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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.Protocol.Parameterizable
org.biomage.Protocol.Protocol
public class Protocol
A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSoftwares |
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HasSoftwares.Softwares_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasHardwares |
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HasHardwares.Hardwares_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasParameterTypes |
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HasParameterTypes.ParameterTypes_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.util.List |
hardwares
Hardware used by this protocol. |
protected java.util.List |
softwares
Software used by this Protocol. |
protected OntologyEntry |
type
The type of a Protocol, a user should provide/use a recommended vocabulary. |
Fields inherited from class org.biomage.Protocol.Parameterizable |
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parameterTypes |
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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Protocol()
Default constructor. |
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Protocol(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToHardwares(Hardware hardware)
Method to add Hardware to Hardwares_list |
void |
addToHardwares(int position,
Hardware hardware)
Method to add Hardware at position to Hardwares_list |
void |
addToSoftwares(int position,
Software software)
Method to add Software at position to Softwares_list |
void |
addToSoftwares(Software software)
Method to add Software to Softwares_list |
boolean |
emptyMAGEobject()
|
Hardware |
getFromHardwares(int position)
Method to get Hardware from Hardwares_list |
Software |
getFromSoftwares(int position)
Method to get Software from Softwares_list |
HasHardwares.Hardwares_list |
getHardwares()
Get method for hardwares |
java.lang.String |
getModelClassName()
|
HasSoftwares.Softwares_list |
getSoftwares()
Get method for softwares |
java.lang.String |
getText()
Get method for text |
java.lang.String |
getTitle()
Get method for title |
OntologyEntry |
getType()
Get method for type |
void |
removeElementAtFromHardwares(int position)
Method to remove by position from Hardwares_list |
void |
removeElementAtFromSoftwares(int position)
Method to remove by position from Softwares_list |
void |
removeFromHardwares(Hardware hardware)
Method to remove first Hardware from Hardwares_list |
void |
removeFromSoftwares(Software software)
Method to remove first Software from Softwares_list |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setHardwares(HasHardwares.Hardwares_list hardwares)
Set method for hardwares |
void |
setSoftwares(HasSoftwares.Softwares_list softwares)
Set method for softwares |
void |
setText(java.lang.String text)
Set method for text |
void |
setTitle(java.lang.String title)
Set method for title |
void |
setType(OntologyEntry type)
Set method for type |
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.Protocol.Parameterizable |
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addToParameterTypes, addToParameterTypes, getFromParameterTypes, getParameterTypes, getURI, removeElementAtFromParameterTypes, removeFromParameterTypes, setParameterTypes, setURI |
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 OntologyEntry type
protected java.util.List hardwares
protected java.util.List softwares
Constructor Detail |
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public Protocol()
public Protocol(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 Parameterizable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Parameterizable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Parameterizable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Parameterizable
java.io.IOException
public void setText(java.lang.String text)
value
- to setpublic java.lang.String getText()
public void setTitle(java.lang.String title)
value
- to setpublic java.lang.String getTitle()
public java.lang.String getModelClassName()
getModelClassName
in class Parameterizable
public void setType(OntologyEntry type)
setType
in interface HasType
value
- to setpublic OntologyEntry getType()
getType
in interface HasType
public void setHardwares(HasHardwares.Hardwares_list hardwares)
setHardwares
in interface HasHardwares
value
- to setpublic HasHardwares.Hardwares_list getHardwares()
getHardwares
in interface HasHardwares
public void addToHardwares(Hardware hardware)
addToHardwares
in interface HasHardwares
public void addToHardwares(int position, Hardware hardware)
addToHardwares
in interface HasHardwares
public Hardware getFromHardwares(int position)
getFromHardwares
in interface HasHardwares
public void removeElementAtFromHardwares(int position)
removeElementAtFromHardwares
in interface HasHardwares
public void removeFromHardwares(Hardware hardware)
removeFromHardwares
in interface HasHardwares
public void setSoftwares(HasSoftwares.Softwares_list softwares)
setSoftwares
in interface HasSoftwares
value
- to setpublic HasSoftwares.Softwares_list getSoftwares()
getSoftwares
in interface HasSoftwares
public void addToSoftwares(Software software)
addToSoftwares
in interface HasSoftwares
public void addToSoftwares(int position, Software software)
addToSoftwares
in interface HasSoftwares
public Software getFromSoftwares(int position)
getFromSoftwares
in interface HasSoftwares
public void removeElementAtFromSoftwares(int position)
removeElementAtFromSoftwares
in interface HasSoftwares
public void removeFromSoftwares(Software software)
removeFromSoftwares
in interface HasSoftwares
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