code_events.html

有趣的模拟进化的程序 由国外一生物学家开发 十分有趣

  * merit (double) default: -1
  *   The initial merit of the organism. If set to -1, this is ignored.
  * lineage label (integer) default: 0
  *   An integer that marks all descendants of this organism.
  * neutral metric (double) default: 0
  *   A double value that randomly drifts over time.
  **/</font>
  <b>:args:</b>
  <font color="#880000">cString</font> <font color="#000088">fname</font>          "START_CREATURE"
  <font color="#880000">int</font>     <font color="#000088">cell_id</font>        0
  <font color="#880000">double</font>  <font color="#000088">merit</font>          -1
  <font color="#880000">int</font>     <font color="#000088">lineage_label</font>  0
  <font color="#880000">double</font>  <font color="#000088">neutral_metric</font> 0
  <b>:body:</b>
  if (<font color="#000088">fname</font> == "START_CREATURE") <font color="#000088">fname</font> = <font color="#880000">cConfig</font>::<font color="#008800">GetStartCreature()</font>;
  <font color="#880000">cGenome</font> <font color="#000088">genome</font> =
     <font color="#880000">cInstUtil</font>::<font color="#008800">LoadGenome</font>(<font color="#000088">fname</font>, <font color="#000088">population</font>-><font color="#008800">GetEnvironment()</font>.<font color="#008800">GetInstLib()</font>);
  <font color="#000088">population</font>-><font color="#008800">Inject</font>(<font color="#000088">genome</font>, <font color="#000088">cell_id</font>, <font color="#000088">merit</font>, <font color="#000088">lineage_label</font>, <font color="#000088">neutral_metric</font>);

</pre>

<p>
As indicated by its description, the "<tt>inject</tt>" command will inject a
single organism into the population.  The user can specify a filename that
contains the organism's genome (or START_CREATURE to use this value from the
genesis file), the cell in which the organism should be
placed, the merit to start the organism with (or -1 to auto-calculate it on
loading), a lineage label to tag all of this organism's offspring,
and a neutral value that will drift over each generation.  Each of
these configuration values is supplied with a default so that the user
is not required to enter any additional information.

<p>
But what actually happens when this event is run?

<p>
First, the <tt>if</tt>-statement checks if the user has entered
(or left as default) the value <tt>"START_CREATURE"</tt> as the filename.
If so, it looks up the proper filename (from the cConfig class that holds
the current state of all the genesis variables -- we'll talk more about it
soon) and sets this variable such that it is now indicating a real file.

<p>
The next line builds an object of class <font color="#880000">cGenome</font>
using a function called <font color="#008800">LoadGenome</font>
in the utility class <font color="#880000">cInstUtil</font>.  This function
needs the filename to load from, and an instruction set to convert the
contents of that file into a genome.  The instruction set is stored within
the population's environment, and therefore requires a series of Methods to
be called to retrieve it.

<p>
Finally, this event takes that newly created genome, and runs the method
<font color="#008800">Inject</font> on the population object.  This method
takes in all of the information about the organism to be injected and then
actually builds the cOrganism object and places into the population.


<h3>Example: The <tt>inject_all</tt> event</h3>

<p>
Below is a slight variation on the <tt>inject</tt> command.  Rather than
injecting a single organism into a specific cell, it will inject identical
organisms into every cell in the population.

<p>

<pre>
  <b>inject_all</b>
  <b>:descr:</b>
  <font color="#886600">/**
  * Injects identical organisms into all cells of the population.
  *
  * Parameters:
  * filename (string)
  *   The filename of the genotype to load. If this is left empty, or the keyword
  *   "START_CREATURE" is given, than the genotype specified in the genesis
  *   file under "START_CREATURE" is used.
  * merit (double) default: -1
  *   The initial merit of the organism. If set to -1, this is ignored.
  * lineage label (integer) default: 0
  *   An integer that marks all descendants of this organism.
  * neutral metric (double) default: 0
  *   A double value that randomly drifts over time.
  **/</font>
  <b>:args:</b>
  <font color="#880000">cString</font> <font color="#000088">fname</font>          "START_CREATURE"
  <font color="#880000">double</font>  <font color="#000088">merit</font>          -1
  <font color="#880000">int</font>     <font color="#000088">lineage_label</font>  0
  <font color="#880000">double</font>  <font color="#000088">neutral_metric</font> 0
  <b>:body:</b>
  if (<font color="#000088">fname</font> == "START_CREATURE") <font color="#000088">fname</font> = <font color="#880000">cConfig</font>::<font color="#008800">GetStartCreature()</font>;
  <font color="#880000">cGenome</font> <font color="#000088">genome</font> =
     <font color="#880000">cInstUtil</font>::<font color="#008800">LoadGenome</font>(<font color="#000088">fname</font>, <font color="#000088">population</font>-><font color="#008800">GetEnvironment()</font>.<font color="#008800">GetInstLib()</font>);
  for (<font color="#880000">int</font> <font color="#000088">i</font> = 0; <font color="#000088">i</font> < <font color="#000088">population</font>-><font color="#008800">GetSize()</font>; <font color="#000088">i</font>++) {
    <font color="#000088">population</font>-><font color="#008800">Inject</font>(<font color="#000088">genome</font>, <font color="#000088">i</font>, <font color="#000088">merit</font>, <font color="#000088">lineage_label</font>, <font color="#000088">neutral_metric</font>);
  }
  <font color="#000088">population</font>-><font color="#008800">SetSyncEvents</font>(true);

</pre>

<p>
The first difference that you should notice is the lack of the
<font color="#000088"><tt>cell_id</tt></font> variable.  Since we are no
longer injecting into just a single cell, no cell ID needs to be
included.  The remaining differences are all in the body of the event.

<p>
The first two commands in the body remain the same; that is, the filename
is finalized, and the genome used to create the organisms is itself
constructed.  The next thing we need to do is actually inject the organisms
into each cell of the population.  To run the Inject command once for each
position we employ a <tt>for</tt> command.  This command has a strange
syntax:

<pre>
  for ( <font color="#886600">setup</font> ; <font color="#886600">continue_test</font> ; <font color="#886600">step_method</font> ) {
    <font color="#886600">loop body</font>
  }

</pre>

<p>
In our case, we want to set a variable to every number that represents
a cell in the population.  These numbers go from zero to the population size
minus one.  To build this loop, we <font color="#886600">setup</font> by
creating a variable called <font color="#000088">i</font> and initialize it
to 0 -- the ID of the first cell we plan to inject into.  We want to
keep injecting into all cells with ID less than the full population size, so
our <font color="#886600">continue_test</font> tells us to keep going as
long as i is less than that number.  Finally our
<font color="#886600">step_method</font> tells the program that after
each execution of the contents of the loop, it should increment the value of
i by one.  The Inject method itself works the same as in the
previous event.

<p>
Finally, we run the method <font color="#008800">SetSyncEvents</font>(true)
on the population object.  This is not necessary, but it helps keep the 
event triggers in proper sync.  Since we just injected organisms into every
site in the population, we have effectively reset the generation of the
population to zero.  This could screw up some events that are triggered based
on generation if we're not careful, so we warn the population that such
trouble may occur, and it should re-sync the events at its earliest
convenience.

<p>
So that isn't so hard is it?  Good!  Now we get to some...

<h3>Try it Out...</h3>

<p>
Here are a couple of example events that you can try implementing.  The
first one of them is the "<b><tt>inject_range</tt></b>" event.  This event
will be used when you want to inject organisms into more than one cell in the
population, but not all of them.  Where the normal <tt>inject</tt> event
took a single cell_id value, this new event should take two of them -- a
starting cell and a stopping cell.  You should then use a <tt>for</tt> loop
(similar to the one in "<tt>inject_all</tt>") to inject the genome into
all cells in range.  Extra credit if you test the order of the two numbers
and swap them if the start_cell is larger than the end_cell.

<p>
The second event you are going to implement is "<b><tt>kill_cell</tt></b>"
This is again somewhat similar to <tt>inject</tt> in code structure, but
you're goal is to kill the organism (if one exists) in the specified cell.
For help with how to do this, take a look at the <tt>apocalypse</tt> event,
which causes a larger scale extinction.