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A
- Audit - class org.biomage.AuditAndSecurity.Audit.
- Tracks information on the contact that creates or modifies an object.
- Audit() - Constructor for class org.biomage.AuditAndSecurity.Audit
- Default constructor.
- Audit(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Audit
- Attribute constructor.
- Audit.Action - class org.biomage.AuditAndSecurity.Audit.Action.
- Inner class for the enumeration values that the attribute action can assume.
- Audit.Action() - Constructor for class org.biomage.AuditAndSecurity.Audit.Action
- AuditAndSecurity_package - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.
- Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
- AuditAndSecurity_package() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Default constructor.
- AuditAndSecurity_package(Attributes) - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Attribute constructor.
- AuditAndSecurity_package.Contact_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list.
- Inner list class for holding multiple entries for attribute contact_list.
- AuditAndSecurity_package.Contact_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list
- AuditAndSecurity_package.Person_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Person_list.
- Inner list class for holding multiple entries for attribute person_list.
- AuditAndSecurity_package.Person_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Person_list
- AuditAndSecurity_package.SecurityGroup_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list.
- Inner list class for holding multiple entries for attribute securityGroup_list.
- AuditAndSecurity_package.SecurityGroup_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list
- AuditAndSecurity_package.Security_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list.
- Inner list class for holding multiple entries for attribute security_list.
- AuditAndSecurity_package.Security_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list
- action - Variable in class org.biomage.AuditAndSecurity.Audit
- Indicates whether an action is a creation or a modification.
- addToContact_list(Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Contact to Contact_list
- addToContact_list(int, Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Contact at position to Contact_list
- addToMembers(Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Method to add Contact to Members_list
- addToMembers(int, Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Method to add Contact at position to Members_list
- addToPerson_list(Person) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Person to Person_list
- addToPerson_list(int, Person) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Person at position to Person_list
- addToReadGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to add SecurityGroup to ReadGroups_list
- addToReadGroups(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to add SecurityGroup at position to ReadGroups_list
- addToRoles(OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
- Method to add OntologyEntry to Roles_list
- addToRoles(int, OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
- Method to add OntologyEntry at position to Roles_list
- addToSecurityGroup_list(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add SecurityGroup to SecurityGroup_list
- addToSecurityGroup_list(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add SecurityGroup at position to SecurityGroup_list
- addToSecurity_list(Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Security to Security_list
- addToSecurity_list(int, Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to add Security at position to Security_list
- addToWriteGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to add SecurityGroup to WriteGroups_list
- addToWriteGroups(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to add SecurityGroup at position to WriteGroups_list
- address - Variable in class org.biomage.AuditAndSecurity.Contact
- affiliation - Variable in class org.biomage.AuditAndSecurity.Person
- The organization a person belongs to.
C
- CREATION - Variable in class org.biomage.AuditAndSecurity.Audit.Action
- Contact - class org.biomage.AuditAndSecurity.Contact.
- A contact is either a person or an organization.
- Contact() - Constructor for class org.biomage.AuditAndSecurity.Contact
- Default constructor.
- Contact(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Contact
- Attribute constructor.
- contact_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- A contact is either a person or an organization.
D
E
F
- fax - Variable in class org.biomage.AuditAndSecurity.Contact
- firstName - Variable in class org.biomage.AuditAndSecurity.Person
G
- getAction() - Method in class org.biomage.AuditAndSecurity.Audit
- Get method for action
- getAddress() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for address
- getAffiliation() - Method in class org.biomage.AuditAndSecurity.Person
- Get method for affiliation
- getContact_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Get method for contact_list
- getDate() - Method in class org.biomage.AuditAndSecurity.Audit
- Get method for date
- getEmail() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for email
- getFax() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for fax
- getFirstName() - Method in class org.biomage.AuditAndSecurity.Person
- Get method for firstName
- getFromContact_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to get Contact from Contact_list
- getFromMembers(int) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Method to get Contact from Members_list
- getFromPerson_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to get Person from Person_list
- getFromReadGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
- Method to get SecurityGroup from ReadGroups_list
- getFromRoles(int) - Method in class org.biomage.AuditAndSecurity.Contact
- Method to get OntologyEntry from Roles_list
- getFromSecurityGroup_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to get SecurityGroup from SecurityGroup_list
- getFromSecurity_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to get Security from Security_list
- getFromWriteGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
- Method to get SecurityGroup from WriteGroups_list
- getLastName() - Method in class org.biomage.AuditAndSecurity.Person
- Get method for lastName
- getMembers() - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Get method for members
- getMidInitials() - Method in class org.biomage.AuditAndSecurity.Person
- Get method for midInitials
- getOwner() - Method in class org.biomage.AuditAndSecurity.Security
- Get method for owner
- getParent() - Method in class org.biomage.AuditAndSecurity.Organization
- Get method for parent
- getPerformer() - Method in class org.biomage.AuditAndSecurity.Audit
- Get method for performer
- getPerson_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Get method for person_list
- getPhone() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for phone
- getReadGroups() - Method in class org.biomage.AuditAndSecurity.Security
- Get method for readGroups
- getRoles() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for roles
- getSecurityGroup_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Get method for securityGroup_list
- getSecurity_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Get method for security_list
- getTollFreePhone() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for tollFreePhone
- getURI() - Method in class org.biomage.AuditAndSecurity.Contact
- Get method for URI
- getWriteGroups() - Method in class org.biomage.AuditAndSecurity.Security
- Get method for writeGroups
L
M
- MODIFICATION - Variable in class org.biomage.AuditAndSecurity.Audit.Action
- members - Variable in class org.biomage.AuditAndSecurity.SecurityGroup
- The members of the Security Group.
- midInitials - Variable in class org.biomage.AuditAndSecurity.Person
N
- nameToValue - Variable in class org.biomage.AuditAndSecurity.Audit.Action
O
- Organization - class org.biomage.AuditAndSecurity.Organization.
- Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
- Organization() - Constructor for class org.biomage.AuditAndSecurity.Organization
- Default constructor.
- Organization(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Organization
- Attribute constructor.
- org.biomage.AuditAndSecurity - package org.biomage.AuditAndSecurity
- owner - Variable in class org.biomage.AuditAndSecurity.Security
- The owner of the security rights.
P
- Person - class org.biomage.AuditAndSecurity.Person.
- A person for which the attributes are self describing.
- Person() - Constructor for class org.biomage.AuditAndSecurity.Person
- Default constructor.
- Person(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Person
- Attribute constructor.
- parent - Variable in class org.biomage.AuditAndSecurity.Organization
- The containing organization (the university or business which a lab belongs to, etc.)
- performer - Variable in class org.biomage.AuditAndSecurity.Audit
- The contact for creating or changing the instance referred to by the Audit.
- person_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- A person for which the attributes are self describing.
- phone - Variable in class org.biomage.AuditAndSecurity.Contact
R
- readGroups - Variable in class org.biomage.AuditAndSecurity.Security
- Specifies which security groups have read permission.
- removeElementAtFromContact_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove by position from Contact_list
- removeElementAtFromMembers(int) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Method to remove by position from Members_list
- removeElementAtFromPerson_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove by position from Person_list
- removeElementAtFromReadGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
- Method to remove by position from ReadGroups_list
- removeElementAtFromRoles(int) - Method in class org.biomage.AuditAndSecurity.Contact
- Method to remove by position from Roles_list
- removeElementAtFromSecurityGroup_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove by position from SecurityGroup_list
- removeElementAtFromSecurity_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove by position from Security_list
- removeElementAtFromWriteGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
- Method to remove by position from WriteGroups_list
- removeFromContact_list(Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove first Contact from Contact_list
- removeFromMembers(Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Method to remove first Contact from Members_list
- removeFromPerson_list(Person) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove first Person from Person_list
- removeFromReadGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to remove first SecurityGroup from ReadGroups_list
- removeFromRoles(OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
- Method to remove first OntologyEntry from Roles_list
- removeFromSecurityGroup_list(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove first SecurityGroup from SecurityGroup_list
- removeFromSecurity_list(Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Method to remove first Security from Security_list
- removeFromWriteGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
- Method to remove first SecurityGroup from WriteGroups_list
- roles - Variable in class org.biomage.AuditAndSecurity.Contact
- The roles (lab equipment sales, contractor, etc.) the contact fills.
S
- Security - class org.biomage.AuditAndSecurity.Security.
- Permission information for an object as to ownership, write and read permissions.
- Security() - Constructor for class org.biomage.AuditAndSecurity.Security
- Default constructor.
- Security(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Security
- Attribute constructor.
- SecurityGroup - class org.biomage.AuditAndSecurity.SecurityGroup.
- Groups contacts together based on their security privileges.
- SecurityGroup() - Constructor for class org.biomage.AuditAndSecurity.SecurityGroup
- Default constructor.
- SecurityGroup(Attributes) - Constructor for class org.biomage.AuditAndSecurity.SecurityGroup
- Attribute constructor.
- securityGroup_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Groups contacts together based on their security privileges.
- security_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Permission information for an object as to ownership, write and read permissions.
- setAction(Audit.Action) - Method in class org.biomage.AuditAndSecurity.Audit
- Set method for action
- setAddress(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for address
- setAffiliation(Organization) - Method in class org.biomage.AuditAndSecurity.Person
- Set method for affiliation
- setContact_list(AuditAndSecurity_package.Contact_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Set method for contact_list
- setDate(Date) - Method in class org.biomage.AuditAndSecurity.Audit
- Set method for date
- setEmail(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for email
- setFax(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for fax
- setFirstName(String) - Method in class org.biomage.AuditAndSecurity.Person
- Set method for firstName
- setLastName(String) - Method in class org.biomage.AuditAndSecurity.Person
- Set method for lastName
- setMembers(HasMembers.Members_list) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- Set method for members
- setMidInitials(String) - Method in class org.biomage.AuditAndSecurity.Person
- Set method for midInitials
- setOwner(Contact) - Method in class org.biomage.AuditAndSecurity.Security
- Set method for owner
- setParent(Organization) - Method in class org.biomage.AuditAndSecurity.Organization
- Set method for parent
- setPerformer(Contact) - Method in class org.biomage.AuditAndSecurity.Audit
- Set method for performer
- setPerson_list(AuditAndSecurity_package.Person_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Set method for person_list
- setPhone(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for phone
- setReadGroups(HasReadGroups.ReadGroups_list) - Method in class org.biomage.AuditAndSecurity.Security
- Set method for readGroups
- setRoles(HasRoles.Roles_list) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for roles
- setSecurityGroup_list(AuditAndSecurity_package.SecurityGroup_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Set method for securityGroup_list
- setSecurity_list(AuditAndSecurity_package.Security_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- Set method for security_list
- setTollFreePhone(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for tollFreePhone
- setURI(String) - Method in class org.biomage.AuditAndSecurity.Contact
- Set method for URI
- setValueByName(String) - Method in class org.biomage.AuditAndSecurity.Audit.Action
- setWriteGroups(HasWriteGroups.WriteGroups_list) - Method in class org.biomage.AuditAndSecurity.Security
- Set method for writeGroups
T
- tollFreePhone - Variable in class org.biomage.AuditAndSecurity.Contact
U
V
- value - Variable in class org.biomage.AuditAndSecurity.Audit.Action
W
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Person
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Security
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Person
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Security
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- writeAttributes
- writeGroups - Variable in class org.biomage.AuditAndSecurity.Security
- Specifies which security groups have write permission.
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Person
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Security
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
- writeMAGEML
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