Trait Information

Overview

A TraitInfo object contains basic information a about a single trait being tracked in an organism. In addition to the name, type, and description of the trait, it also describes: the TARGET method, the ACCESS method, the INIT method, the ARCHIVE method, and the SUMMARY method.

TARGET method

The TARGET indicates what type of object the trait should be applied to.

  • ORGANISM Every organism in MABE must have this trait.

  • POPULATION Collections of organisms must have this trait.

  • MODULE Every module attached to MABE must have this trait.

  • MANAGER Every OrganismManager must have this trait.

ACCESS method

The ACCESS method to be used for a trait by each module. A trait can be

  • PRIVATE Only this module can modify the trait; no others should even read it.

  • OWNED Only this module can modify the trait, but other modules can read it.

  • GENERATED Only this module can modify the trait, but other modules MUST read it.

  • SHARED This module will read and write this trait, but others are allowed to as well.

  • REQUIRED This module will read the trait; another module must write to it.

  • OPTIONAL This module can read the trait; must first check if it exists.

INIT method

The INIT method describes how a trait should be initialized in a new offspring. (note that injected organisms always get the DEFAULT value.)

  • DEFAULT Always initialize this trait to its default value.

  • FIRST Initialize trait to the first parent’s value (only parent for asexual runs)

  • AVERAGE Initialize trait to the average value of all parents.

  • MINIMUM Initialize trait to the minimum value of all parents.

  • MAXIMUM Initialize trait to the maximum value of all parents.

The default INIT method is DEFAULT.

ARCHIVE method

The ARCHIVE method determines how many older values should be saved with each organism.

  • NONE Only the most recent value should be tracked, no archived values.

  • AT_BIRTH Store value of this trait was born with in “birth_(name)”.

  • LAST_REPRO Store value of trait at the last reproduction in “last_(name)”.

  • ALL_REPROS Store all value of trait at each reproduction event in “archive_(name)”.

  • ALL_VALUES Store every value change of trait at any time in “sequence_(name)”.

The default ARCHIVE method is NONE.

SUMMARY method

The SUMMARY method determines how a trait should be summarized over a collection of organisms.

  • IGNORE Don’t include this trait in phyla records.

  • AVERAGE Average of current value of all organisms (or final value at death).

  • SUMMARY Basic summary (min, max, count, ave) of current/final values.

  • FULL Store ALL current/final values for organisms.

The default SUMMARY method is NONE.

Helper Functions

The TraitInfo class comes with a number of public helper functions.

Getter Functions

const std::string & GetName() const

const std::string & GetDesc() const

emp::TypeID GetType() const

Init GetInit() const

Archive GetArchive()

Summary GetSummary()

const emp::vector<emp::TypeID> & GetAltTypes() const

What other types are allowed?

bool HasDefault() const

Was a default value set for this trait?

const T & GetDefault() const

Setter Functions

TraitInfo & SetName(const std::string & in_name)

TraitInfo & SetDesc(const std::string & in_desc)

TraitInfo & AddAccess(const std::string & in_name, mod_ptr_t in_mod, Access access)

Add a module that can access this trait.

virtual void Register(emp::DataMap & dm)

Register this trait in the provided DataMap.

Parent Functions

bool GetResetParent() const

TraitInfo & SetInheritParent()

Set the current value of this trait to be automatically inherited by offspring.

To set the average, minimum, or maximum across parents for this trait to be automatically inherited by offspring use the corresponding setter function. For example, to set the average use the function:

TraitInfo & SetInheritAverage()

TraitInfo & SetParentReset()

Set the parent to ALSO reset to the same value as the offspring on divide.

To set the the previous value or ALL previous values of this trait to be stored on birth or reset use the corresponding setter function. For example, to set only the pervious value use the function:

TraitInfo & SetArchiveLast()

Type Functions

void SetAltTypes(const emp::vector<emp::TypeID> & in_alt_types)

template <typename T> bool IsType() const

bool IsAllowedType(emp::TypeID test_type) const

template <typename T> bool IsAllowedType() const

Module/Access Functions

Access GetAccess(mod_ptr_t mod_ptr) const

Determine what kind of access a module has.

bool HasAccess(mod_ptr_t mod_ptr) const

Determine if a module has any knd of access to this trait.

size_t GetModuleCount() const

How many modules can access this trait?

size_t GetAccessCount(Access access) const

How many modules can access this trait using a specified access mode?

To determine the specific access mode of a trait use the boolean function for that access mode. For example, to determine if a trait has Private access use the function:

bool IsPrivate() const

To determine the number of traits with a specified access mode use the corresponding getter function. For example, to determine the number of traits with Private access use the function:

size_t GetPrivateCount() const

emp::vector<std::string> GetModuleNames() const

emp::vector<std::string> GetModuleNames(Access test_access)

What specific modules have a given access mode?

To determine the specific modules with a specified mode use the corresponding getter function. For example, to determine the specific modules with Private access is use the function:

emp::vector<std::string> GetPrivateNames() const