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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.Software
public class Software
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSoftwareManufacturers |
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HasSoftwareManufacturers.SoftwareManufacturers_list |
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.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 Hardware |
hardware
Associates Hardware and Software together. |
protected java.util.List |
softwareManufacturers
Contact for information on the software. |
protected java.util.List |
softwares
Software packages this software uses, i.e. |
protected OntologyEntry |
type
The type of a piece of Software. |
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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Software()
Default constructor. |
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Software(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToSoftwareManufacturers(Contact contact)
Method to add Contact to SoftwareManufacturers_list |
void |
addToSoftwareManufacturers(int position,
Contact contact)
Method to add Contact at position to SoftwareManufacturers_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()
|
Contact |
getFromSoftwareManufacturers(int position)
Method to get Contact from SoftwareManufacturers_list |
Software |
getFromSoftwares(int position)
Method to get Software from Softwares_list |
Hardware |
getHardware()
Get method for hardware |
java.lang.String |
getModelClassName()
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HasSoftwareManufacturers.SoftwareManufacturers_list |
getSoftwareManufacturers()
Get method for softwareManufacturers |
HasSoftwares.Softwares_list |
getSoftwares()
Get method for softwares |
OntologyEntry |
getType()
Get method for type |
void |
removeElementAtFromSoftwareManufacturers(int position)
Method to remove by position from SoftwareManufacturers_list |
void |
removeElementAtFromSoftwares(int position)
Method to remove by position from Softwares_list |
void |
removeFromSoftwareManufacturers(Contact contact)
Method to remove first Contact from SoftwareManufacturers_list |
void |
removeFromSoftwares(Software software)
Method to remove first Software from Softwares_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setHardware(Hardware hardware)
Set method for hardware |
void |
setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers)
Set method for softwareManufacturers |
void |
setSoftwares(HasSoftwares.Softwares_list softwares)
Set method for softwares |
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 Hardware hardware
protected java.util.List softwares
protected java.util.List softwareManufacturers
Constructor Detail |
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public Software()
public Software(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 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 setHardware(Hardware hardware)
setHardware
in interface HasHardware
value
- to setpublic Hardware getHardware()
getHardware
in interface HasHardware
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
public void setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers)
setSoftwareManufacturers
in interface HasSoftwareManufacturers
value
- to setpublic HasSoftwareManufacturers.SoftwareManufacturers_list getSoftwareManufacturers()
getSoftwareManufacturers
in interface HasSoftwareManufacturers
public void addToSoftwareManufacturers(Contact contact)
addToSoftwareManufacturers
in interface HasSoftwareManufacturers
public void addToSoftwareManufacturers(int position, Contact contact)
addToSoftwareManufacturers
in interface HasSoftwareManufacturers
public Contact getFromSoftwareManufacturers(int position)
getFromSoftwareManufacturers
in interface HasSoftwareManufacturers
public void removeElementAtFromSoftwareManufacturers(int position)
removeElementAtFromSoftwareManufacturers
in interface HasSoftwareManufacturers
public void removeFromSoftwareManufacturers(Contact contact)
removeFromSoftwareManufacturers
in interface HasSoftwareManufacturers
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