interfaceSubstanceInterface
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getSynonyme
- Specified by:
getSynonyme
in interfaceSubstanceInterface
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getFuncat
- Specified by:
getFuncat
in interfaceSubstanceInterface
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getInfo
- Specified by:
getInfo
in interfaceSubstanceInterface
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getMaximumSynonymeIndex
public int getMaximumSynonymeIndex(int returnIfNoSynonymes)- Specified by:
getMaximumSynonymeIndex
in interfaceSubstanceInterface
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getAverage
public double getAverage()- Specified by:
getAverage
in interfaceSubstanceInterface
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setAttribute
public void setAttribute(org.jdom2.Attribute attr)- Specified by:
setAttribute
in interfaceMappingDataEntity
- Specified by:
setAttribute
in interfaceSubstanceInterface
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setData
public boolean setData(org.jdom2.Element experimentElement)- Specified by:
setData
in interfaceMappingDataEntity
- Specified by:
setData
in interfaceSubstanceInterface
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setDataOfChildElement
public void setDataOfChildElement(org.jdom2.Element childElement)- Specified by:
setDataOfChildElement
in interfaceMappingDataEntity
- Specified by:
setDataOfChildElement
in interfaceSubstanceInterface
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setDataOfChildElement
public void setDataOfChildElement(org.jdom2.Element childElement, org.jdom2.Element experimentChildElement)- Specified by:
setDataOfChildElement
in interfaceSubstanceInterface
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getSubstanceString
- Specified by:
getSubstanceString
in interfaceSubstanceInterface
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compareTo
- Specified by:
compareTo
in interfaceComparable<SubstanceInterface>
- Specified by:
compareTo
in interfaceSubstanceInterface
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setRowId
- Specified by:
setRowId
in interfaceSubstanceInterface
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getRowId
- Specified by:
getRowId
in interfaceSubstanceInterface
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setName
- Specified by:
setName
in interfaceSubstanceInterface
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getName
- Specified by:
getName
in interfaceSubstanceInterface
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setFuncat
- Specified by:
setFuncat
in interfaceSubstanceInterface
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setInfo
- Specified by:
setInfo
in interfaceSubstanceInterface
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setFormula
- Specified by:
setFormula
in interfaceSubstanceInterface
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getFormula
- Specified by:
getFormula
in interfaceSubstanceInterface
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setSubstancegroup
- Specified by:
setSubstancegroup
in interfaceSubstanceInterface
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getSubstancegroup
- Specified by:
getSubstancegroup
in interfaceSubstanceInterface
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setClusterId
- Specified by:
setClusterId
in interfaceSubstanceInterface
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getClusterId
- Specified by:
getClusterId
in interfaceSubstanceInterface
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setSpot
- Specified by:
setSpot
in interfaceSubstanceInterface
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getSpot
- Specified by:
getSpot
in interfaceSubstanceInterface
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setNewBlast
- Specified by:
setNewBlast
in interfaceSubstanceInterface
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getNewBlast
- Specified by:
getNewBlast
in interfaceSubstanceInterface
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setNewBlastEval
- Specified by:
setNewBlastEval
in interfaceSubstanceInterface
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getNewBlastEval
- Specified by:
getNewBlastEval
in interfaceSubstanceInterface
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setNewBlastScore
- Specified by:
setNewBlastScore
in interfaceSubstanceInterface
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getNewBlastScore
- Specified by:
getNewBlastScore
in interfaceSubstanceInterface
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setAffyHit
- Specified by:
setAffyHit
in interfaceSubstanceInterface
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getAffyHit
- Specified by:
getAffyHit
in interfaceSubstanceInterface
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setScore
- Specified by:
setScore
in interfaceSubstanceInterface
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getScore
- Specified by:
getScore
in interfaceSubstanceInterface
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setSecure
- Specified by:
setSecure
in interfaceSubstanceInterface
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getSecure
- Specified by:
getSecure
in interfaceSubstanceInterface
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validate
- Throws:
Exception
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getDataPointCount
public int getDataPointCount(boolean returnAvgValues)- Specified by:
getDataPointCount
in interfaceSubstanceInterface
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getSum
public double getSum()- Specified by:
getSum
in interfaceSubstanceInterface
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getConditions
- Specified by:
getConditions
in interfaceSubstanceInterface
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add
- Specified by:
add
in interfaceCollection<ConditionInterface>
- Specified by:
add
in interfaceSubstanceInterface
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iterator
- Specified by:
iterator
in interfaceCollection<ConditionInterface>
- Specified by:
iterator
in interfaceIterable<ConditionInterface>
- Specified by:
iterator
in interfaceSubstanceInterface
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addAll
- Specified by:
addAll
in interfaceCollection<ConditionInterface>
- Specified by:
addAll
in interfaceSubstanceInterface
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clear
public void clear()- Specified by:
clear
in interfaceCollection<ConditionInterface>
- Specified by:
clear
in interfaceSubstanceInterface
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contains
- Specified by:
contains
in interfaceCollection<ConditionInterface>
- Specified by:
contains
in interfaceSubstanceInterface
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containsAll
- Specified by:
containsAll
in interfaceCollection<ConditionInterface>
- Specified by:
containsAll
in interfaceSubstanceInterface
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isEmpty
public boolean isEmpty()- Specified by:
isEmpty
in interfaceCollection<ConditionInterface>
- Specified by:
isEmpty
in interfaceSubstanceInterface
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remove
- Specified by:
remove
in interfaceCollection<ConditionInterface>
- Specified by:
remove
in interfaceSubstanceInterface
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removeAll
- Specified by:
removeAll
in interfaceCollection<ConditionInterface>
- Specified by:
removeAll
in interfaceSubstanceInterface
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retainAll
- Specified by:
retainAll
in interfaceCollection<ConditionInterface>
- Specified by:
retainAll
in interfaceSubstanceInterface
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size
public int size()- Specified by:
size
in interfaceCollection<ConditionInterface>
- Specified by:
size
in interfaceSubstanceInterface
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toArray
- Specified by:
toArray
in interfaceCollection<ConditionInterface>
- Specified by:
toArray
in interfaceSubstanceInterface
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toArray
public <T> T[] toArray(T[] a)- Specified by:
toArray
in interfaceCollection<ConditionInterface>
- Specified by:
toArray
in interfaceSubstanceInterface
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fillAttributeMap
- Specified by:
fillAttributeMap
in interfaceAttributeValuePairSupport
- Specified by:
fillAttributeMap
in interfaceSubstanceInterface
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clone
- Specified by:
clone
in interfaceSubstanceInterface
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equals
- Specified by:
equals
in interfaceCollection<ConditionInterface>
- Overrides:
equals
in classObject
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hashCode
public int hashCode()- Specified by:
hashCode
in interfaceCollection<ConditionInterface>
- Overrides:
hashCode
in classObject
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