ambit2.core.data.experiment
Class StudyTemplate

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<TemplateField>
              ambit2.core.data.experiment.StudyTemplate

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<TemplateField>, java.util.Collection<TemplateField>, java.util.List<TemplateField>, java.util.RandomAccess

public class StudyTemplate
extends java.util.ArrayList<TemplateField>

Study templates are introduced in order to provide generic framework for storing experimental data results, without predefined fieldnames, which may not be relevant to all endpoints (e.g. species strain or vehicle is not relevant to all species or endpoints). On other hand, fields with the same meaning have to have the same name to make queries feasible (e.g. “species” field should be the same across all endpoints in order to be able to search for species).
A template consists of a name, fields defining study conditions and fields defining study results. Each field has a name, units and a flag specifying whether it is a condition or a result. See DefaultTemplate , DSSToxCarcinogenicityTemplate, DSSToxERBindingTemplate, DSSToxLC50Template for specific examples.

See Also:

Serialized Form

Field Summary

protected int	id
protected java.lang.String	name
protected TemplateField	query
protected java.lang.String	source

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

StudyTemplate(java.lang.String name)

Method Summary

void	addFields(java.lang.String fieldName, java.lang.String units, boolean numeric, boolean isResult)
protected org.w3c.dom.Document	buildDocument()
TemplateField	getField(java.lang.Object field)
int	getId()
java.lang.String	getName()
java.lang.String	getSource()
void	getStudyConditions(java.util.Hashtable properties)
void	getStudyResults(java.util.Hashtable properties)
boolean	load(java.io.InputStream in)
boolean	load(java.io.Reader reader)
boolean	save(java.io.OutputStream out)
boolean	save(java.io.Writer writer)
void	setId(int id)
void	setName(java.lang.String name)
void	setSource(java.lang.String source)
java.lang.String	toString()

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

source

protected java.lang.String source

query

protected TemplateField query

name

protected java.lang.String name

id

protected int id

Constructor Detail

StudyTemplate

public StudyTemplate(java.lang.String name)

Method Detail

addFields

public void addFields(java.lang.String fieldName,
                      java.lang.String units,
                      boolean numeric,
                      boolean isResult)

getField

public TemplateField getField(java.lang.Object field)

save

public boolean save(java.io.OutputStream out)
             throws ambit2.base.exceptions.AmbitIOException

Throws:

ambit2.base.exceptions.AmbitIOException

save

public boolean save(java.io.Writer writer)
             throws ambit2.base.exceptions.AmbitIOException

Throws:

ambit2.base.exceptions.AmbitIOException

buildDocument

protected org.w3c.dom.Document buildDocument()

load

public boolean load(java.io.InputStream in)
             throws ambit2.base.exceptions.AmbitIOException

Throws:

ambit2.base.exceptions.AmbitIOException

load

public boolean load(java.io.Reader reader)
             throws ambit2.base.exceptions.AmbitIOException

Throws:

ambit2.base.exceptions.AmbitIOException

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<TemplateField>

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)

getStudyConditions

public void getStudyConditions(java.util.Hashtable properties)

getStudyResults

public void getStudyResults(java.util.Hashtable properties)

getId

public int getId()

setId

public void setId(int id)

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)