|
public static getMediumFromId ( int id, LinkedList |
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| id | int | |
| list | LinkedList |
|
| return | Medium, | |
/*!
* \brief Adds an IReaction to a medium
* \param mediumId The medium ID.
* \param reaction The reaction to add.
*/
public void addReactionToMedium(int mediumId, IReaction reaction)
{
Logger.Log("ReactionEngine::addReactionToMedium(" + mediumId + ", " + reaction + ")", Logger.Level.INFO);
Medium med = ReactionEngine.getMediumFromId(mediumId, _mediums);
if (med == null)
{
Logger.Log("ReactionEngine::addReactionToMedium medium #" + mediumId + "not found", Logger.Level.WARN);
return;
}
/*TODO FIXME USEFULNESS?/////////////////////////////////////////////////////////////////////
* ReactionSet reactionsSet = null;
* string medName = med.getName()+"Reactions";
* foreach (ReactionSet rs in _reactionsSets) {
* if (rs.id == medName) reactionsSet = rs;
* }
* if (reactionsSet != null) {
* reactionsSet.reactions.AddLast(IReaction.copyReaction(reaction));
* } else {
* Logger.Log("ReactionEngine::addReactionToMedium reactionsSet == null", Logger.Level.WARN);
* }
* //////////////////////////////////////////////////////////////////////////////////////////*/
med.addReaction(IReaction.copyReaction(reaction));
}
void OnTriggerEnter(Collider collider)
{
Logger.Log("PhenoFickContact::OnTriggerEnter collider=" + collider, Logger.Level.DEBUG);
PhysicalMedium PMext = collider.gameObject.GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter collider.PMext == null", Logger.Level.TRACE);
return;
}
int colliderMediumIdExt = PMext.MediumId;
Medium colliderMediumExt = ReactionEngine.getMediumFromId(colliderMediumIdExt, _reactionEngine.getMediumList());
if (colliderMediumExt == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter The collided medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
PhysicalMedium PM = GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter this.PMext == null", Logger.Level.TRACE);
return;
}
int mediumId = PM.MediumId;
Medium medium = ReactionEngine.getMediumFromId(mediumId, _reactionEngine.getMediumList());
if (medium == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter The medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
float surface = Math.Min(PM.Size, PMext.Size);
Fick fick = _reactionEngine.getFick();
FickReaction reaction = Fick.getFickReactionFromIds(colliderMediumIdExt, mediumId, fick.getFickReactions());
if (reaction == null)
{
Logger.Log("PhenoFickContact::OnTriggerEnter This FickReaction does not exist.", Logger.Level.WARN);
return;
}
reaction.setSurface(surface);
// set medium as medium of collider
Logger.Log("colliderMediumIdExt : " + colliderMediumIdExt, Logger.Level.INFO);
configureExternalDisplays(colliderMediumIdExt);
_collidedMediumIds.AddLast(colliderMediumIdExt);
/*
* Logger.Log("PhenoFickContact::OnTriggerEnter"
+" reaction.setSurface("+surface+")"
+" _collidedMediumIds.Count="+_collidedMediumIds.Count
+" _collidedMediumIds.Last.Value="+_collidedMediumIds.Last.Value
* ,Logger.Level.);
*/
}
void Start()
{
_reactionEngine = ReactionEngine.get();
_graphWindow = gameObject.GetComponentInChildren <GraphWindow>();
if (setMedium(ReactionEngine.getMediumFromId(_mediumId, _reactionEngine.getMediumList())) == false)
{
Logger.Log("Failed to load medium curves", Logger.Level.ERROR);
}
}
/*!
* \brief remove a reaction from a medium
* \param mediumId The medium ID.
* \param name The reaction's name.
*/
public void removeReactionFromMediumByName(int mediumId, string name)
{
Medium med = ReactionEngine.getMediumFromId(mediumId, _mediums);
if (med == null)
{
return;
}
med.removeReactionByName(name);
}
private void initializeIfNecessary()
{
//???
//gameObject.SetActive(true);
_isAlive = true;
//LinkedList<Medium> mediums = ReactionEngine.get ().getMediumList();
_medium = ReactionEngine.getMediumFromId(1, ReactionEngine.get().getMediumList());
_maxMediumEnergy = _medium.getMaxEnergy();
_energy = _medium.getEnergy() / _maxMediumEnergy;
}
/*!
* \brief This method gets all molecular concentrations
* \sa Molecule
* \sa Molecule.getConcentration()
*/
public void initMolecules()
{
LinkedList <Medium> mediums = _reactionEngine.getMediumList();
_mediumRef = ReactionEngine.getMediumFromId(_mediumId, mediums);
if (_mediumRef != null && _molecules == null)
{
_molecules = _mediumRef.getMolecules();
}
}
/* !
* \brief Remove from the specified medium the reaction that has the same characteristics as the one given as parameter
* \param mediumId The Id of the medium to remove from.
* \param reaction The model of reaction to remove.
* \param checkNameAndMedium Whether the name and medium must be taken into account or not.
*/
public void removeReaction(int mediumId, IReaction reaction, bool checkNameAndMedium = false)
{
Medium med = ReactionEngine.getMediumFromId(mediumId, _mediums);
if (med == null)
{
Logger.Log("ReactionEngine::removeReaction could not find medium with id " + mediumId, Logger.Level.WARN);
return;
}
med.removeReaction(reaction, checkNameAndMedium);
}
/*!
* \brief Load a list of properties in order to convert it into a ActiveTransportReaction
* \param props The list of ActiveTransportProperties
* \param mediums The list of mediums
*/
public void loadActiveTransportReactionsFromProperties(LinkedList <ActiveTransportProperties> props, LinkedList <Medium> mediums)
{
ActiveTransportReaction reaction;
Medium med;
foreach (ActiveTransportProperties prop in props)
{
reaction = new ActiveTransportReaction();
reaction.setName(prop.name);
reaction.setSubstrate(prop.substrate);
reaction.setEnzyme(prop.enzyme);
reaction.setKcat(prop.Kcat);
reaction.setEffector(prop.effector);
reaction.setAlpha(prop.alpha);
reaction.setBeta(prop.beta);
reaction.setKm(prop.Km);
reaction.setKi(prop.Ki);
reaction.setEnergyCost(prop.energyCost);
foreach (Product p in prop.products)
{
reaction.addProduct(p);
}
med = ReactionEngine.getMediumFromId(prop.srcMediumId, mediums);
if (med == null)
{
Debug.Log("Cannot load Active Transport properties because the medium Id : " + prop.srcMediumId + " is unknown.");
break;
}
reaction.setSrcMedium(med);
med = ReactionEngine.getMediumFromId(prop.dstMediumId, mediums);
if (med == null)
{
Debug.Log("Cannot load Active Transport properties because the medium Id : " + prop.dstMediumId + " is unknown.");
break;
}
reaction.setDstMedium(med);
med = ReactionEngine.getMediumFromId(prop.mediumId, mediums);
if (med == null)
{
Debug.Log("Cannot load Active Transport properties because the medium Id : " + prop.mediumId + " is unknown.");
break;
}
reaction.setMedium(med);
med.addReaction(reaction);
}
}
public static IReaction buildFickReactionFromProps(FickProperties props, LinkedList <Medium> mediums)
{
FickReaction reaction = new FickReaction();
Medium med1 = ReactionEngine.getMediumFromId(props.MediumId1, mediums);
Medium med2 = ReactionEngine.getMediumFromId(props.MediumId2, mediums);
if (med1 == null || med2 == null)
{
Debug.Log("failed to build FickReaction from FickProperties beacause one or all the medium id don't exist");
return(null);
}
reaction.setSurface(props.surface);
reaction.setPermCoef(props.P);
reaction.setMedium1(med1);
reaction.setMedium2(med2);
reaction.setEnergyCost(props.energyCost);
return(reaction);
}
public void setMedium(int mediumId)
{
if (!safeLazyInit())
{
return;
}
_mediumId = mediumId;
Medium medium = ReactionEngine.getMediumFromId(_mediumId, _mediums);
if (medium == null)
{
Logger.Log("VectrosityPanel Can't find the given medium (" + _mediumId + ")", Logger.Level.ERROR);
return;
}
_molecules = medium.getMolecules();
if (_molecules == null)
{
Logger.Log("VectrosityPanel Can't find molecules in medium (" + _mediumId + ")", Logger.Level.ERROR);
return;
}
VectrosityPanelLine line;
foreach (Molecule m in _molecules)
{
line = _lines.Find(l => m.getName() == l.moleculeName);
if (null == line)
{
_lines.Add(new Line(width, height, infos, _mediumId, m.getName()));
}
}
drawLines(true);
lineCount = _lines.Count;
}
public void OnTriggerExit(Collider collider)
{
Logger.Log("PhenoFickContact::OnTriggerExit collider=" + collider, Logger.Level.DEBUG);
PhysicalMedium PMext = collider.gameObject.GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit collider.PMext == null", Logger.Level.TRACE);
return;
}
int colliderMediumIdExt = PMext.MediumId;
Medium colliderMediumExt = ReactionEngine.getMediumFromId(colliderMediumIdExt, _reactionEngine.getMediumList());
if (colliderMediumExt == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit The collided medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
PhysicalMedium PM = GetComponent <PhysicalMedium>();
if (PMext == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit this.PMext == null", Logger.Level.TRACE);
return;
}
int mediumId = PM.MediumId;
Medium medium = ReactionEngine.getMediumFromId(mediumId, _reactionEngine.getMediumList());
if (medium == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit The medium does not exist in the reaction Engine. Load it or change the MediumId number in the PhysicalMedium script.", Logger.Level.WARN);
return;
}
// un-set medium as medium of collider
_collidedMediumIds.Remove(colliderMediumIdExt);
//string nullLast = (null != _collidedMediumIds.Last)?_collidedMediumIds.Last.Value.ToString():"null";
/*
* Logger.Log("PhenoFickContact::OnTriggerExit"
+" _collidedMediumIds.Count="+_collidedMediumIds.Count
+" _collidedMediumIds.Last.Value="+nullLast
* ,Logger.Level.);
*/
//Logger.Log("PhenoFickContact::OnTriggerExit _collidedMediumIds.Last.Value="+nullLast, Logger.Level.);
if (null != _collidedMediumIds.Last)
{
// TODO consider the current medium as superposition of mediums the ids of which are _collidedMediumIds
configureExternalDisplays(_collidedMediumIds.Last.Value);
}
else
{
//not in any Fick contact anymore
configureExternalDisplays(_vectroPanelInitMediumId);
Fick fick = _reactionEngine.getFick();
FickReaction reaction = Fick.getFickReactionFromIds(colliderMediumIdExt, mediumId, fick.getFickReactions());
if (reaction == null)
{
Logger.Log("PhenoFickContact::OnTriggerExit This FickReaction does not exist.", Logger.Level.WARN);
}
reaction.setSurface(0);
}
}