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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.ArrayDesign.ArrayDesign
public class ArrayDesign
Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications |
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HasProtocolApplications.ProtocolApplications_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeGroups |
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HasCompositeGroups.CompositeGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDesignProviders |
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HasDesignProviders.DesignProviders_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterGroups |
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HasReporterGroups.ReporterGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureGroups |
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HasFeatureGroups.FeatureGroups_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected java.lang.String |
additionalReporterFileLocation
|
protected java.util.List |
compositeGroups
The grouping of like CompositeSequence together. |
protected boolean |
deleted
|
protected java.util.List |
designProviderRoles
The providers of the ArrayDesign that have a role which describes how he/she contributes the ArrayDesign, e.g. |
protected java.util.List |
featureGroups
The grouping of like Features together. |
protected java.util.List |
protocolApplications
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array. |
protected java.lang.String |
reporterFileLocation
|
protected java.lang.String |
reporterFileType
|
protected java.util.List |
reporterGroups
The grouping of like Reporter together. |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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ArrayDesign()
Default constructor. |
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ArrayDesign(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToCompositeGroups(CompositeGroup compositeGroup)
Method to add CompositeGroup to CompositeGroups_list |
void |
addToCompositeGroups(int position,
CompositeGroup compositeGroup)
Method to add CompositeGroup at position to CompositeGroups_list |
void |
addToDesignProviderRoles(DesignProviderRole providerRole)
Method to add Contact to DesignProviders_list |
void |
addToDesignProviderRoles(int position,
DesignProviderRole providerRole)
Adds a provider of this experiment that has a role |
void |
addToDesignProviders(Contact contact)
Method to add Contact to DesignProviders_list |
void |
addToDesignProviders(int position,
Contact contact)
Method to add Contact at position to DesignProviders_list |
void |
addToFeatureGroups(FeatureGroup featureGroup)
Method to add FeatureGroup to FeatureGroups_list |
void |
addToFeatureGroups(int position,
FeatureGroup featureGroup)
Method to add FeatureGroup at position to FeatureGroups_list |
void |
addToProtocolApplications(int position,
ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list |
void |
addToProtocolApplications(ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list |
void |
addToProviderRoles(DesignProviderRole providerRole)
Adds a provider of this experiment that has a role |
void |
addToReporterGroups(int position,
ReporterGroup reporterGroup)
Method to add ReporterGroup at position to ReporterGroups_list |
void |
addToReporterGroups(ReporterGroup reporterGroup)
Method to add ReporterGroup to ReporterGroups_list |
boolean |
emptyMAGEobject()
|
java.lang.String |
getAdditionalReporterFileLocation()
|
HasCompositeGroups.CompositeGroups_list |
getCompositeGroups()
Get method for compositeGroups |
java.util.ArrayList |
getDesignProviderRoles()
|
HasDesignProviders.DesignProviders_list |
getDesignProviders()
Get method for designProviders |
HasFeatureGroups.FeatureGroups_list |
getFeatureGroups()
Get method for featureGroups |
CompositeGroup |
getFromCompositeGroups(int position)
Method to get CompositeGroup from CompositeGroups_list |
DesignProviderRole |
getFromDesignProviderRoles(int position)
|
Contact |
getFromDesignProviders(int position)
Method to get Contact from DesignProviders_list |
FeatureGroup |
getFromFeatureGroups(int position)
Method to get FeatureGroup from FeatureGroups_list |
ProtocolApplication |
getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list |
ReporterGroup |
getFromReporterGroups(int position)
Method to get ReporterGroup from ReporterGroups_list |
java.lang.String |
getModelClassName()
|
java.lang.Integer |
getNumberOfFeatures()
Get method for numberOfFeatures |
HasProtocolApplications.ProtocolApplications_list |
getProtocolApplications()
Get method for protocolApplications |
java.lang.String |
getReporterFileLocation()
|
java.lang.String |
getReporterFileType()
|
HasReporterGroups.ReporterGroups_list |
getReporterGroups()
Get method for reporterGroups |
java.lang.String |
getVersion()
Get method for version |
boolean |
isDeleted()
|
void |
removeElementAtFromCompositeGroups(int position)
Method to remove by position from CompositeGroups_list |
void |
removeElementAtFromDesignProviderRoles(int position)
|
void |
removeElementAtFromDesignProviders(int position)
Method to remove by position from DesignProviders_list |
void |
removeElementAtFromFeatureGroups(int position)
Method to remove by position from FeatureGroups_list |
void |
removeElementAtFromProtocolApplications(int position)
Method to remove by position from ProtocolApplications_list |
void |
removeElementAtFromReporterGroups(int position)
Method to remove by position from ReporterGroups_list |
void |
removeFromCompositeGroups(CompositeGroup compositeGroup)
Method to remove first CompositeGroup from CompositeGroups_list |
void |
removeFromDesignProviderRoles(DesignProviderRole providerRole)
|
void |
removeFromDesignProviders(Contact contact)
Method to remove first Contact from DesignProviders_list |
void |
removeFromFeatureGroups(FeatureGroup featureGroup)
Method to remove first FeatureGroup from FeatureGroups_list |
void |
removeFromProtocolApplications(ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list |
void |
removeFromReporterGroups(ReporterGroup reporterGroup)
Method to remove first ReporterGroup from ReporterGroups_list |
void |
setAdditionalReporterFileLocation(java.lang.String string)
|
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setCompositeGroups(HasCompositeGroups.CompositeGroups_list compositeGroups)
Set method for compositeGroups |
void |
setDeleted(boolean deleted)
Mark this ArrayDesign as deleted. |
void |
setDesignProviderRoles(java.util.ArrayList providerRoles)
The specified providerRoles must be instantiable List subclass for creation by reflection to work. |
void |
setDesignProviders(HasDesignProviders.DesignProviders_list designProviders)
Set method for designProviders |
void |
setFeatureGroups(HasFeatureGroups.FeatureGroups_list featureGroups)
Set method for featureGroups |
void |
setNumberOfFeatures(java.lang.Integer numberOfFeatures)
Set method for numberOfFeatures |
void |
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
Set method for protocolApplications |
void |
setReporterFileLocation(java.lang.String string)
|
void |
setReporterFileType(java.lang.String string)
|
void |
setReporterGroups(HasReporterGroups.ReporterGroups_list reporterGroups)
Set method for reporterGroups |
void |
setVersion(java.lang.String version)
Set method for version |
void |
writeAssociations(java.io.Writer out)
writeAssociations This method is responsible for assembling the association data into XML. |
void |
writeAttributes(java.io.Writer out)
writeAttributes This method is responsible for assembling the attribute data into XML. |
void |
writeMAGEML(java.io.Writer out)
writeMAGEML This method is responsible for assembling the attribute and association data into XML. |
Methods inherited from class org.biomage.Common.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.lang.String reporterFileLocation
protected java.lang.String reporterFileType
protected java.lang.String additionalReporterFileLocation
protected boolean deleted
protected java.util.List protocolApplications
protected java.util.List featureGroups
protected java.util.List reporterGroups
protected java.util.List compositeGroups
protected java.util.List designProviderRoles
Constructor Detail |
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public ArrayDesign()
public ArrayDesign(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public void setVersion(java.lang.String version)
value
- to setpublic java.lang.String getVersion()
public void setNumberOfFeatures(java.lang.Integer numberOfFeatures)
value
- to setpublic java.lang.Integer getNumberOfFeatures()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
setProtocolApplications
in interface HasProtocolApplications
value
- to setpublic HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
getProtocolApplications
in interface HasProtocolApplications
public void addToProtocolApplications(ProtocolApplication protocolApplication)
addToProtocolApplications
in interface HasProtocolApplications
public void addToProtocolApplications(int position, ProtocolApplication protocolApplication)
addToProtocolApplications
in interface HasProtocolApplications
public ProtocolApplication getFromProtocolApplications(int position)
getFromProtocolApplications
in interface HasProtocolApplications
public void removeElementAtFromProtocolApplications(int position)
removeElementAtFromProtocolApplications
in interface HasProtocolApplications
public void removeFromProtocolApplications(ProtocolApplication protocolApplication)
removeFromProtocolApplications
in interface HasProtocolApplications
public void setFeatureGroups(HasFeatureGroups.FeatureGroups_list featureGroups)
setFeatureGroups
in interface HasFeatureGroups
value
- to setpublic HasFeatureGroups.FeatureGroups_list getFeatureGroups()
getFeatureGroups
in interface HasFeatureGroups
public void addToFeatureGroups(FeatureGroup featureGroup)
addToFeatureGroups
in interface HasFeatureGroups
public void addToFeatureGroups(int position, FeatureGroup featureGroup)
addToFeatureGroups
in interface HasFeatureGroups
public FeatureGroup getFromFeatureGroups(int position)
getFromFeatureGroups
in interface HasFeatureGroups
public void removeElementAtFromFeatureGroups(int position)
removeElementAtFromFeatureGroups
in interface HasFeatureGroups
public void removeFromFeatureGroups(FeatureGroup featureGroup)
removeFromFeatureGroups
in interface HasFeatureGroups
public void setReporterGroups(HasReporterGroups.ReporterGroups_list reporterGroups)
setReporterGroups
in interface HasReporterGroups
value
- to setpublic HasReporterGroups.ReporterGroups_list getReporterGroups()
getReporterGroups
in interface HasReporterGroups
public void addToReporterGroups(ReporterGroup reporterGroup)
addToReporterGroups
in interface HasReporterGroups
public void addToReporterGroups(int position, ReporterGroup reporterGroup)
addToReporterGroups
in interface HasReporterGroups
public ReporterGroup getFromReporterGroups(int position)
getFromReporterGroups
in interface HasReporterGroups
public void removeElementAtFromReporterGroups(int position)
removeElementAtFromReporterGroups
in interface HasReporterGroups
public void removeFromReporterGroups(ReporterGroup reporterGroup)
removeFromReporterGroups
in interface HasReporterGroups
public void setCompositeGroups(HasCompositeGroups.CompositeGroups_list compositeGroups)
setCompositeGroups
in interface HasCompositeGroups
value
- to setpublic HasCompositeGroups.CompositeGroups_list getCompositeGroups()
getCompositeGroups
in interface HasCompositeGroups
public void addToCompositeGroups(CompositeGroup compositeGroup)
addToCompositeGroups
in interface HasCompositeGroups
public void addToCompositeGroups(int position, CompositeGroup compositeGroup)
addToCompositeGroups
in interface HasCompositeGroups
public CompositeGroup getFromCompositeGroups(int position)
getFromCompositeGroups
in interface HasCompositeGroups
public void removeElementAtFromCompositeGroups(int position)
removeElementAtFromCompositeGroups
in interface HasCompositeGroups
public void removeFromCompositeGroups(CompositeGroup compositeGroup)
removeFromCompositeGroups
in interface HasCompositeGroups
public void setDesignProviders(HasDesignProviders.DesignProviders_list designProviders)
setDesignProviders
in interface HasDesignProviders
value
- to setpublic void setDesignProviderRoles(java.util.ArrayList providerRoles)
providerRoles
- public HasDesignProviders.DesignProviders_list getDesignProviders()
getDesignProviders
in interface HasDesignProviders
public java.util.ArrayList getDesignProviderRoles()
public void addToDesignProviders(Contact contact)
addToDesignProviders
in interface HasDesignProviders
public void addToDesignProviderRoles(DesignProviderRole providerRole)
public void addToProviderRoles(DesignProviderRole providerRole)
providerRole
- - A provider who has a role such as investigator,
primary contact, etc.public void addToDesignProviders(int position, Contact contact)
addToDesignProviders
in interface HasDesignProviders
public void addToDesignProviderRoles(int position, DesignProviderRole providerRole)
public Contact getFromDesignProviders(int position)
getFromDesignProviders
in interface HasDesignProviders
public DesignProviderRole getFromDesignProviderRoles(int position)
public void removeElementAtFromDesignProviders(int position)
removeElementAtFromDesignProviders
in interface HasDesignProviders
public void removeElementAtFromDesignProviderRoles(int position)
public void removeFromDesignProviders(Contact contact)
removeFromDesignProviders
in interface HasDesignProviders
public void removeFromDesignProviderRoles(DesignProviderRole providerRole)
public java.lang.String getReporterFileLocation()
public java.lang.String getReporterFileType()
public void setReporterFileLocation(java.lang.String string)
string
- public void setReporterFileType(java.lang.String string)
string
- public java.lang.String getAdditionalReporterFileLocation()
public void setAdditionalReporterFileLocation(java.lang.String string)
string
- public boolean isDeleted()
public void setDeleted(boolean deleted)
b
-
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