All Superinterfaces:: AttributeValuePairSupport, Collection<ConditionInterface>, Comparable<SubstanceInterface>, HelperClass, Iterable<ConditionInterface>, MappingDataEntity

All Known Implementing Classes:: Substance

public interface SubstanceInterface
extends MappingDataEntity, Comparable<SubstanceInterface>, Collection<ConditionInterface>, HelperClass

Field Summary

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

Method Summary

Modifier and Type	Method	Description
`boolean`	`add(ConditionInterface e)`
`boolean`	`addAll(Collection<? extends ConditionInterface> c)`
`ConditionInterface`	`addAndMergeData(ConditionInterface seriesnew)`
`void`	`clear()`
`int`	`clearSynonyms()`
`SubstanceInterface`	`clone()`
`int`	`compareTo(SubstanceInterface o)`
`boolean`	`contains(Object o)`
`boolean`	`containsAll(Collection<?> c)`
`void`	`fillAttributeMap(Map<String,Object> attributeValueMap)`
`String`	`getAffyHit()`
`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()`
`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()`

Methods inherited from interface java.util.Collection

equals, hashCode, parallelStream, removeIf, spliterator, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Method Details
- setMappedData
  
  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> ...
- addAndMergeData
  
  ConditionInterface addAndMergeData(ConditionInterface seriesnew)
- getXMLstring
  
  String getXMLstring()
- toString
  
  String toString()
  
  Overrides:
  
  toString in class Object
- getXMLAttributeString
  
  void getXMLAttributeString(StringBuilder s)
  
  Specified by:
  
  getXMLAttributeString in interface MappingDataEntity
- getStringOfChildren
  
  void getStringOfChildren(StringBuilder s)
  
  Specified by:
  
  getStringOfChildren in interface MappingDataEntity
- getDataPoints
  
  Collection<MyComparableDataPoint> getDataPoints(boolean returnAvgValues, boolean removeEmptyConditions)
- getSynonyms
  
  Collection<String> getSynonyms()
  
  Returns:
  
  Null or eventually empty list of synonyms.
- getSynonymMap
  
  HashMap<Integer,String> getSynonymMap()
- getNumberOfDifferentTimePoints
  
  int getNumberOfDifferentTimePoints()
- clearSynonyms
  
  int clearSynonyms()
- setSynonyme
  
  void setSynonyme(int idx, String value)
- getSynonyme
  
  String getSynonyme(int idx)
- getFuncat
  
  String getFuncat()
- getInfo
  
  String getInfo()
- getMaximumSynonymeIndex
  
  int getMaximumSynonymeIndex(int returnIfNoSynonymes)
- getAverage
  
  double getAverage()
- setAttribute
  
  void setAttribute(org.jdom2.Attribute attr)
  
  Specified by:
  
  setAttribute in interface MappingDataEntity
- setData
  
  boolean setData(org.jdom2.Element experimentElement)
  
  Specified by:
  
  setData in interface MappingDataEntity
- setDataOfChildElement
  
  void setDataOfChildElement(org.jdom2.Element childElement)
  
  Specified by:
  
  setDataOfChildElement in interface MappingDataEntity
- setDataOfChildElement
  
  void setDataOfChildElement(org.jdom2.Element childElement, org.jdom2.Element experimentChildElement)
- getSubstanceString
  
  void getSubstanceString(StringBuilder r)
- compareTo
  
  int compareTo(SubstanceInterface o)
  
  Specified by:
  
  compareTo in interface Comparable<SubstanceInterface>
- setRowId
  
  void setRowId(String rowId)
- getRowId
  
  String getRowId()
- setName
  
  void setName(String name)
- getName
  
  String getName()
- setFuncat
  
  void setFuncat(String funcat)
- setInfo
  
  void setInfo(String info)
- setFormula
  
  void setFormula(String formula)
- getFormula
  
  String getFormula()
- setSubstancegroup
  
  void setSubstancegroup(String substancegroup)
- getSubstancegroup
  
  String getSubstancegroup()
- setClusterId
  
  void setClusterId(String cluster_id)
- getClusterId
  
  String getClusterId()
- setSpot
  
  void setSpot(String spot)
- getSpot
  
  String getSpot()
- setNewBlast
  
  void setNewBlast(String new_blast)
- getNewBlast
  
  String getNewBlast()
- setNewBlastEval
  
  void setNewBlastEval(String new_blast_e_val)
- getNewBlastEval
  
  String getNewBlastEval()
- setNewBlastScore
  
  void setNewBlastScore(String new_blast_score)
- getNewBlastScore
  
  String getNewBlastScore()
- setAffyHit
  
  void setAffyHit(String affy_hit)
- getAffyHit
  
  String getAffyHit()
- setScore
  
  void setScore(String score)
- getScore
  
  String getScore()
- setSecure
  
  void setSecure(String secure)
- getSecure
  
  String getSecure()
- getDataPointCount
  
  int getDataPointCount(boolean returnAvgValues)
- getSum
  
  double getSum()
- getConditions
  
  Collection<ConditionInterface> getConditions(Collection<String> validConditons)
- add
  
  boolean add(ConditionInterface e)
  
  Specified by:
  
  add in interface Collection<ConditionInterface>
- iterator
  
  Iterator<ConditionInterface> iterator()
  
  Specified by:
  
  iterator in interface Collection<ConditionInterface>
  
  Specified by:
  
  iterator in interface Iterable<ConditionInterface>
- addAll
  
  boolean addAll(Collection<? extends ConditionInterface> c)
  
  Specified by:
  
  addAll in interface Collection<ConditionInterface>
- clear
  
  void clear()
  
  Specified by:
  
  clear in interface Collection<ConditionInterface>
- contains
  
  boolean contains(Object o)
  
  Specified by:
  
  contains in interface Collection<ConditionInterface>
- containsAll
  
  boolean containsAll(Collection<?> c)
  
  Specified by:
  
  containsAll in interface Collection<ConditionInterface>
- isEmpty
  
  boolean isEmpty()
  
  Specified by:
  
  isEmpty in interface Collection<ConditionInterface>
- remove
  
  boolean remove(Object o)
  
  Specified by:
  
  remove in interface Collection<ConditionInterface>
- removeAll
  
  boolean removeAll(Collection<?> c)
  
  Specified by:
  
  removeAll in interface Collection<ConditionInterface>
- retainAll
  
  boolean retainAll(Collection<?> c)
  
  Specified by:
  
  retainAll in interface Collection<ConditionInterface>
- size
  
  int size()
  
  Specified by:
  
  size in interface Collection<ConditionInterface>
- toArray
  
  Object[] toArray()
  
  Specified by:
  
  toArray in interface Collection<ConditionInterface>
- toArray
  
  <T> T[] toArray(T[] a)
  
  Specified by:
  
  toArray in interface Collection<ConditionInterface>
- fillAttributeMap
  
  void fillAttributeMap(Map<String,Object> attributeValueMap)
  
  Specified by:
  
  fillAttributeMap in interface AttributeValuePairSupport
- setSynonyme
  
  void setSynonyme(HashMap<Integer,String> hashMap)
- clone
  
  SubstanceInterface clone()

Interface SubstanceInterface

Field Summary

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

Method Summary

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Method Details

setMappedData

addAndMergeData

getXMLstring

toString

getXMLAttributeString

getStringOfChildren

getDataPoints

getSynonyms

getSynonymMap

getNumberOfDifferentTimePoints

clearSynonyms

setSynonyme

getSynonyme

getFuncat

getInfo

getMaximumSynonymeIndex

getAverage

setAttribute

setData

setDataOfChildElement

setDataOfChildElement

getSubstanceString

compareTo

setRowId

getRowId

setName

getName

setFuncat

setInfo

setFormula

getFormula

setSubstancegroup

getSubstancegroup

setClusterId

getClusterId

setSpot

getSpot

setNewBlast

getNewBlast

setNewBlastEval

getNewBlastEval

setNewBlastScore

getNewBlastScore

setAffyHit

getAffyHit

setScore

getScore

setSecure

getSecure

getDataPointCount

getSum

getConditions

add

iterator

addAll

clear

contains

containsAll

isEmpty

remove

removeAll

retainAll

size

toArray

toArray

fillAttributeMap

setSynonyme

clone