protected override DNABit produceDNABit()
{
LinkedList <BioBrick> deviceBricks = new LinkedList <BioBrick>();
string[] bricks = new string[] { promoterName, rbsName, geneName, terminatorName };
foreach (string brickName in bricks)
{
BioBrick brick = AvailableBioBricksManager.get().getBioBrickFromAll(brickName);
if (brick != null)
{
deviceBricks.AddLast(brick);
}
else
{
Logger.Log("PickableDeviceRef4Bricks::produceDNABit failed to add brick with name " + brickName + "!", Logger.Level.WARN);
}
}
if (ExpressionModule.isBioBricksSequenceValid(deviceBricks))
{
ExpressionModule deviceModule = new ExpressionModule(deviceName, deviceBricks);
LinkedList <ExpressionModule> deviceModules = new LinkedList <ExpressionModule>();
deviceModules.AddLast(deviceModule);
Device result = Device.buildDevice(deviceName, deviceModules);
return(result);
}
else
{
Logger.Log("PickableDeviceRef4Bricks::produceDNABit failed to produce DNABit - BioBrick sequence is incorrect: list=" + Logger.ToString <BioBrick>(deviceBricks), Logger.Level.WARN);
return(null);
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// utilities
private Device getDeviceFromBricks(LinkedList <BioBrick> bricks)
{
Logger.Log("CraftZoneManager::getDeviceFromBricks(" + Logger.ToString <BioBrick>(bricks) + ")", Logger.Level.TRACE);
if (!ExpressionModule.isBioBricksSequenceValid(bricks))
{
Logger.Log("CraftZoneManager::getDeviceFromBricks invalid biobricks sequence", Logger.Level.TRACE);
return(null);
}
ExpressionModule module = new ExpressionModule("test", bricks);
LinkedList <ExpressionModule> modules = new LinkedList <ExpressionModule>();
modules.AddLast(module);
Device device = Device.buildDevice(modules);
if (device != null)
{
Logger.Log("CraftZoneManager::getDeviceFromBricks produced " + device, Logger.Level.TRACE);
}
else
{
Logger.Log("CraftZoneManager::getDeviceFromBricks device==null with bricks=" + Logger.ToString <BioBrick>(bricks)
, Logger.Level.WARN);
}
return(device);
}
private PromoterProperties getPromoterReaction(ExpressionModule em, int id)
{
Logger.Log("Device::getPromoterReaction(" + em.ToString() + ", " + id + ")", Logger.Level.TRACE);
PromoterProperties prom = new PromoterProperties();
prom.energyCost = _energyPerBasePair * em.getSize();
//promoter only
//prom.energyCost = _energyPerBasePair*em.getBioBricks().First.Value.getSize();
LinkedList <BioBrick> bricks = em.getBioBricks();
//TODO fix this: create good properties' name
prom.name = _internalName + id;
PromoterBrick p = bricks.First.Value as PromoterBrick;
prom.formula = p.getFormula();
prom.beta = p.getBeta();
bricks.RemoveFirst();
prom.products = getProductsFromBiobricks(bricks);
TerminatorBrick tb = bricks.First.Value as TerminatorBrick;
prom.terminatorFactor = tb.getTerminatorFactor();
bricks.RemoveFirst();
if (bricks.Count != 0)
{
Logger.Log("Device::getPromoterReaction Warning: bricks.Count =" + bricks.Count, Logger.Level.TRACE);
}
return(prom);
}
public ExpressionModule(ExpressionModule m)
{
_name = m._name;
_bioBricks = new LinkedList<BioBrick>();
foreach (BioBrick b in m.getBioBricks())
_bioBricks.AddLast(b);
}
protected override DNABit produceDNABit()
{
LinkedList<BioBrick> deviceBricks = new LinkedList<BioBrick>();
string[] bricks = new string[]{promoterName, rbsName, geneName, terminatorName};
foreach(string brickName in bricks)
{
BioBrick brick = AvailableBioBricksManager.get().getBioBrickFromAll(brickName);
if(brick != null) {
deviceBricks.AddLast(brick);
} else {
Logger.Log("PickableDeviceRef4Bricks::produceDNABit failed to add brick with name "+brickName+"!", Logger.Level.WARN);
}
}
if(ExpressionModule.isBioBricksSequenceValid(deviceBricks))
{
ExpressionModule deviceModule = new ExpressionModule(deviceName, deviceBricks);
LinkedList<ExpressionModule> deviceModules = new LinkedList<ExpressionModule>();
deviceModules.AddLast(deviceModule);
Device result = Device.buildDevice(deviceName, deviceModules);
return result;
} else {
Logger.Log("PickableDeviceRef4Bricks::produceDNABit failed to produce DNABit - BioBrick sequence is incorrect: list="+Logger.ToString<BioBrick>(deviceBricks), Logger.Level.WARN);
return null;
}
}
public static Device buildDevice(ExpressionModule em)
{
Logger.Log("Device::buildDevice(em) with em=" + em + ")", Logger.Level.INFO);
LinkedList <ExpressionModule> modules = new LinkedList <ExpressionModule>();
modules.AddLast(em);
return(buildDevice(em.getInternalName(), modules));
}
public static Device buildDevice(LinkedList <BioBrick> bricks)
{
Logger.Log("Device::buildDevice(bricks) with bricks=" + bricks, Logger.Level.INFO);
ExpressionModule em = new ExpressionModule(bricks);
return(buildDevice(em));
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick("PromY2", 75f, "[0.01,2]Y");
RBSBrick rbs = new RBSBrick("RBS3", 3.0f);
GeneBrick gene = new GeneBrick("MOV", "MOV");
TerminatorBrick term = new TerminatorBrick("T1", 1.0f);
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(new List<BioBrick>(){prom, rbs, gene, term});
ExpressionModule module = new ExpressionModule("expr", bricks);
return Device.buildDevice("DEV", new LinkedList<ExpressionModule>(new List<ExpressionModule>(){module}));
}
//copy constructor
public ExpressionModule(ExpressionModule m)
{
Logger.Log("ExpressionModule::ExpressionModule(" + m + ")", Logger.Level.DEBUG);
_name = m._name;
_bioBricks = new LinkedList <BioBrick>();
foreach (BioBrick b in m.getBioBricks())
{
_bioBricks.AddLast(b.copy());
}
}
public void ParseTest1()
{
ExpressionModule ex;
ex = new ExpressionModule("(50)");
Assert.AreEqual(ex.Parse(), 50);
ex = new ExpressionModule("(+50)");
Assert.AreEqual(ex.Parse(), 50);
ex = new ExpressionModule("(-50)");
Assert.AreEqual(ex.Parse(), -50);
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick(promoterName, promoterBeta, promoterFormula);
RBSBrick rbs = new RBSBrick(rbsName, rbsFactor);
GeneBrick gene = new GeneBrick(geneName, geneProteinName);
TerminatorBrick term = new TerminatorBrick(terminatorName, terminatorFactor);
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(new List<BioBrick>(){prom, rbs, gene, term});
ExpressionModule module = new ExpressionModule(expressionModuleName, bricks);
Device result = Device.buildDevice(deviceName, new LinkedList<ExpressionModule>(new List<ExpressionModule>(){module}));
return result;
}
public void ParseTest2()
{
ExpressionModule ex;
ex = new ExpressionModule("2+3");
Assert.AreEqual(ex.Parse(), 5);
ex = new ExpressionModule("3*3+3");
Assert.AreEqual(ex.Parse(), 12);
ex = new ExpressionModule("(2*2)+2");
Assert.AreEqual(ex.Parse(), 6);
ex = new ExpressionModule("(2+2)*2");
Assert.AreEqual(ex.Parse(), 8);
}
public void ParseTest3()
{
ExpressionModule ex;
ex = new ExpressionModule("2+-3");
Assert.AreEqual(ex.Parse(), -1);
ex = new ExpressionModule("3*3--3");
Assert.AreEqual(ex.Parse(), 12);
ex = new ExpressionModule("(2*-2)+2");
Assert.AreEqual(ex.Parse(), -2);
ex = new ExpressionModule("-(2+2)*2");
Assert.AreEqual(ex.Parse(), -8);
}
private void SolveButton_OnClick(object sender, RoutedEventArgs e)
{
ExpressionModule expr = new ExpressionModule(InputTextBox.Text);
try
{
AnswerText.Text = "Ответ: " + expr.Parse();
}
catch (Exception exception)
{
AnswerText.Text = String.Format("Ошибка {0}:\n{1}", exception.GetType(), exception.Message);
}
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick("PromY2", 75f, "[0.01,2]Y");
RBSBrick rbs = new RBSBrick("RBS3", 3.0f);
GeneBrick gene = new GeneBrick("MOV", "MOV");
TerminatorBrick term = new TerminatorBrick("T1", 1.0f);
LinkedList <BioBrick> bricks = new LinkedList <BioBrick>(new List <BioBrick>()
{
prom, rbs, gene, term
});
ExpressionModule module = new ExpressionModule("expr", bricks);
return(Device.buildDevice("DEV", new LinkedList <ExpressionModule>(new List <ExpressionModule>()
{
module
})));
}
public bool hasSameBricks(ExpressionModule module)
{
if (module._bioBricks.Count != _bioBricks.Count)
{
return(false);
}
IEnumerator <BioBrick> enumerator1 = module._bioBricks.GetEnumerator();
IEnumerator <BioBrick> enumerator2 = _bioBricks.GetEnumerator();
while (enumerator1.MoveNext() && enumerator2.MoveNext())
{
if (!enumerator1.Current.Equals(enumerator2.Current))
{
return(false);
}
}
return(true);
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick(promoterName, promoterBeta, promoterFormula);
RBSBrick rbs = new RBSBrick(rbsName, rbsFactor);
GeneBrick gene = new GeneBrick(geneName, geneProteinName);
TerminatorBrick term = new TerminatorBrick(terminatorName, terminatorFactor);
LinkedList <BioBrick> bricks = new LinkedList <BioBrick>(new List <BioBrick>()
{
prom, rbs, gene, term
});
ExpressionModule module = new ExpressionModule(expressionModuleName, bricks);
Device result = Device.buildDevice(deviceName, new LinkedList <ExpressionModule>(new List <ExpressionModule>()
{
module
}));
return(result);
}
public PromoterProprieties getPromoterReaction(ExpressionModule em, int id)
{
PromoterProprieties prom = new PromoterProprieties();
LinkedList<BioBrick> bricks = em.getBioBricks();
prom.name = _name + id;
PromoterBrick p = bricks.First.Value as PromoterBrick;
prom.formula = p.getFormula();
prom.beta = p.getBeta();
bricks.RemoveFirst();
prom.products = getProductsFromBiobricks(bricks);
TerminatorBrick tb = bricks.First.Value as TerminatorBrick;
prom.terminatorFactor = tb.getTerminatorFactor();
bricks.RemoveFirst();
prom.energyCost = getSize();
return prom;
}
private PromoterProperties getPromoterReaction(ExpressionModule em, int id)
{
Logger.Log("Device::getPromoterReaction("+em.ToString()+", "+id+")", Logger.Level.TRACE);
PromoterProperties prom = new PromoterProperties();
prom.energyCost = _energyPerBasePair*em.getSize();
//promoter only
//prom.energyCost = _energyPerBasePair*em.getBioBricks().First.Value.getSize();
LinkedList<BioBrick> bricks = em.getBioBricks();
//TODO fix this: create good properties' name
prom.name = _internalName + id;
PromoterBrick p = bricks.First.Value as PromoterBrick;
prom.formula = p.getFormula();
prom.beta = p.getBeta();
bricks.RemoveFirst();
prom.products = getProductsFromBiobricks(bricks);
TerminatorBrick tb = bricks.First.Value as TerminatorBrick;
prom.terminatorFactor = tb.getTerminatorFactor();
bricks.RemoveFirst();
if(bricks.Count != 0) {
Logger.Log("Device::getPromoterReaction Warning: bricks.Count ="+bricks.Count, Logger.Level.TRACE);
}
return prom;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// utilities
private Device getDeviceFromBricks(LinkedList<BioBrick> bricks){
Logger.Log("CraftZoneManager::getDeviceFromBricks("+Logger.ToString<BioBrick>(bricks)+")", Logger.Level.TRACE);
if(!ExpressionModule.isBioBricksSequenceValid(bricks))
{
Logger.Log("CraftZoneManager::getDeviceFromBricks invalid biobricks sequence", Logger.Level.TRACE);
return null;
}
ExpressionModule module = new ExpressionModule("test", bricks);
LinkedList<ExpressionModule> modules = new LinkedList<ExpressionModule>();
modules.AddLast(module);
Device device = Device.buildDevice(modules);
if(device != null)
{
Logger.Log("CraftZoneManager::getDeviceFromBricks produced "+device, Logger.Level.TRACE);
}
else
{
Logger.Log ("CraftZoneManager::getDeviceFromBricks device==null with bricks="+Logger.ToString<BioBrick>(bricks)
, Logger.Level.WARN);
}
return device;
}
//copy constructor
public ExpressionModule(ExpressionModule m)
{
Logger.Log("ExpressionModule::ExpressionModule("+m+")", Logger.Level.DEBUG);
_name = m._name;
_bioBricks = new LinkedList<BioBrick>();
foreach (BioBrick b in m.getBioBricks())
{
_bioBricks.AddLast(b.copy());
}
}
public static Device buildDevice(LinkedList<BioBrick> bricks)
{
Logger.Log("Device::buildDevice(bricks) with bricks="+bricks, Logger.Level.INFO);
ExpressionModule em = new ExpressionModule(bricks);
return buildDevice(em);
}
public bool hasSameBricks(ExpressionModule module) {
if(module._bioBricks.Count != _bioBricks.Count) {
return false;
}
IEnumerator<BioBrick> enumerator1 = module._bioBricks.GetEnumerator();
IEnumerator<BioBrick> enumerator2 = _bioBricks.GetEnumerator();
while(enumerator1.MoveNext() && enumerator2.MoveNext()) {
if(!enumerator1.Current.Equals(enumerator2.Current)) {
return false;
}
}
return true;
}
public static Device buildDevice(ExpressionModule em)
{
Logger.Log("Device::buildDevice(em) with em="+em+")", Logger.Level.INFO);
LinkedList<ExpressionModule> modules = new LinkedList<ExpressionModule>();
modules.AddLast(em);
return buildDevice(em.getInternalName(), modules);
}
private static bool checkModuleValidity(ExpressionModule module)
{
if (module == null)
return false;
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(module.getBioBricks());
if (bricks == null)
return false;
if (bricks.Count == 0 || bricks.First.Value == null)
return false;
if (checkPromoter(bricks.First.Value) == false)
return false;
bricks.RemoveFirst();
if (checkOperon(bricks) == false)
return false;
if (bricks.Count == 0 || bricks.First.Value != null || checkTerminator(bricks.First.Value) == false)
return false;
bricks.RemoveFirst();
if (bricks.Count != 0)
return false;
return true;
}
public LinkedList <Device> loadDevicesFromFile(string filePath)
{
Logger.Log("DeviceLoader::loadDevicesFromFile(" + filePath + ")", Logger.Level.INFO);
LinkedList <Device> resultDevices = new LinkedList <Device>();
XmlDocument xmlDoc = Tools.getXmlDocument(filePath);
XmlNodeList deviceList = xmlDoc.GetElementsByTagName(BioBricksXMLTags.DEVICE);
reinitVars();
foreach (XmlNode deviceNode in deviceList)
{
try
{
deviceName = deviceNode.Attributes[BioBricksXMLTags.ID].Value;
}
catch (NullReferenceException exc)
{
Logger.Log("DeviceLoader::loadDevicesFromFile bad xml, missing field \"id\"\n" + exc, Logger.Level.WARN);
continue;
}
catch (Exception exc)
{
Logger.Log("DeviceLoader::loadDevicesFromFile failed, got exc=" + exc, Logger.Level.WARN);
continue;
}
Logger.Log("DeviceLoader::loadDevicesFromFile got id=" + deviceName
, Logger.Level.TRACE);
bool processSuccess = true;
if (checkString(deviceName))
{
// processes longer grammars that use explicit brick nodes names
if (0 != deviceNode.ChildNodes.Count)
{
foreach (XmlNode attr in deviceNode)
{
if (attr.Name == BioBricksXMLTags.BIOBRICK)
{
//find brick in existing bricks
string brickName = attr.Attributes[BioBricksXMLTags.ID].Value;
if (!processBrick(brickName, filePath))
{
// processes even longer grammar that uses explicit brick description
// because the brick wasn't found neither in 'available' nor 'all' biobricks lists
brick = bLoader.loadBioBrick(attr);
if (null != brick)
{
AvailableBioBricksManager.get().addAvailableBioBrick(brick);
deviceBricks.AddLast(brick);
}
else
{
processSuccess = false;
break;
}
}
}
else
{
Logger.Log("DeviceLoader::loadDevicesFromFile unknown attr " + attr.Name, Logger.Level.WARN);
}
}
}
else
{
// processes shortened grammar that uses only device name
foreach (string brickName in deviceName.Split(':'))
{
if (!processBrick(brickName, filePath))
{
processSuccess = false;
break;
}
}
}
if (processSuccess)
{
ExpressionModule deviceModule = new ExpressionModule(deviceName, deviceBricks);
LinkedList <ExpressionModule> deviceModules = new LinkedList <ExpressionModule>();
deviceModules.AddLast(deviceModule);
device = Device.buildDevice(deviceName, deviceModules);
if (device != null)
{
resultDevices.AddLast(device);
}
}
}
else
{
Logger.Log("DeviceLoader::loadDevicesFromFile Error : missing attribute id in Device node", Logger.Level.WARN);
}
reinitVars();
}
return(resultDevices);
}
public LinkedList<Device> loadDevicesFromFile(string filePath)
{
Logger.Log("DeviceLoader::loadDevicesFromFile(" + filePath + ")", Logger.Level.INFO);
LinkedList<Device> resultDevices = new LinkedList<Device>();
XmlDocument xmlDoc = Tools.getXmlDocument(filePath);
XmlNodeList deviceList = xmlDoc.GetElementsByTagName(BioBricksXMLTags.DEVICE);
reinitVars();
foreach (XmlNode deviceNode in deviceList)
{
try
{
deviceName = deviceNode.Attributes[BioBricksXMLTags.ID].Value;
}
catch (NullReferenceException exc)
{
Logger.Log("DeviceLoader::loadDevicesFromFile bad xml, missing field \"id\"\n" + exc, Logger.Level.WARN);
continue;
}
catch (Exception exc)
{
Logger.Log("DeviceLoader::loadDevicesFromFile failed, got exc=" + exc, Logger.Level.WARN);
continue;
}
Logger.Log("DeviceLoader::loadDevicesFromFile got id=" + deviceName
, Logger.Level.TRACE);
bool processSuccess = true;
if (checkString(deviceName))
{
// processes longer grammars that use explicit brick nodes names
if (0 != deviceNode.ChildNodes.Count)
{
foreach (XmlNode attr in deviceNode)
{
if (attr.Name == BioBricksXMLTags.BIOBRICK)
{
//find brick in existing bricks
string brickName = attr.Attributes[BioBricksXMLTags.ID].Value;
if (!processBrick(brickName, filePath))
{
// processes even longer grammar that uses explicit brick description
// because the brick wasn't found neither in 'available' nor 'all' biobricks lists
brick = bLoader.loadBioBrick(attr);
if (null != brick)
{
AvailableBioBricksManager.get().addAvailableBioBrick(brick);
deviceBricks.AddLast(brick);
}
else
{
processSuccess = false;
break;
}
}
}
else
{
Logger.Log("DeviceLoader::loadDevicesFromFile unknown attr " + attr.Name, Logger.Level.WARN);
}
}
}
else
{
// processes shortened grammar that uses only device name
foreach (string brickName in deviceName.Split(':'))
{
if (!processBrick(brickName, filePath))
{
processSuccess = false;
break;
}
}
}
if (processSuccess)
{
ExpressionModule deviceModule = new ExpressionModule(deviceName, deviceBricks);
LinkedList<ExpressionModule> deviceModules = new LinkedList<ExpressionModule>();
deviceModules.AddLast(deviceModule);
device = Device.buildDevice(deviceName, deviceModules);
if (device != null)
{
resultDevices.AddLast(device);
}
}
}
else
{
Logger.Log("DeviceLoader::loadDevicesFromFile Error : missing attribute id in Device node", Logger.Level.WARN);
}
reinitVars();
}
return resultDevices;
}
