/// <summary>
/// Create a list of Channels, using the mesh hierarchy to get the visible frames representing the channels,
/// and the gene or the physiology to get the species-specific parameters such as chemical selectivity
/// </summary>
/// <param name="gene"></param>
/// <returns></returns>
private Channel[] LoadChannels(Gene gene)
{
// Read any channels defined by the gene
Channel[] channel = gene.GetChannels();
// If none are defined, create some and load with the default chemical#s from the cell type
if (channel.Length == 0)
{
ChannelData[] chanData = physiology.GetChannelData(); // read the default src, dst, chem
if (chanData != null)
{
channel = new Channel[chanData.GetLength(0)]; // create enough channels
for (int c = 0; c < channel.Length; c++) // copy in the default chemical selectivity
{
channel[c] = new Channel();
channel[c].chemical = chanData[c].Chemical;
channel[c].constant = chanData[c].Constant; // and default for user-definable constant
}
}
}
//// Get a list of the "chan#" frames (visible organelles), in order, then copy to the channels
//JointFrame[] channelFrame = null;
//try
//{
// channelFrame = JointFrame.IndexFrameType(rootFrame, JointFrame.FrameType.Channel);
// for (int c = 0; c < channel.Length; c++)
// {
// channel[c].organelle = channelFrame[c];
// }
//}
//catch
//{
// throw new SDKException(this.name + " has different numbers of channels in the cell type ("
// + channel.Length + ") and the mesh (" + channelFrame.Length + ")");
//}
return channel;
}
/// <summary>
/// Get a clone of this Cell from the library, loading it first if necessary
/// </summary>
/// <returns>A modifiable clone of the named Cell</returns>
/// <param name="gene">The gene containing the cell's properties, orientation and wiring</param>
/// <param name="owner">The organism that owns me</param>
public static Cell Get(Gene gene, Organism owner)
{
Cell cell = null;
// Get name of the cell from the gene
string fullname = gene.XFile();
// if the library already contains a Cell of that name, that's what we'll clone from
if (library.ContainsKey(fullname))
{
cell = (Cell)library[fullname];
// Debug.WriteLine(" Cell: Created new Cell instance: "+name+":"+cell.instance);
}
// otherwise, create a new entry in the library by loading a whole X file
else
{
cell = new Cell(fullname);
// Debug.WriteLine(" Cell: Created new Cell archetype: "+name+":"+cell.instance);
}
// Return a cloned instance of this Cell
Cell newCell = cell.Clone(gene, owner);
newCell.CreateBoundMarker(); // temp: create marker to show bounding sphere
return newCell;
}
/// <summary>
/// Given the gene that has/would be used to create this cell, update its parameters
/// to reflect the current wiring setup, etc. Then recurse through children and siblings
/// until the whole tree has been constructed
/// </summary>
/// <param name="gene"></param>
public void UpdateGene(Gene gene)
{
// The gene type is our cell type, which we get from ToString()
gene.Type = physiology.ToString();
// Create a new list of channels from the user-defined wiring
gene.Channels = new List<Channel>();
gene.Channels.AddRange(channel);
// Get our current plug orientation matrix
gene.Orientation = PlugOrientation;
// Get the name of our parent socket (if we're not the root)
if (parentSocket != null)
{
gene.Socket = parentSocket.Name.Substring(0,4); // convert "skt3-0" to skt3
}
// Recursively build up the rest of the genome...
// If we have a child, create a new gene for it, link it into the genome tree and ask the child to update this gene
if (this.firstChild != null)
{
gene.FirstChild = new Gene();
this.firstChild.UpdateGene(gene.FirstChild);
}
// If we have a sibling, blah blah blah
if (this.sibling != null)
{
gene.Sibling = new Gene();
this.sibling.UpdateGene(gene.Sibling);
}
}
/// <summary>
/// Clone this cell
/// </summary>
/// <param name="gene">The gene specifying this cell instance's orientation, wiring, etc.</param>
/// <param name="owner">The organism that owns me</param>
private Cell Clone(Gene gene, Organism owner)
{
// Make a shallow copy of all members
Cell newCell = (Cell)this.MemberwiseClone();
// Replace members that are CLONED copies of objects in the master...
newCell.rootFrame = JointFrame.CloneHierarchy(rootFrame); // my unique copy of the frame hierarchy
// TODO: Clone any other members here
// Replace or create members that are UNIQUE to this instance...
newCell.instance = instance++; // my instance number (tally in master)
newCell.PlugOrientation = gene.Orientation; // my orientation in the parent socket
newCell.owner = owner; // my owning organism
newCell.joint = JointFrame.IndexFrameType(
newCell.rootFrame,JointFrame.FrameType.Animating); // lists of my animation, hotspot & skt frames
newCell.hotspot = JointFrame.IndexFrameType(
newCell.rootFrame, JointFrame.FrameType.Hotspot);
newCell.socket = JointFrame.IndexFrameType(
newCell.rootFrame, JointFrame.FrameType.Socket);
newCell.physiology = Physiology.LoadPhysiology(newCell.group, newCell.name, newCell.variantName, // my Physiology class containing functionality
newCell,
newCell.joint.Length,
newCell.socket.Length);
newCell.GetMyVariantIndex(); // Convert variant name into an index before trying to access channel data
newCell.channel = newCell.LoadChannels(gene); // lists of channel info from gene AND mesh frames
newCell.collisionFrames = new List<JointFrame>();
newCell.GetMeshFrames(newCell.rootFrame, newCell.collisionFrames, false); // a list of mesh-containing frames for collision tests
// Set all the internal (organelle) frames to invisible, because they aren't normally rendered
newCell.HideOrganelles();
// TODO: Initialise other instance-specific members here
// Now that everything is set up, call the Physiology subclass's Init() method to allow the physiology to initialise itself
newCell.physiology.Init();
// Add a device reset handler to rebuild this cell's resources
Engine.Device.DeviceReset += new System.EventHandler(newCell.OnReset);
return newCell;
}
/// <summary>
/// Recursively walk the gene tree, extract the Cell filenames, clone the Cell from the library and
/// record their interconnections (root->joint)
/// </summary>
/// <param name="gene">the gene being expressed</param>
/// <param name="parent">the Cell that is the parent of this new one</param>
/// <returns>the Cell created by this gene</returns>
private Cell GetCells(Gene gene, Cell parent)
{
// Get the X filename from the gene and either load or fetch that Cell from the library,
Cell s = Cell.Get(gene, this);
// Add it to the flat partlist
partList[numParts++] = s;
// Locate this cell's SOCKET by locating the frame with the correct name in the
// parent (if any)
if (parent!=null)
s.Attach(parent, gene.Socket);
// if the gene has any siblings, recursively attach their structures as siblings of this one
if (gene.Sibling!=null)
s.Sibling = GetCells(gene.Sibling, parent); // we share a parent
// if the gene has a child, recursively attach this as the child of this one
if (gene.FirstChild!=null)
s.FirstChild = GetCells(gene.FirstChild, s); // I am the parent
return s; // return the new Cell to the parent/sibling
}
/// <summary>
/// Add a cell of the selected type to the creature at the selected socket (if any)
/// </summary>
public void Add(string name)
{
// If no socket is selected, quit
if (Lab.SelectedSocket == null) return;
// If the selected socket already has a cell attached to it, we mustn't add another!
if (SelectedSocketIsOccupied())
return;
// OK to add
try
{
Gene gene = new Gene(name); // Create a gene for the cell type
Cell newCell = Cell.Get(gene, Lab.SelectedOrg); // create a cell from the gene
if (Lab.SelectedCell.FirstChild == null) // if the selected cell has no children
Lab.SelectedCell.FirstChild = newCell; // attach the new cell to it as the first child
else // otherwise, drop to the first child and find its last
{ // sibling. The new cell becomes the youngest sibling
Cell sib = Lab.SelectedCell.FirstChild;
while (sib.Sibling != null)
sib = sib.Sibling;
sib.Sibling = newCell;
}
newCell.Attach(Lab.SelectedCell, Lab.SelectedSocket); // record the cell's .parent and .parentSocket
Refresh(); // update org's part list, channels, etc.
Lab.SelectedCell = newCell; // Select the cell we've just added
newCell.SelectFirst(); // and the first socket on that cell
}
catch (Exception e)
{
throw new SDKException("Unable to create new cell of selected type: " + name, e);
}
}
/// <summary>
/// Read genome from XML stream
/// </summary>
/// <param name="xml"></param>
private void Read(XmlTextReader xml)
{
string tag = "";
while (xml.Read()) // for each node in the file...
{
if (xml.NodeType == XmlNodeType.Element) // <tag> rather than final </document>
{
switch (xml.Name) // depending on tag...
{
case "gene": // <gene> the ROOT gene </gene>
root = Gene.RecursiveRead(xml,null); // read recursively to support part hierarchy
break;
// Any other root level tags go here
// anything else must be a data tag, so wait for its text to arrive
default:
tag = xml.Name;
break;
}
}
// text within tags
else if (xml.NodeType == XmlNodeType.Text)
{
switch (tag)
{
// data tags relating to the Genome as a whole (not a gene) go here
default:
throw new XmlException("unexpected tag type: "+tag);
}
}
}
}
/// <summary>
/// Print an entire genome's hierarchy to the debug output stream
/// </summary>
/// <param name="root">root of hierarchy</param>
/// <param name="level">current depth into hierarchy (set this to 0)</param>
/// <returns></returns>
public static void DebugHierarchy(Gene root, int level)
{
// set up an indent level
string indent = "";
for (int i=0; i<level; i++)
indent += "\t";
Debug.WriteLine(indent+"*** GENE ["+root.Type+"] ***");
Debug.WriteLine(indent+" Socket: ["+root.Socket+"]");
// continue walking the tree
if (root.FirstChild!=null)
{
DebugHierarchy(root.FirstChild, level+1);
}
if (root.Sibling!=null)
{
DebugHierarchy(root.Sibling, level);
}
}
/// <summary>
/// Create a minimal genome for building a new creature.
/// The genome consists of a single gene defining a CORE cell
/// </summary>
public Genome()
{
root = new Gene("Core");
}
/// <summary>
/// Recurse through a genome writing the genes to an XML file
/// </summary>
/// <param name="xml">The output stream</param>
/// <param name="gene">The gene to write (and then descend into)</param>
public static void RecursiveWrite(XmlWriter xml, Gene gene)
{
xml.WriteStartElement("gene");
xml.WriteElementString("type", gene.Type);
if (gene.Socket!=null)
xml.WriteElementString("socket", gene.Socket);
xml.WriteElementString("orientation", EncodeMatrix(gene.Orientation));
// Write <channel> nodes
foreach (Channel c in gene.Channels)
{
c.WriteXml(xml);
}
// If this gene has children, nest them inside
if (gene.FirstChild != null)
RecursiveWrite(xml, gene.FirstChild);
// Close the </gene>
xml.WriteEndElement();
// If this gene has siblings, write them at the same level
if (gene.Sibling != null)
RecursiveWrite(xml, gene.Sibling);
}
/// <summary>
/// Read this <gene></gene> and any nested genes too
/// </summary>
/// <param name="xml"></param>
/// <param name="previous">previous SIBLING of the gene being created</param>
/// <returns></returns>
public static Gene RecursiveRead(XmlTextReader xml, Gene previous)
{
Gene gene = null;
Gene elder = null;
string tag = "";
while (xml.Read()) // for each node...
{
// <tag>
if (xml.NodeType == XmlNodeType.Element)
{
// Handle the tag
switch (xml.Name) // depending on tag...
{
// A child gene definition is nested inside this one, so create it recursively
case "gene":
// the first such gene is the child of this one
if (gene.FirstChild==null)
{
gene.FirstChild = RecursiveRead(xml,null);
elder = gene.FirstChild;
}
// subsequent genes are siblings of each other
else
{
elder.Sibling = RecursiveRead(xml,null);
elder = elder.Sibling;
}
break;
// A channel
case "channel":
gene.Channels.Add(ReadChannel(xml));
break;
// anything else must be a standalone <tag>text</tag>, so wait for its text to arrive
default:
tag = xml.Name;
break;
}
}
// text within tags
else if (xml.NodeType == XmlNodeType.Text)
{
switch (tag) // action depends on the tag this text is part of
{
// create the named gene as a sibling of the previous one
case "type": // <type> this gene's type </type>
gene = new Gene(); // start a new gene
gene.Type = xml.Value; // store its type name
break;
// <attachment>
case "socket":
gene.Socket = xml.Value;
break;
// <position>
case "orientation":
gene.Orientation = ReadMatrix(xml.Value);
break;
// Other gene initialisers here
default:
throw new XmlException("unexpected gene tag type: "+tag);
}
}
// closing tag
else if (xml.NodeType == XmlNodeType.EndElement)
{
if (xml.Name == "gene")
{
return gene; // return the gene I just created
}
}
}
throw new XmlException("missing </gene> tag"); // should always return before end of file
}
