/// <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>
/// Read a channel node (note: not all members of Channel are filled (e.g. mesh frames))
/// </summary>
/// <param name="xml"></param>
/// <returns></returns>
public static Channel ReadChannel(XmlTextReader xml)
{
string tag = "";
Channel channel = new Channel();
while (xml.Read()) // for each node...
{
// <tag>
if (xml.NodeType == XmlNodeType.Element)
{
tag = xml.Name;
}
// text within tags
else if (xml.NodeType == XmlNodeType.Text)
{
channel.ReadXml(xml, tag);
}
// closing tag
else if (xml.NodeType == XmlNodeType.EndElement)
{
if (xml.Name == "channel")
{
return channel; // return the channel I just created
}
}
}
throw new XmlException("missing </channel> tag"); // should always return before end of file
}