//! Load the diffusion reactions from an array of files and a Medium list
/*!
* \param files Array of files which contain information about diffusion reaction.
* \param mediums The list of all the mediums.
*
* This function loads the diffusion reactions based on Fick model. It takes an Array of file paths
* and a list of Medium that should contain all the mediums of the simulation.
* This function creates the list of all the reactions between all Medium which exist and initialize their parameters to 0.
* Only the reactions explicitly defined in files are initialized to the values explicited in files.
* If a parameter of a fick reaction is not specified in files then this parameter will be equal to 0.
*/
public void loadFicksReactionsFromFiles(string[] files, LinkedList <Medium> mediums)
{
Logger.Log("Fick::loadFicksReactionsFromFiles("
+ Logger.EnumerableToString <string> (files)
+ ") starts"
, Logger.Level.INFO);
LinkedList <FickProperties> propsList = new LinkedList <FickProperties> ();
LinkedList <FickProperties> newPropList;
foreach (string file in files)
{
newPropList = loadObjectsFromFile <FickProperties> (file, "ficks");
if (newPropList != null)
{
LinkedListExtensions.AppendRange <FickProperties> (propsList, newPropList);
}
}
_reactions = FickReaction.getFickReactionsFromMediumList(mediums);
finalizeFickReactionFromProps(propsList, _reactions);
Logger.Log("Fick::loadFicksReactionsFromFiles("
+ Logger.EnumerableToString <string> (files)
+ ") starts"
, Logger.Level.INFO);
}
/*!
* \brief Load all the properties from multiple files
* \param files All the files
* \return A list of all the properties
*/
public LinkedList <ActiveTransportProperties> getActiveTransportPropertiesFromFiles(IEnumerable <string> files)
{
Logger.Log("ActiveTransport::getActiveTransportPropertiesFromFiles("
+ Logger.EnumerableToString <string>(files)
+ ") starts"
, Logger.Level.DEBUG);
LinkedList <ActiveTransportProperties> propsList = new LinkedList <ActiveTransportProperties>();
LinkedList <ActiveTransportProperties> newPropList;
foreach (string file in files)
{
newPropList = loadObjectsFromFile <ActiveTransportProperties>(file, "activeTransports");
if (null != newPropList)
{
LinkedListExtensions.AppendRange <ActiveTransportProperties>(propsList, newPropList);
}
}
Logger.Log("ActiveTransport::getActiveTransportPropertiesFromFiles("
+ Logger.EnumerableToString <string>(files)
+ ") returns " + Logger.ToString <ActiveTransportProperties>(propsList)
, Logger.Level.DEBUG);
return(propsList);
}
private void updateDisplayedBioBricks()
{
Logger.Log("AvailableBioBricksManager::updateDisplayedBioBricks", Logger.Level.DEBUG);
LinkedList <BioBrick> availablePromoters = new LinkedList <BioBrick>();
LinkedListExtensions.AppendRange <BioBrick>(availablePromoters, getAvailableBioBricksOfType(BioBrick.Type.PROMOTER));
LinkedList <BioBrick> availableRBS = new LinkedList <BioBrick>();
LinkedListExtensions.AppendRange <BioBrick>(availableRBS, getAvailableBioBricksOfType(BioBrick.Type.RBS));
LinkedList <BioBrick> availableGenes = new LinkedList <BioBrick>();
LinkedListExtensions.AppendRange <BioBrick>(availableGenes, getAvailableBioBricksOfType(BioBrick.Type.GENE));
LinkedList <BioBrick> availableTerminators = new LinkedList <BioBrick>();
LinkedListExtensions.AppendRange <BioBrick>(availableTerminators, getAvailableBioBricksOfType(BioBrick.Type.TERMINATOR));
_displayableAvailablePromoters = getDisplayableAvailableBioBricks(
availablePromoters
, getDisplayableAvailableBioBrick
);
_displayableAvailableRBS = getDisplayableAvailableBioBricks(
availableRBS
, getDisplayableAvailableBioBrick
);
_displayableAvailableGenes = getDisplayableAvailableBioBricks(
availableGenes
, getDisplayableAvailableBioBrick
);
_displayableAvailableTerminators = getDisplayableAvailableBioBricks(
availableTerminators
, getDisplayableAvailableBioBrick
);
Logger.Log("AvailableBioBricksManager::updateDisplayedBioBricks"
+ "\n\navailablePromoters=" + Logger.ToString <BioBrick>(availablePromoters)
+ ",\n\navailableRBS=" + Logger.ToString <BioBrick>(availableRBS)
+ ",\n\navailableGenes=" + Logger.ToString <BioBrick>(availableGenes)
+ ",\n\navailableTerminators=" + Logger.ToString <BioBrick>(availableTerminators)
+ ",\n\n_displayableAvailablePromoters=" + Logger.ToString <AvailableDisplayedBioBrick>(_displayableAvailablePromoters)
+ ",\n\n_displayableAvailableRBS=" + Logger.ToString <AvailableDisplayedBioBrick>(_displayableAvailableRBS)
+ ",\n\n_displayableAvailableGenes=" + Logger.ToString <AvailableDisplayedBioBrick>(_displayableAvailableGenes)
+ ",\n\n_displayableAvailableTerminators=" + Logger.ToString <AvailableDisplayedBioBrick>(_displayableAvailableTerminators)
, Logger.Level.TRACE);
displayPromoters();
}
// Warning: inputFiles is an array of names of files inside 'biobrickFilesPathPrefix'
private void loadBioBricks(string[] inputFiles, LinkedList <BioBrick> destination)
{
Logger.Log("AvailableBioBricksManager::loadBioBricks", Logger.Level.INFO);
//load biobricks from xml
BioBrickLoader bLoader = new BioBrickLoader();
//_availableBioBricks = new LinkedList<BioBrick>();
string files = "";
foreach (string file in inputFiles)
{
string fullPath = biobrickFilesPathPrefix + file;
Logger.Log("AvailableBioBricksManager::loadBioBricks loads biobrick file " + fullPath, Logger.Level.DEBUG);
LinkedList <BioBrick> bb = bLoader.loadBioBricksFromFile(fullPath);
Logger.Log("AvailableBioBricksManager::loadBioBricks appended bb=" + bb.Count.ToString() + " from file " + fullPath, Logger.Level.DEBUG);
LinkedListExtensions.AppendRange <BioBrick>(destination, bb);
if (!string.IsNullOrEmpty(files))
{
files += ", ";
}
files += fullPath;
}
Logger.Log("AvailableBioBricksManager::loadBioBricks loaded " + files + " so that destination=" + destination.Count, Logger.Level.DEBUG);
}
//! This function is called at the initialisation of the simulation (like a Constructor)
void Awake()
{
_instance = this;
FileLoader fileLoader = new FileLoader();
_reactionsSets = new LinkedList <ReactionSet>();
_moleculesSets = new LinkedList <MoleculeSet>();
_mediums = new LinkedList <Medium>();
//TODO there is only one file in _moleculesFiles and in _reactionsFiles
foreach (string file in _reactionsFiles)
{
LinkedList <ReactionSet> lr = fileLoader.loadObjectsFromFile <ReactionSet>(file, "reactions");
if (null != lr)
{
LinkedListExtensions.AppendRange <ReactionSet>(_reactionsSets, lr);
}
}
foreach (string file in _moleculesFiles)
{
Logger.Log("ReactionEngine::Awake() loading molecules from file", Logger.Level.DEBUG);
LinkedList <MoleculeSet> lm = fileLoader.loadObjectsFromFile <MoleculeSet>(file, "molecules");
if (null != lm)
{
LinkedListExtensions.AppendRange <MoleculeSet>(_moleculesSets, lm);
}
Logger.Log("ReactionEngine::Awake() loading molecules from file done"
+ ": _moleculesSets=" + Logger.ToString <MoleculeSet>(_moleculesSets)
, Logger.Level.DEBUG);
}
foreach (string file in _mediumsFiles)
{
LinkedList <Medium> lmed = fileLoader.loadObjectsFromFile <Medium>(file, "Medium");
if (null != lmed)
{
LinkedListExtensions.AppendRange <Medium>(_mediums, lmed);
}
}
foreach (Medium medium in _mediums)
{
medium.Init(_reactionsSets, _moleculesSets);
medium.enableSequential(enableSequential);
medium.enableNoise(enableNoise);
medium.enableEnergy(enableEnergy);
medium.enableShufflingReactionOrder = enableShufflingReactionOrder;
}
Logger.Log("ReactionEngine::Awake() FickReactions starting", Logger.Level.INFO);
_fick = new Fick();
_fick.loadFicksReactionsFromFiles(_fickFiles, _mediums);
Logger.Log("ReactionEngine::Awake() activeTransport starting", Logger.Level.INFO);
_activeTransport = new ActiveTransport();
_activeTransport.loadActiveTransportReactionsFromFiles(_activeTransportFiles, _mediums);
Logger.Log("ReactionEngine::Awake() done", Logger.Level.INFO);
}
