structure.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

of helper classes:

<p>
<table cellpadding=6>
<tr><td valign=top><tt><font color="#000088">fitness_matrix.??</font></tt>
    <td valign=top>The cFitnessMatrix class is used to calculate the
	quasi-species around a genotype.
<tr><td valign=top><tt><font color="#000088">landscape.??</font></tt>
    <td valign=top>The cLandscape class is used to study the local region
	of genotype space around a genotype.  All possible single (or more,
	if desired) mutations are performed, and statistics are kept about
	the results.
<tr><td valign=top><tt><font color="#000088">pop_interface.??</font></tt>
    <td valign=top>The cPopulationInterface class is used by organisms
	to interact back with the population (or test CPU).
<tr><td valign=top><tt><font color="#000088">primitive.cc</font></tt>
    <td valign=top>This file defines the primitive avida driver, when no
	interactive user interface is being used.
<tr><td valign=top><tt><font color="#000088">reaction.??</font></tt>
    <td valign=top>The cReaction class contains all of the information for
	what triggers a reaction, its restrictions, and the process that
	occurs.
<tr><td valign=top><tt><font color="#000088">reaction_result.??</font></tt>
    <td valign=top>The cReactionResult class contains all of the information
	about the results of a reaction after one occurs, such as the amount
	of resources consumed, what the merit change is, what tasks triggered
	it, etc.
<tr><td valign=top><tt><font color="#000088">resource.??</font></tt>
    <td valign=top>The cResource class contains information about a single
	resource, such as its inflow rate, outflow, name, etc.
<tr><td valign=top><tt><font color="#000088">resource_count.??</font></tt>
    <td valign=top>The resource count keeps track of how much of each
	resource is present in the region being tracked.
<tr><td valign=top><tt><font color="#000088">species.??</font></tt>
    <td valign=top>The cSpecies class represents a group of genotypes that
	can be crossed over with a high probability of producing a viable
	result.
<tr><td valign=top><tt><font color="#000088">tasks.??</font></tt>
    <td valign=top>These files contain all of the information associated
	with tasks, including the cTaskLibrary, and the cTaskEntry classes.
	A task entry contains the task name and a pointer to the function
	that will check its completion.
</table>

<p>
Finally, we have the utility classes.  A utility class is different from
normal classes in that they include <i>only</i> methods and no data.  This
is basically for collecting functions that don't need to be part of a
class, but I want to keep them nice, neat and organized.

<p>
<table cellpadding=6>
<tr><td valign=top><tt><font color="#000088">analyze_util.??</font></tt>
    <td valign=top>The cAnalyzeUtil class contains functions to analyze the
	state of avida populations.
<tr><td valign=top><tt><font color="#000088">callback_util.??</font></tt>
    <td valign=top>The cCallbackUtil class contains functions to enable
	the cPopulationInterface to interact smoothly with the population.
<tr><td valign=top><tt><font color="#000088">genome_util.??</font></tt>
    <td valign=top>The cGenomeUtil class contains functions to analyze
	individual genomes, such as scanning if they contain a specific
	instruction or to find the edit distance between two genomes.
<tr><td valign=top><tt><font color="#000088">inst_util.??</font></tt>
    <td valign=top>The cInstUtil class is for functions that used both
	a genome and the instruction library, such as loading a new genome
	or randomizing a genome.
</table>



<h3>Directory: <tt><font color="#008844">current/source/cpu/</font></tt></h3>

This sub-directory contains the files used to define the virtual CPUs in
Avida.

<p>
<table cellpadding=6>

<tr><td valign=top><tt><font color="#000088">cpu_defs.hh</font></tt>
    <td valign=top>This header file only contains definitions relating
	to virtual CPUs.
<tr><td valign=top><tt><font color="#000088">cpu_memory.??</font></tt>
    <td valign=top>The cCPUMemory class inherits from the cGenome class,
	extending its functionality to facilitate insertions and deletions.
	It also associates flags with each instruction in the genome to
	mark if they have been executed, copied, mutated, etc.
<tr><td valign=top><tt><font color="#000088">cpu_stack.??</font></tt>
    <td valign=top>The cCPUStack class is an integer-stack component in the
	virtual CPUs.
<tr><td valign=top><tt><font color="#000088">cpu_stats.hh</font></tt>
    <td valign=top>The cCPUStats class tracks mutations that have
	occurred during an organism's life, and the number
	of times each instruction has been executed.
<tr><td valign=top><tt><font color="#000088">hardware_base.??</font></tt>
    <td valign=top>The cHardwareBase class is an abstract base class that
	all other hardware types must be overloaded from.  It has minimal
	built in functionality.
<tr><td valign=top><tt><font color="#000088">hardware_cpu.??</font></tt>
    <td valign=top>The cHardwareCPU class extends cHardwareBase into a
	proper virtual CPU, with registers, stacks, memory, IO Buffers,
	etc.
<tr><td valign=top><tt><font color="#000088">hardware_factory.??</font></tt>
    <td valign=top>The cHardwareFactory manages the building of new hardware
	as well as the recycling of old hardware after an organism dies.
	Recycling hardware rather than making a new one each time can 
	provide a performance increase.
<tr><td valign=top><tt><font color="#000088">hardware_util.??</font></tt>
    <td valign=top>The cHardwareUtil class is a utility class that currently
	only manages the loading of instruction sets into a virtual CPU.
<tr><td valign=top><tt><font color="#000088">head.hh</font></tt>
    <td valign=top>The cCPUHead class implements a head pointing to a
	position in the memory of a virtual CPU.
<tr><td valign=top><tt><font color="#000088">label.hh</font></tt>
    <td valign=top>The cLabel class marks labels (series of no-operation
	instruction) in a genome.  These are used when a
	label needs to be used as an instruction argument.
<tr><td valign=top><tt><font color="#000088">test_cpu.hh</font></tt>
    <td valign=top>The cTestCPU class maintains a test environment to
	run organisms in that we don't want to be able to directly affect
	the real population.
<tr><td valign=top><tt><font color="#000088">test_util.hh</font></tt>
    <td valign=top>The cTestUtil utility class is for test-related functions
	that require a test CPU, such as printing out a genome to a file with
	collected information.
</table>


<h3>Directory: <tt><font color="#008844">current/source/events/</font></tt></h3>

<p>
The events sub-directory contains files that manage the scheduling and
processing of user-defined events.  Many of the files here are actually
automatically generated by the
<font color="#000088"><tt>make_events.pl</tt></font> script, which is written
in the language Perl, and automatically run by the Makefile.  This script
will convert <font color="#000088"><tt>cPopulation.events</tt></font> into
the proper C++ files.

<h3>Directory: <tt><font color="#008844">current/source/tools/</font></tt></h3>

<p>
The tools sub-directory contains C++ source code that is used throughout 
avida, but is not specific to the project.  I will list the proper classes
first, and then the template class.

<p>
<table cellpadding=6>
<tr><td valign=top><tt><font color="#000088">assert.??</font></tt>
    <td valign=top>A collection of tests that start up the debugger if any
  of the tests fail.  When running the code in an optimized mode, these tests
  are not performed for speedup.
<tr><td valign=top><tt><font color="#000088">data_entry.??</font></tt>
    <td valign=top>Associates data names with functions for printing out data
  file with a user specified format.
<tr><td valign=top><tt><font color="#000088">data_manager.??</font></tt>
    <td valign=top>This class manages a collection of data entries and handles
  the creation and output of user-designed data files at runtime.
<tr><td valign=top><tt><font color="#000088">datafile.??</font></tt>
    <td valign=top>A set of classes useful for handling output files, and
  a manager to track output files by name.
<tr><td valign=top><tt><font color="#000088">debug.??</font></tt>
    <td valign=top>This is used to track of problems with the
  code.  You can call methods in a debug object to set errors, warnings
  or leave comments.  In practice, assert is cleaner.
<tr><td valign=top><tt><font color="#000088">file.??</font></tt>
    <td valign=top>A set of classes useful for loading input files and removing
	comments.
<tr><td valign=top><tt><font color="#000088">functions.hh</font></tt>
    <td valign=top>Some useful math functions such as Min, Max, and Log.
<tr><td valign=top><tt><font color="#000088">help.??</font></tt>
    <td valign=top>This still needs to be integrated into avida proper, (it
  is being used some in analyze mode) but can output useful HTML help files.
<tr><td valign=top><tt><font color="#000088">merit.??</font></tt>
    <td valign=top>Provides a very large integer number, dissectable in useful
  ways.
<tr><td valign=top><tt><font color="#000088">random.??</font></tt>
    <td valign=top>A powerful random number generator, that can output numbers
  in a variety of formats.
<tr><td valign=top><tt><font color="#000088">slice.??</font></tt>
    <td valign=top> A scheduling class that can operate at high precision.
<tr><td valign=top><tt><font color="#000088">stat.??</font></tt>
    <td valign=top>A set of classes used to collect statistics on data.
<tr><td valign=top><tt><font color="#000088">string.??</font></tt>
    <td valign=top>A standard string object, but with lots of functionality.
<tr><td valign=top><tt><font color="#000088">string_list.??</font></tt>
    <td valign=top>A specialized class for collections of strings, with added
  functionality over a normal list.
<tr><td valign=top><tt><font color="#000088">string_util.??</font></tt>
    <td valign=top>Contains a bunch of static methods to manipulate and compare
  strings.
<tr><td valign=top><tt><font color="#000088">tools.hh</font></tt>
    <td valign=top>A collection of global objects (for debug, random, and
  default directory) and a flags class.
</table>

<p>
Templates are special classes that interact with another data-type
that doesn't need to be specified until the programmer instantiates an object
in the class.  Its a hard concepts to get used, but allows for remarkably
flexible programming, and makes very reusable code.  The
main drawback (other than brain-strain) is that
templates must be entirely defined in header files since separate code is
generated for each class the template interacts with.

<p>
<table cellpadding=6>
<tr><td valign=top><tt><font color="#000088">tArray.hh</font></tt>
    <td valign=top>A fixed-length array template; array sizes may be adjusted
  manually when needed.
<tr><td valign=top><tt><font color="#000088">tBuffer.hh</font></tt>
    <td valign=top>A container that keeps only the last N entries,
  indexed with the most recent first.
<tr><td valign=top><tt><font color="#000088">tDictionary.hh</font></tt>
    <td valign=top>A container template that allows the user to search for
  a target object based on a keyword.
<tr><td valign=top><tt><font color="#000088">tList.hh</font></tt>
    <td valign=top>A reasonably powerful linked list and iterators.  The list
  will keep track of the iterators and never allow them to have an illegal
  value.
<tr><td valign=top><tt><font color="#000088">tMatrix.hh</font></tt>
    <td valign=top> A fixed size matrix template with arbitrary indexing.
<tr><td valign=top><tt><font color="#000088">tMemTrack.hh</font></tt>
    <td valign=top>This is a template that can be put over any class or data
  type to keep track of it.  If all creations of objects in the class are
  done through this template rather than (or in conjunction with) "new",
  memory leaks should be detectable.
  This is new, and not yet used in avida.
<tr><td valign=top><tt><font color="#000088">tVector.hh</font></tt>
    <td valign=top>A variable-length array object; array sizes will be
  automatically adjusted to accommodate any positions accessed in it.
</table>


<h3>Directories: <tt><font color="#008844">current/source/viewers/</font></tt>
 and <tt><font color="#008844">current/source/qt-viewer/</font></tt></h3>

<p>
These directories contain the source code for the avida viewers, which I'm
not planning on going into at this point.  The first directory contains
the files for the text viewers (both the ncurses viewer and the Windows ASCII
viewer), while the second one contains the files for the Qt graphical viewer
thats still under development.  If people are interested in this later in the
course, I will come back to it in more detail.

<h3>Directory: <tt><font color="#008844">current/source/support/</font></tt></h3>

<p>
This directory contains all of the originals of the files that are
copied into the <tt><font color="#008844">current/work/</font></tt> directory
on the installation process for the user to modify.  There is also
a <tt><font color="#008844">config/</font></tt> sub-directory under here
with additional, optional configuration files that you may want to look at
to see other possible pre-configured settings.