code_environment.html

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<h3>Building a Reaction</h3>

<p>
The reaction class keeps track of all of the information associated with
a single possible environmental reaction.  The class appears as follows:

<pre>
  class <font color="#880000">cReaction</font> {
  private:
    <font color="#880000">cString</font> <font color="#000088">name</font>;
    <font color="#880000">int</font> <font color="#000088">id</font>;
    <font color="#880000">cTaskEntry</font> * <font color="#000088">task</font>;
    <font color="#880000">tList</font><<font color="#880000">cReactionRequisite</font>> <font color="#000088">requisite_list</font>;
    <font color="#880000">tList</font><<font color="#880000">cReactionProcess</font>> <font color="#000088">process_list</font>;
  public:
    <font color="#008800">cReaction</font>(const <font color="#880000">cString</font> & <font color="#000088">_name</font>, <font color="#880000">int</font> <font color="#000088">_id</font>);
    ~<font color="#008800">cReaction</font>();

    const <font color="#880000">cString</font> & <font color="#008800">GetName</font>() const { return <font color="#000088">name</font>; }
    <font color="#880000">int</font> <font color="#008800">GetID</font>() const { return <font color="#000088">id</font>; }
    <font color="#880000">cTaskEntry</font> * <font color="#008800">GetTask</font>() { return <font color="#000088">task</font>; }
    const <font color="#880000">tList</font><<font color="#880000">cReactionRequisite</font>> & <font color="#008800">GetRequisites</font>()
      { return <font color="#000088">requisite_list</font>; }
    const <font color="#880000">tList</font><<font color="#880000">cReactionProcess</font>> & <font color="#008800">GetProcesses</font>() { return <font color="#000088">process_list</font>; }

    void <font color="#008800">SetTask</font>(<font color="#880000">cTaskEntry</font> * <font color="#000088">_task</font>) { <font color="#000088">task</font> = <font color="#000088">_task</font>; }
    <font color="#880000">cReactionProcess</font> * <font color="#008800">AddProcess</font>();
    <font color="#880000">cReactionRequisite</font> * <font color="#008800">AddRequisite</font>();
  };
</pre>

<p>
Each reaction must have a unique name and a unique numerical ID associated
with them.  In addition to those data, a reaction object also has a task that
acts as its trigger, a list of other requisites that must be met for the
trigger to work, and a list of processes that will occur if the reaction goes
off.  The cReaction object acts a a single place to store all of this
information.

<h3>Resources</h3>

<p>
Resources are a little more complicated than task entries to manage
and understand.  An object
of type <font color="#880000">cResource</font> contains 18 pieces of
data, and the associated accessors.  Like all of the other individual 
units we have discussed, resources have a unique 
<font color="#000088">name</font> and numerical
<font color="#000088">id</font>.  For all resource we store the quantities
associated with their <font color="#000088">inflow</font>,
<font color="#000088">outflow</font>, and
<font color="#000088">initial</font> count (each stored as a
<font color="#880000">double</font>) as well as the 
<font color="#000088">geometry</font> of that resource.

<p>
For spatial resources we need to be able to describe how a resource
exists in space so we store data for:
<ul>
  <li>
    <font color="#000088">inflowX1</font>, <font
    color="#000088">inflowX2</font>, <font
    color="#000088">inflowY1</font>, and  <font
    color="#000088">inflowY2</font> to describe a rectangle where
    resources flow in
  </li>
  <li>
    <font color="#000088">outflowX1</font>, <font
    color="#000088">outflowX2</font>, <font
    color="#000088">outflowY1</font>, and  <font
    color="#000088">outfowY2</font> for a rectangle where resources flow
    out of
  </li>
  <li>
    <font color="#000088">xdiffuse</font> and <font
    color="#000088">ydiffuse</font> describe how fast resources will
    flow from cells of higher amounts of that resource to cells with
    lower amounts of that resource
  </li>
  <li>
    <font color="#000088">xgravity</font> and <font
    color="#000088">ygravity</font> describe the preferential flow of
    resource in a given direction
  </li>
</ul>                                   
<p>
This class describes the dynamics of a resource, not its current count 
(since, for example, we might want local resources where each cell 
would have its own count).  However, every time a
resource is needed, any changes in its quantity from the last time it was
used can be calculated using these numbers.


<h3>Tying it all together: The Environment</h3>

<p>
The cEnvironment class is used to maintain the details of how the environments
work using the classes described above and a few others.  Below is an
abbreviated version of this class:

<pre>
class <font color="#880000">cEnvironment</font> {
private:
  <font color="#886600">// Keep libraries of resources, reactions, and tasks.</font>
  <font color="#880000">cResourceLib</font> <font color="#000088">resource_lib</font>;
  <font color="#880000">cReactionLib</font> <font color="#000088">reaction_lib</font>;
  <font color="#880000">cTaskLib</font> <font color="#000088">task_lib</font>;
  <font color="#880000">cInstLib</font> <font color="#000088">inst_lib</font>;
  <font color="#880000">cMutationRates</font> <font color="#000088">mut_rates</font>;

public:
  <font color="#008800">cEnvironment</font>();
  <font color="#008800">cEnvironment</font>(const <font color="#880000">cString</font> & <font color="#000088">filename</font>);
  ~<font color="#008800">cEnvironment</font>() { ; }

  <font color="#880000">bool</font> <font color="#008800">Load</font>(const <font color="#880000">cString</font> & <font color="#000088">filename</font>);

  <font color="#886600">// Interaction with the organisms</font>
  <font color="#880000">bool</font> <font color="#008800">TestOutput</font>(  <font color="#880000">cReactionResult</font> & <font color="#000088">result</font>,
                    const <font color="#880000">tBuffer</font><<font color="#880000">int</font>> & <font color="#000088">inputs</font>,
                    const <font color="#880000">tBuffer</font><<font color="#880000">int</font>> & <font color="#000088">outputs</font>,
                    const <font color="#880000">tArray</font><<font color="#880000">int</font>> & <font color="#000088">task_count</font>,
                    const <font color="#880000">tArray</font><<font color="#880000">int</font>> & <font color="#000088">reaction_count</font>,
                    const <font color="#880000">tArray</font><<font color="#880000">double</font>> & <font color="#000088">resource_count</font> ) const;
};
</pre>

<p>
The private data members include all of the libraries needed to specify
the environment, plus its mutation rates.  The
<font color="#008800">Load</font>() method takes a filename (environment.cfg
by default) and will fill out all of the libraries in this environment.  The
most important feature of this class is the
<font color="#008800">TestOutput</font>() method, which takes in all sorts
of information about the current state of the organism that has just done
an output and fills out an object of type
<font color="#880000">cReactionResult</font> with information about what
happened.  It also directly returns a bool that will indicate if there have
been any changes at all.  The specific information it uses to determine
the results are the <font color="#000088">inputs</font> the organism has
taken in and the <font color="#000088">outputs</font> it has produced --
both needed to determine what tasks have been done, and therefore what
reactions may have been triggered.  That organism's previous
<font color="#000088">task_count</font> and
<font color="#000088">resource_count</font> are also needed to determine
if the reactions requisites have been met.  And finally the
<font color="#000088">resource_count</font> available to the organisms is
needed to determine how much of each resource can be used in the reactions.