void Awake(){
if(Instance != null && Instance != this)
{
Destroy(gameObject);
}
Instance = this;
DontDestroyOnLoad(gameObject);
if(deleteProgressAtStart){
PlayerPrefs.DeleteAll();
//TODO neue levelSequence
}//else{
// load();
// }
player = GameObject.FindWithTag("Player");
// Debug.Log(player.transform.position.x);
playerDataPerScene = new Dictionary<string, PlayerData>();
currentScene = "Stadt";
load();
}
private void Update(){
if (globalVariables == null && !EditorApplication.isCompiling) {
globalVariables = GlobalVariables.Load();
if (globalVariables == null) {
if (!System.IO.Directory.Exists(Application.dataPath + "/ICode/Resources")) {
AssetDatabase.CreateFolder("Assets/ICode", "Resources");
}
globalVariables= AssetCreator.CreateAsset<GlobalVariables>("Assets/ICode/Resources/"+GlobalVariables.assetName+".asset");
EditorUtility.DisplayDialog("Created GlobalVariables!",
"Do not delete or rename the Resource folder and the GlobalVariables asset.", "Ok");
}
Array.Sort(globalVariables.Variables,(a, b) => a.Group.CompareTo(b.Group));
}
}
public virtual bool GlobalLocked(TDto dto)
{
return(!this.genericRepository.VersionValidate(GlobalVariables.ConfigID, GlobalVariables.ConfigVersionID(GlobalVariables.ConfigID)) || dto.EntryDate <= this.genericRepository.GetEditLockedDate(this.LocationID, this.nmvnTaskID));
}
public async Task <User> Add(PaymentNotification paymentNotification, IFormFile[] images)
{
var user = await _context.Users.Where(x => x.Email == paymentNotification.Email).FirstOrDefaultAsync();
if (user == null)
{
throw new AppException("User is not found");
}
if (images != null)
{
for (int i = 0; i < images.Length; i++)
{
if (images[i] != null && images[i].Length > 0)
{
var file = images[i];
if (file.Length > 0)
{
if (!file.ContentType.StartsWith("image"))
{
var fileLength = file.Length / 1024;
var maxFileLength = 5120;
if (fileLength > maxFileLength)
{
throw new AppException("Uploaded file must not be more than 5MB!");
}
}
}
}
}
}
if (images != null)
{
for (int i = 0; i < images.Length; i++)
{
Bitmap originalFile = null;
Bitmap resizedFile = null;
int imgWidth = 0;
int imgHeigth = 0;
if ((i == 0) && (images[i] != null) && (images[i].Length > 0))
{
var uploads = Path.GetFullPath(Path.Combine(GlobalVariables.ImagePath, @"images\payment"));
var file = images[i];
if (file.Length > 0)
{
var fileName = ContentDispositionHeaderValue.Parse(file.ContentDisposition).FileName.Trim();
string uniqueFileName = paymentNotification.FirstName.Substring(0, 5) + i + DateTime.Now + file.FileName;
string uniqueFileNameTrimmed = uniqueFileName.Replace(":", "").Replace("-", "").Replace(" ", "").Replace("/", "");
using (var fileStream = new FileStream(Path.Combine(uploads, uniqueFileNameTrimmed), FileMode.Create))
{
await file.CopyToAsync(fileStream);
paymentNotification.ImageNames = uniqueFileNameTrimmed;
if (file.ContentType.StartsWith("image"))
{
int width = 200;
int height = 200;
originalFile = new Bitmap(fileStream);
resizedFile = ResizeImage.GetResizedImage(fileStream, width, height, width, height);
}
}
if (resizedFile != null)
{
imgWidth = resizedFile.Width;
imgHeigth = resizedFile.Height;
using (var fileStreamUp = new FileStream(Path.Combine(uploads, uniqueFileNameTrimmed), FileMode.Create))
{
resizedFile.Save(fileStreamUp, ImageFormat.Jpeg);
}
}
}
}
}
}
DateTime paymentNotificationLocalDate_Nigeria = new DateTime();
string windowsTimeZone = GetWindowsFromOlson.GetWindowsFromOlsonFunc("Africa/Lagos");
paymentNotificationLocalDate_Nigeria = TimeZoneInfo.ConvertTime(DateTime.UtcNow, TimeZoneInfo.FindSystemTimeZoneById(windowsTimeZone));
paymentNotification.DateAdded = paymentNotificationLocalDate_Nigeria;
int length = GlobalVariables.RandomStringLengthShort();
var randomKey = "";
var keyIsAlreadyPresent = true;
do
{
randomKey = GlobalVariables.RandomString(length);
keyIsAlreadyPresent = _context.PaymentNotifications.Any(x => x.Reference == randomKey);
} while (keyIsAlreadyPresent);
paymentNotification.Reference = randomKey;
paymentNotification.Confirmed = "No";
paymentNotification.UpdateAllowed = true;
await _context.PaymentNotifications.AddAsync(paymentNotification);
if (paymentNotification.TransactionType == "Activation")
{
user.ActivationRequested = true;
_context.Users.Update(user);
}
await _context.SaveChangesAsync();
//ThreadPool.QueueUserWorkItem(o => {
string body = "Dear " + paymentNotification.FirstName + ",<br/><br/>Thank you for submitting your payment notification.<br/><br/>" +
"We will confirm your payment and update your online profile.<br/><br/>" +
"You will also receive an email from us as soon as we have confirmed your payment<br/><br/>" +
"Thanks,<br/>The RotatePay Team<br/>";
var message = new Message(new string[] { paymentNotification.Email }, "[RotatePay] Payment Notification Received", body, null);
_emailSenderService.SendEmail(message);
string body1 = paymentNotification.FirstName + "(" + paymentNotification.Email + ") has submitted the payment notification form.<br/><br/><br/>";
var message1 = new Message(new string[] { GlobalVariables.AdminEmail }, "[RotatePay] Payment receipt by " + paymentNotification.Email, body1, images);
_emailSenderService.SendEmail(message1);
//});
//await _logService.Create(log);
return(user);
}
public MasterMDI(GlobalEnums.NmvnTaskID nmvnTaskID, Form loadedView)
{
InitializeComponent();
try
{
this.nmvnTaskID = nmvnTaskID;
this.moduleAPIs = new ModuleAPIs(CommonNinject.Kernel.Get <IModuleAPIRepository>());
switch (this.nmvnTaskID)
{
case GlobalEnums.NmvnTaskID.SmartCoding:
this.buttonLoading.Visible = false;
this.buttonNew.Visible = false;
this.buttonEdit.Visible = false;
this.buttonSave.Visible = false;
this.buttonDelete.Visible = false;
this.buttonImport.Visible = false;
this.buttonExport.Visible = false;
this.toolStripSeparatorImport.Visible = false;
this.buttonApprove.Visible = false;
this.buttonVoid.Visible = false;
this.toolStripSeparatorApprove.Visible = false;
this.toolStripSeparatorVoid.Visible = false;
this.buttonPrint.Visible = false;
this.buttonPrintPreview.Visible = false;
this.toolStripSeparatorPrint.Visible = false;
this.toolStripTopHead.Visible = false;
break;
case GlobalEnums.NmvnTaskID.Batch:
this.Size = new Size(1388, 740);
this.FormBorderStyle = System.Windows.Forms.FormBorderStyle.FixedDialog;
this.MinimizeBox = false; this.MaximizeBox = false; this.WindowState = FormWindowState.Normal;
this.panelTopRight.Visible = false;
this.panelTopLeft.Dock = DockStyle.Fill;
break;
case GlobalEnums.NmvnTaskID.BatchMaster:
if (GlobalVariables.ConfigID != (int)GlobalVariables.FillingLine.BatchMaster)
{
this.Size = new Size(1388, 740);
this.FormBorderStyle = System.Windows.Forms.FormBorderStyle.FixedDialog;
this.MinimizeBox = false; this.MaximizeBox = false; this.WindowState = FormWindowState.Normal;
}
//this.panelTopRight.Visible = false;
//this.panelTopLeft.Dock = DockStyle.Fill;
break;
case GlobalEnums.NmvnTaskID.Commodity:
this.Size = new Size(1388, 740);
this.FormBorderStyle = System.Windows.Forms.FormBorderStyle.FixedDialog;
this.MinimizeBox = false; this.MaximizeBox = false; this.WindowState = FormWindowState.Normal;
this.panelTopRight.Visible = false;
this.panelTopLeft.Dock = DockStyle.Fill;
break;
default:
break;
}
this.beginingDateBinding = this.textFillterLowerDate.TextBox.DataBindings.Add("Text", GlobalEnums.GlobalOptionSetting, "LowerFillterDate", true);
this.endingDateBinding = this.textFillterUpperDate.TextBox.DataBindings.Add("Text", GlobalEnums.GlobalOptionSetting, "UpperFillterDate", true);
this.beginingDateBinding.BindingComplete += new BindingCompleteEventHandler(CommonControl_BindingComplete);
this.endingDateBinding.BindingComplete += new BindingCompleteEventHandler(CommonControl_BindingComplete);
this.buttonNaviBarHeaderVisibleBinding = this.buttonNaviBarHeader.DataBindings.Add("Visible", this.naviBarModuleMaster, "Collapsed", true, DataSourceUpdateMode.OnPropertyChanged);
this.buttonNaviBarHeaderVisibleBinding.Parse += new ConvertEventHandler(buttonNaviBarHeaderVisibleBinding_Parse);
this.buttonNaviBarHeaderVisibleBinding.Format += new ConvertEventHandler(buttonNaviBarHeaderVisibleBinding_Format);
this.listViewTaskMaster.Dock = DockStyle.Fill;
this.listViewTaskMaster.Columns.Add(new ColumnHeader()
{
Width = this.listViewTaskMaster.Width
});
if (loadedView != null)
{
this.naviBarModuleMaster.Visible = false;
this.OpenView(loadedView);
}
else
{
this.InitializeModuleMaster();
this.buttonNaviBarHeader_Click(this.buttonNaviBarHeader, new EventArgs());
}
DateTime buildDate = new FileInfo(Assembly.GetExecutingAssembly().Location).LastWriteTime;
this.statusVersion.Text = "Version 1.0." + GlobalVariables.ConfigVersionID(GlobalVariables.ConfigID).ToString() + ", Date: " + buildDate.ToString("dd/MM/yyyy HH:mm:ss");
this.comboSearchBarcode.Text = this.searchPlaceHolder;
this.toolUserReferences.Enabled = true; //ContextAttributes.User.IsDatabaseAdmin;
this.statusUserDescription.Text = ContextAttributes.User.FullyQualifiedUserName;
this.panelTop.Height = this.nmvnTaskID == GlobalEnums.NmvnTaskID.SmartCoding ? 61 : 39;
}
catch (Exception exception)
{
ExceptionHandlers.ShowExceptionMessageBox(this, exception);
}
}
// Use this for initialization
void Awake()
{
variables = this;
}
private bool VersionValidate()
{
try
{
foreach (GlobalVariables.FillingLine fillingLine in Enum.GetValues(typeof(GlobalVariables.FillingLine)))
{
this.baseRepository.ExecuteStoreCommand("UPDATE Configs SET VersionID = " + GlobalVariables.ConfigVersionID((int)fillingLine) + " WHERE ConfigID = " + (int)fillingLine + " AND VersionID < " + GlobalVariables.ConfigVersionID((int)fillingLine), new ObjectParameter[] { });
}
if (this.baseRepository.VersionValidate(GlobalVariables.ConfigID, GlobalVariables.ConfigVersionID(GlobalVariables.ConfigID)))
{
CommonConfigs.AddUpdateAppSetting("VersionID", GlobalVariables.ConfigVersionID(GlobalVariables.ConfigID).ToString());
}
return(true);
}
catch (Exception exception)
{
CommonConfigs.AddUpdateAppSetting("VersionID", "-9");
throw exception;
}
}
public static void Load(GlobalVariables globalVariables, string version)
{
if (globalVariables == null)
{
return;
}
if (string.IsNullOrEmpty(version))
{
BinaryDeserializationDeprecated.Load(globalVariables);
return;
}
globalVariables.Variables = null;
FieldSerializationData fieldSerializationData;
if (globalVariables.VariableData == null || (fieldSerializationData = globalVariables.VariableData.fieldSerializationData).byteData == null || fieldSerializationData.byteData.Count == 0)
{
return;
}
if (fieldSerializationData.typeName.Count > 0)
{
BinaryDeserializationDeprecated.Load(globalVariables);
return;
}
VariableSerializationData variableData = globalVariables.VariableData;
fieldSerializationData.byteDataArray = fieldSerializationData.byteData.ToArray();
BinaryDeserialization.updatedSerialization = (globalVariables.Version.CompareTo("1.5.7") >= 0);
if (BinaryDeserialization.updatedSerialization)
{
BinaryDeserialization.shaHashSerialization = (globalVariables.Version.CompareTo("1.5.9") >= 0);
}
if (variableData.variableStartIndex != null)
{
List <SharedVariable> list = new List <SharedVariable>();
Dictionary <int, int> dictionary = ObjectPool.Get <Dictionary <int, int> >();
for (int i = 0; i < variableData.variableStartIndex.Count; i++)
{
int num = variableData.variableStartIndex[i];
int num2;
if (i + 1 < variableData.variableStartIndex.Count)
{
num2 = variableData.variableStartIndex[i + 1];
}
else
{
num2 = fieldSerializationData.startIndex.Count;
}
dictionary.Clear();
for (int j = num; j < num2; j++)
{
dictionary.Add(fieldSerializationData.fieldNameHash[j], fieldSerializationData.startIndex[j]);
}
SharedVariable sharedVariable = BinaryDeserialization.BytesToSharedVariable(fieldSerializationData, dictionary, fieldSerializationData.byteDataArray, variableData.variableStartIndex[i], globalVariables, false, 0);
if (sharedVariable != null)
{
list.Add(sharedVariable);
}
}
ObjectPool.Return <Dictionary <int, int> >(dictionary);
globalVariables.Variables = list;
}
}
public static void TestUserModSelectionInPrunedDB()
{
List <(string, string)> listOfModsFixed = new List <(string, string)> {
("Common Fixed", "Carbamidomethyl of C"), ("Common Fixed", "Carbamidomethyl of U")
};
//Create Search Task
SearchTask task5 = new SearchTask
{
SearchParameters = new SearchParameters
{
WritePrunedDatabase = true,
SearchTarget = true,
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
},
CommonParameters = new CommonParameters(listOfModsFixed: listOfModsFixed)
};
task5.SearchParameters.ModsToWriteSelection["Mod"] = 0;
task5.SearchParameters.ModsToWriteSelection["Common Fixed"] = 1;
task5.SearchParameters.ModsToWriteSelection["Glycan"] = 2;
task5.SearchParameters.ModsToWriteSelection["missing"] = 3;
//add task 1 to task list
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("task5", task5)
};
ModificationMotif.TryGetMotif("P", out ModificationMotif motif);
ModificationMotif.TryGetMotif("E", out ModificationMotif motif2);
var connorMod = new Modification(_originalId: "ModToNotAppear", _modificationType: "Mod", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
var connorMod2 = new Modification(_originalId: "Default(Mod in DB and Observed)", _modificationType: "Common Fixed", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
var connorMod3 = new Modification(_originalId: "ModToAlwaysAppear", _modificationType: "Glycan", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
var connorMod4 = new Modification(_originalId: "ModObservedNotinDB", _modificationType: "missing", _target: motif2, _locationRestriction: "Anywhere.", _monoisotopicMass: 5);
GlobalVariables.AddMods(new List <Modification>
{
connorMod,
connorMod2,
connorMod3,
connorMod4
}, false);
//create modification lists
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => task5.CommonParameters.ListOfModsVariable.Contains
((b.ModificationType, b.IdWithMotif))).ToList();
List <Modification> fixedModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => task5.CommonParameters.ListOfModsFixed.Contains
((b.ModificationType, b.IdWithMotif))).ToList();
//add modification to Protein object
var dictHere = new Dictionary <int, List <Modification> >();
Modification modToAdd = connorMod;
Modification modToAdd2 = connorMod2;
Modification modToAdd3 = connorMod3;
Modification modToAdd4 = connorMod4;
//add Fixed modifcation so can test if mod that is observed and not in DB
fixedModifications.Add(connorMod4);
listOfModsFixed.Add((connorMod4.ModificationType, connorMod4.IdWithMotif));
dictHere.Add(1, new List <Modification> {
modToAdd
});
dictHere.Add(2, new List <Modification> {
modToAdd2
}); //default
dictHere.Add(3, new List <Modification> {
modToAdd3
}); //Alway Appear
var dictHere2 = new Dictionary <int, List <Modification> >
{
{ 1, new List <Modification> {
modToAdd
} },
{ 2, new List <Modification> {
modToAdd2
} }, //default
{ 3, new List <Modification> {
modToAdd3
} }, //Alway Appear
{ 4, new List <Modification> {
modToAdd4
} } //observed
};
//protein Creation (One with mod and one without)
Protein TestProteinWithModForDB = new Protein("PPPPPPPPPPE", "accession1", "organism", new List <Tuple <string, string> >(), dictHere);
Protein TestProteinWithModObsevred = new Protein("PPPPPPPPPPE", "accession1", "organism", new List <Tuple <string, string> >(), dictHere2);
//First Write XML Database
string xmlName = "selectedMods.xml";
string xmlName2 = "selectedModsObvs.xml";
//Add Mod to list and write XML input database
Dictionary <string, HashSet <Tuple <int, Modification> > > modList = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
var Hash = new HashSet <Tuple <int, Modification> >
{
new Tuple <int, Modification>(1, modToAdd),
new Tuple <int, Modification>(2, modToAdd2),
new Tuple <int, Modification>(3, modToAdd3),
new Tuple <int, Modification>(4, modToAdd4), //Observed Only
};
modList.Add("test", Hash);
ProteinDbWriter.WriteXmlDatabase(modList, new List <Protein> {
TestProteinWithModForDB
}, xmlName);
//Add Observed Only
modList.Add("test2", Hash);
ProteinDbWriter.WriteXmlDatabase(modList, new List <Protein> {
TestProteinWithModObsevred
}, xmlName2);
//now create MZML data
var protein = ProteinDbLoader.LoadProteinXML(xmlName2, true, DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> ok);
var digestedList = protein[0].Digest(task5.CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
//Set Peptide with 1 mod at position 3
PeptideWithSetModifications pepWithSetMods1 = digestedList[0];
PeptideWithSetModifications pepWithSetMods2 = digestedList[1];
PeptideWithSetModifications pepWithSetMods3 = digestedList[2];
PeptideWithSetModifications pepWithSetMods4 = digestedList[3];
PeptideWithSetModifications pepWithSetMods5 = digestedList[4];
//CUSTOM PEP
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
pepWithSetMods1, pepWithSetMods2, pepWithSetMods3, pepWithSetMods4, pepWithSetMods5
});
string mzmlName = @"newMzml.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
//make sure this runs correctly
//run!
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestUserModSelectionInPrunedDB");
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mzmlName
}, new List <DbForTask> {
new DbForTask(xmlName, false)
}, outputFolder);
engine.Run();
string final = Path.Combine(MySetUpClass.outputFolder, "task5", "selectedModspruned.xml");
var proteins = ProteinDbLoader.LoadProteinXML(final, true, DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out ok);
var Dlist = proteins[0].GetVariantProteins().SelectMany(vp => vp.Digest(task5.CommonParameters.DigestionParams, fixedModifications, variableModifications)).ToList();
Assert.AreEqual(Dlist[0].NumFixedMods, 1);
//check length
Assert.AreEqual(proteins[0].OneBasedPossibleLocalizedModifications.Count, 3);
List <Modification> listOfLocalMods = new List <Modification>();
listOfLocalMods.AddRange(proteins[0].OneBasedPossibleLocalizedModifications[2]);
listOfLocalMods.AddRange(proteins[0].OneBasedPossibleLocalizedModifications[3]);
listOfLocalMods.AddRange(proteins[0].OneBasedPossibleLocalizedModifications[11]);
//check Type, count, ID
Assert.AreEqual(listOfLocalMods[0].ModificationType, "Common Fixed");
Assert.AreEqual(listOfLocalMods[2].ModificationType, "missing");
Assert.IsFalse(listOfLocalMods.Contains(connorMod)); //make sure that mod set not to show up is not in mod list
Assert.AreEqual(listOfLocalMods[0].IdWithMotif, "Default(Mod in DB and Observed) on P");
Assert.AreEqual(listOfLocalMods[1].IdWithMotif, "ModToAlwaysAppear on P");
//Makes sure Mod that was not in the DB but was observed is in pruned DB
Assert.AreEqual(listOfLocalMods[2].IdWithMotif, "ModObservedNotinDB on E");
Assert.AreEqual(listOfLocalMods.Count, 3);
Directory.Delete(outputFolder, true);
File.Delete(mzmlName);
File.Delete(xmlName);
File.Delete(xmlName2);
}
public string GenerateTimePeriodCV(string startMonth, int?startYear, string endMonth, int?endYear)
{
string timePeriod = GlobalVariables.GenerateTimePeriodFormat(startMonth, startYear, endMonth, endYear);
return(!string.IsNullOrWhiteSpace(timePeriod) ? timePeriod.Substring(1, timePeriod.Length - 2) : timePeriod);
}
// Update is called once per frame
void Update()
{
GlobalVariables.getGameTime().addSeconds(Time.deltaTime);
}
public PointCloud AlignCloudsFromDirectory_StartFromLast(string directory, int numberOfCloudPairs)
{
GlobalVariables.ResetTime();
PointCloud pSource;
PointCloud pTarget = null;
string[] files = System.IO.Directory.GetFiles(directory, "*.obj");
string pathResult = directory + "\\result";
if (!System.IO.Directory.Exists(pathResult))
{
System.IO.Directory.CreateDirectory(pathResult);
}
int numberOfCloudsCurrent = 0;
int numberOfCloudsResult = -1;
int iteratorFile = -1;
for (int i = 0; i < 1000; i++)
{
numberOfCloudsCurrent++;
iteratorFile++;
if (numberOfCloudsCurrent == numberOfCloudPairs)
{
numberOfCloudsCurrent = 1;
numberOfCloudsResult++;
pTarget.ToObjFile(pathResult + "\\Result" + numberOfCloudsResult.ToString() + ".obj");
// iteratorFile--;
}
if (pTarget != null && iteratorFile == (files.Length - 2))
{
numberOfCloudsResult++;
pTarget.ToObjFile(pathResult + "\\Result" + numberOfCloudsResult.ToString() + ".obj");
return(pTarget);
}
//first iteration
if (numberOfCloudsCurrent == 1)
{
//pTarget = PointCloud.FromObjFile(files[iteratorFile]);
pTarget = PointCloud.FromObjFile(files[files.Length - iteratorFile - 1]);
}
//pSource = PointCloud.FromObjFile(files[iteratorFile + 1]);
pSource = PointCloud.FromObjFile(files[files.Length - iteratorFile - 2]);
//------------------
//ICP
Reset_RealData();
pTarget = PerformICP(pSource, pTarget);
System.Diagnostics.Debug.WriteLine("###### ICP for point cloud: " + pSource.Name + " - points added: " + PointsAdded.ToString());
// this.registrationMatrix = icp.Matrix;
// registrationMatrix.Save(GLSettings.Path + GLSettings.PathModels, "registrationMatrix.txt");
}
GlobalVariables.ShowLastTimeSpan("--> Time for ICP ");
return(pTarget);
}
public Visit(GlobalVariables.Visit.IVisit iVisit)
{
_iVisit = iVisit;
}
private static int Run(CommandLineSettings settings)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Welcome to MetaMorpheus");
Console.WriteLine(GlobalVariables.MetaMorpheusVersion);
}
int errorCode = 0;
try
{
settings.ValidateCommandLineSettings();
CommandLineSettings = settings;
}
catch (Exception e)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("MetaMorpheus encountered the following error:" + Environment.NewLine + e.Message);
}
errorCode = 2;
return(errorCode);
}
if (settings.GenerateDefaultTomls)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Generating default tomls at location: " + settings.OutputFolder);
}
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
return(errorCode);
}
// set up microvignette
if (settings.RunMicroVignette)
{
// set up the spectra file
settings.Spectra.Clear();
settings.Spectra.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallCalibratible_Yeast.mzML"));
// set up the database
settings.Databases.Clear();
settings.Databases.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallYeast.fasta"));
// set up the tasks (calibration, GPTMD, search)
settings.Tasks.Clear();
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "CalibrationTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "GptmdTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "SearchTask.toml"));
}
MetaMorpheusEngine.WarnHandler += WarnHandler;
MetaMorpheusEngine.OutProgressHandler += MyEngine_outProgressHandler;
MetaMorpheusEngine.StartingSingleEngineHander += MyEngine_startingSingleEngineHander;
MetaMorpheusEngine.FinishedSingleEngineHandler += MyEngine_finishedSingleEngineHandler;
MetaMorpheusTask.WarnHandler += WarnHandler;
MetaMorpheusTask.LogHandler += LogHandler;
MetaMorpheusTask.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
bool containsRawFiles = settings.Spectra.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(v => v == ".raw");
if (containsRawFiles && !GlobalVariables.GlobalSettings.UserHasAgreedToThermoRawFileReaderLicence)
{
// write the Thermo RawFileReader licence agreement
Console.WriteLine(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
Console.WriteLine("\nIn order to search Thermo .raw files, you must agree to the above terms. Do you agree to the above terms? y/n\n");
string res = Console.ReadLine().ToLowerInvariant();
if (res == "y")
{
var newGlobalSettings = new GlobalSettings
{
UserHasAgreedToThermoRawFileReaderLicence = true,
WriteExcelCompatibleTSVs = GlobalVariables.GlobalSettings.WriteExcelCompatibleTSVs
};
Toml.WriteFile <GlobalSettings>(newGlobalSettings, Path.Combine(GlobalVariables.DataDir, @"settings.toml"));
GlobalVariables.GlobalSettings = newGlobalSettings;
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting MetaMorpheus. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
errorCode = 3;
return(errorCode);
}
}
foreach (var db in settings.Databases)
{
if (!Path.GetExtension(db).Equals(".fasta"))
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(db).OfType <Modification>(), true);
// print any error messages reading the mods to the console
foreach (var error in GlobalVariables.ErrorsReadingMods)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(error);
}
}
GlobalVariables.ErrorsReadingMods.Clear();
}
}
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>();
var tasks = settings.Tasks.ToList();
for (int i = 0; i < tasks.Count; i++)
{
var filePath = tasks[i];
var toml = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (toml.Get <string>("TaskType"))
{
case "Search":
var searchTask = Toml.ReadFile <SearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "SearchTask", searchTask));
break;
case "Calibrate":
var calibrationTask = Toml.ReadFile <CalibrationTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "CalibrationTask", calibrationTask));
break;
case "Gptmd":
var GptmdTask = Toml.ReadFile <GptmdTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GptmdTask", GptmdTask));
break;
case "XLSearch":
var XlTask = Toml.ReadFile <XLSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "XLSearchTask", XlTask));
break;
case "GlycoSearch":
var GlycoTask = Toml.ReadFile <GlycoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GlycoSearchTask", GlycoTask));
break;
default:
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(toml.Get <string>("TaskType") + " is not a known task type! Skipping.");
}
break;
}
}
List <string> startingRawFilenameList = settings.Spectra.Select(b => Path.GetFullPath(b)).ToList();
List <DbForTask> startingXmlDbFilenameList = settings.Databases.Select(b => new DbForTask(Path.GetFullPath(b), IsContaminant(b))).ToList();
EverythingRunnerEngine a = new EverythingRunnerEngine(taskList, startingRawFilenameList, startingXmlDbFilenameList, settings.OutputFolder);
try
{
a.Run();
}
catch (Exception e)
{
while (e.InnerException != null)
{
e = e.InnerException;
}
var message = "Run failed, Exception: " + e.Message;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(message);
}
errorCode = 4;
}
return(errorCode);
}
public static void TestPrunedDatabase()
{
//Create Search Task
SearchTask task1 = new SearchTask
{
SearchParameters = new SearchParameters
{
WritePrunedDatabase = true,
SearchTarget = true,
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
ModsToWriteSelection = new Dictionary <string, int>
{
{ "ConnorModType", 1 }
}
},
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5))
};
//add task to task list
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>
{
("task1", task1)
};
ModificationMotif.TryGetMotif("P", out ModificationMotif motif);
var connorMod = new Modification(_originalId: "ConnorMod on P", _modificationType: "ConnorModType", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
GlobalVariables.AddMods(new List <Modification>
{
connorMod
}, false);
//create modification lists
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>()
.Where(b => task1.CommonParameters.ListOfModsVariable.Contains((b.ModificationType, b.IdWithMotif))).ToList();
//add modification to Protein object
var dictHere = new Dictionary <int, List <Modification> >();
Modification modToAdd = connorMod;
Modification modToAdd2 = connorMod;
dictHere.Add(1, new List <Modification> {
modToAdd
});
dictHere.Add(3, new List <Modification> {
modToAdd2
});
//protein Creation (One with mod and one without)
Protein TestProteinWithMod = new Protein("PEPTID", "accession1", "organism", new List <Tuple <string, string> >(), dictHere);
//First Write XML Database
string xmlName = "okkk.xml";
//Add Mod to list and write XML input database
Dictionary <string, HashSet <Tuple <int, Modification> > > modList = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
var Hash = new HashSet <Tuple <int, Modification> >
{
new Tuple <int, Modification>(3, modToAdd)
};
modList.Add("test", Hash);
ProteinDbWriter.WriteXmlDatabase(modList, new List <Protein> {
TestProteinWithMod
}, xmlName);
//now write MZML file
var protein = ProteinDbLoader.LoadProteinXML(xmlName, true,
DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> ok);
//Dictionary 'ok' contains unknown modifications. There are no unknown modifications in this test.
Assert.AreEqual(0, ok.Count);
//One protein is read from the .xml database and one decoy is created. Therefore, the list of proteins contains 2 entries.
Assert.AreEqual(2, protein.Count);
//The original database had two localized mods on the protein. Therefore. both protein and decoy should have two mods.
Assert.AreEqual(2, protein[0].OneBasedPossibleLocalizedModifications.Count);
List <int> foundResidueIndicies = protein[0].OneBasedPossibleLocalizedModifications.Select(k => k.Key).ToList();
List <int> expectedResidueIndices = new List <int>()
{
1, 3
};
Assert.That(foundResidueIndicies, Is.EquivalentTo(expectedResidueIndices));
Assert.AreEqual(2, protein[1].OneBasedPossibleLocalizedModifications.Count);
foundResidueIndicies = protein[1].OneBasedPossibleLocalizedModifications.Select(k => k.Key).ToList();
expectedResidueIndices = new List <int>()
{
4, 6
}; //originally modified residues are now at the end in the decoy
Assert.That(foundResidueIndicies, Is.EquivalentTo(expectedResidueIndices));
var thisOk = ok; //for debugging
var commonParamsAtThisPoint = task1.CommonParameters.DigestionParams; //for debugging
var digestedList = protein[0].Digest(task1.CommonParameters.DigestionParams, new List <Modification> {
},
variableModifications).ToList();
Assert.AreEqual(4, digestedList.Count);
//Set Peptide with 1 mod at position 3
PeptideWithSetModifications pepWithSetMods1 = digestedList[1];
//Finally Write MZML file
Assert.AreEqual("PEP[ConnorModType:ConnorMod on P]TID", pepWithSetMods1.FullSequence);//this might be base sequence
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetMods1
});
string mzmlName = @"hello.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
//run!
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPrunedDatabase");
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mzmlName
},
new List <DbForTask> {
new DbForTask(xmlName, false)
}, outputFolder);
engine.Run();
string final = Path.Combine(MySetUpClass.outputFolder, "task1", "okkkpruned.xml");
var proteins = ProteinDbLoader.LoadProteinXML(final, true, DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out ok);
//check length
Assert.AreEqual(1, proteins[0].OneBasedPossibleLocalizedModifications.Count);
//check location (key)
Assert.AreEqual(true, proteins[0].OneBasedPossibleLocalizedModifications.ContainsKey(3));
List <Modification> listOfMods = proteins[0].OneBasedPossibleLocalizedModifications[3];
//check Type, count, ID
Assert.AreEqual(listOfMods[0].ModificationType, "ConnorModType");
Assert.AreEqual(listOfMods[0].IdWithMotif, "ConnorMod on P");
Assert.AreEqual(listOfMods.Count, 1);
Directory.Delete(outputFolder, true);
File.Delete(xmlName);
File.Delete(mzmlName);
}
public GlobalVariablesWrapper(GlobalVariables globalVariables)
{
this.globalVariables = globalVariables;
}
private void LicenseTerms_Load(object sender, EventArgs e)
{
DateTime buildDate = new FileInfo(Assembly.GetExecutingAssembly().Location).LastWriteTime;
this.labelVersion.Text = "Version 1.0." + GlobalVariables.ConfigVersionID(GlobalVariables.ConfigID).ToString() + ", Date: " + buildDate.ToString("dd/MM/yyyy HH:mm:ss");
}
// Use this for initialization
void Start()
{
instance = this;
CurrentFallingSpeed = RegularFallingSpeed;
}
public ActionResult Login(string command, AppUserLoginInfo data)
{
if (ModelState.IsValid)
{
switch (command)
{
case "Log In":
try
{
string MD5_Password = mainDAL.CalculateMD5Hash(data.Password);
User _user = db.Users.Where(w => w.Username.ToLower() == data.Username.ToLower() && w.Password == MD5_Password && !w.IsDeleted).FirstOrDefault();
if (_user != null)
{
string IsAdmin = _user.UserRole.RoleName == GlobalVariables.AdminRoleName ? "True" : "False";
GlobalVariables.StoreInCookie("NYCUser", IPGlobalProperties.GetIPGlobalProperties().DomainName, "Username", _user.Username, DateTime.Now.AddDays(2), false);
GlobalVariables.StoreInCookie("NYCUser", IPGlobalProperties.GetIPGlobalProperties().DomainName, "IsLogged", "True", DateTime.Now.AddDays(2), false);
GlobalVariables.StoreInCookie("NYCUser", IPGlobalProperties.GetIPGlobalProperties().DomainName, "IsAdmin", IsAdmin, DateTime.Now.AddDays(2), false);
if (MD5_Password == mainDAL.CalculateMD5Hash(GlobalVariables.InitPassword))
{
return(RedirectToAction("ChangePassword"));
}
else
{
return(RedirectToAction("Index", "Home"));
}
}
else
{
TempData["ErrorMessage"] = "Your username or password is not correct";
return(View(data));
}
}
catch (Exception ex)
{
string message = ex.InnerException != null ? "Message: " + ex.Message + Environment.NewLine + "InnerException: " + ex.InnerException.Message : "Message: " + ex.Message;
mainDAL.RecordInLogger("ERROR", "Login", message, "", "");
return(View(data));
}
case "Sign Up":
try
{
if (db.Users.Any(w => w.Username.ToLower() == data.Username.ToLower()))
{
TempData["ErrorMessage"] = "This username is taken. Please choose other one";
return(View(data));
}
else
{
User _user = new User
{
Username = data.Username,
Password = mainDAL.CalculateMD5Hash(data.Password),
Role_ID = GlobalVariables.ViewerRoleID,
IsDeleted = false
};
db.Users.Add(_user);
db.SaveChanges();
TempData["InfoMessage"] = "You are registered successfully";
return(RedirectToAction("Login"));
}
}
catch (Exception ex)
{
string message = ex.InnerException != null ? "Message: " + ex.Message + Environment.NewLine + "InnerException: " + ex.InnerException.Message : "Message: " + ex.Message;
mainDAL.RecordInLogger("ERROR", "Sign Up", message, "", "");
TempData["ErrorMessage"] = "Some error happens and you are not registered successfully";
return(View(data));
}
}
}
return(View(data));
}
// Start is called before the first frame update
void Start()
{
gameManager = GameObject.Find("GameManager");
globalV = gameManager.GetComponent <GlobalVariables>();
}
private void checkInput()
{
if (!unitSelected)
{
// Check to see if the player made some input that we need to do something with
for (int i = 0; i < 6; i++)
{
if (unitSelected = Input.GetKeyDown(unitKeys[i]))
{
unitType = unitPrefabs[i];
if (isLeftSideBox)
{
GlobalVariables.leftSelectedUnit = i + 1;
}
else
{
GlobalVariables.rightSelectedUnit = i + 1;
}
break;
}
}
}
else if (unitSelected)
{
// Check all the selection keys to see if the player selected something
for (int i = 0; i < 6; i++)
{
if (Input.GetKeyDown(unitKeys[i]))
{
// If any unit is tried to be placed on any tile of the same side,
// go back to checking for a unit instead
unitSelected = false;
// De-highlight the unit summoned
if (isLeftSideBox)
{
GlobalVariables.leftSelectedUnit = -1;
}
else
{
GlobalVariables.rightSelectedUnit = -1;
}
// Only summon the unit corresponding to the key pressed and only if
// a unit is not summoned on that spot already
if (unitKeys[i] == selectionBoxKey && (currentUnit == null || currentUnit.GetComponent <Unit>().health <= 0))
{
// Check if we have the currency to buy the unit
// Check the left side if we are on it
if (isLeftSideBox)
{
if (!GlobalVariables.payLeftHoneyCount(1 + unitPrefabs.IndexOf(unitType)))
{
break;
}
}
// Otherwise check the right side
else
{
if (!GlobalVariables.payRightHoneyCount(1 + unitPrefabs.IndexOf(unitType)))
{
break;
}
}
// Summon the unit of the selected key
currentUnit = Instantiate(unitType, rigidbody2d.position, Quaternion.identity);
// If the unit is on the right, change it's direction
if (!isLeftSideBox)
{
currentUnit.GetComponent <Unit>().direction = -1;
}
// Hide the selection box since the unit was just summoned
unitAlive = true;
gameObject.GetComponent <Renderer>().enabled = false;
// Don't summon any more units
break;
}
}
}
}
}
private void BuildFile()
{
this.Enabled = false;
string uploadKey = tbUploadKey.txtbox.Text;
string time = nudInterval.Value.ToString();
string mutex = Random();
if (string.IsNullOrEmpty(uploadKey) || string.IsNullOrEmpty(time))
{
this.Enabled = true;
return;
}
tbBuildLog.Text += "> Upload Key: " + uploadKey + Environment.NewLine;
tbBuildLog.Text += "> Log Interval: " + time + Environment.NewLine;
tbBuildLog.Text += "> Mutex: " + mutex + Environment.NewLine;
bool installFile = cbInstallFile.Checked;
string processName = tbProcessName.txtbox.Text;
string folder = tbFolder.txtbox.Text;
string directory = cbDirectory.Text;
bool hkcu = cbHKCU.Checked;
bool hklm = cbHKLM.Checked;
string hkcuKey = tbHKCU.txtbox.Text;
string hklmKey = tbHKLM.txtbox.Text;
bool meltFile = cbMeltFile.Checked;
bool antis = cbAntis.Checked;
bool sendScreenshots = cbSendScreenshots.Checked;
bool hideFile = cbHideFile.Checked;
bool pinlogger = cbPinlogger.Checked;
bool stealers = cbStealers.Checked;
string title = tbTitle.txtbox.Text;
string description = tbDescription.txtbox.Text;
string product = tbProduct.txtbox.Text;
string copyright = tbCopyright.txtbox.Text;
string version = tbVersion.txtbox.Text;
string guid = tbGUID.txtbox.Text;
string iconPath = tbIconPath.txtbox.Text;
bool changeIcon = !string.IsNullOrEmpty(tbIconPath.txtbox.Text);
byte[] iconFile = null;
if (changeIcon)
{
iconFile = File.ReadAllBytes(iconPath);
}
using (PayloadWriter pw = new PayloadWriter())
{
pw.WriteByte(0x03);
pw.WriteString(uploadKey);
pw.WriteString(time);
pw.WriteString(mutex);
pw.WriteBool(installFile);
if (installFile)
{
pw.WriteString(processName);
pw.WriteString(folder);
pw.WriteString(directory);
}
pw.WriteBool(hkcu);
if (hkcu)
{
pw.WriteString(hkcuKey);
}
pw.WriteBool(hklm);
if (hklm)
{
pw.WriteString(hklmKey);
}
pw.WriteBool(meltFile);
pw.WriteBool(antis);
pw.WriteBool(sendScreenshots);
pw.WriteBool(hideFile);
pw.WriteBool(pinlogger);
pw.WriteBool(stealers);
pw.WriteString(title);
pw.WriteString(description);
pw.WriteString(product);
pw.WriteString(copyright);
pw.WriteString(version);
pw.WriteString(guid);
pw.WriteBool(changeIcon);
if (changeIcon)
{
pw.WriteInteger(iconFile.Length);
pw.WriteBytes(iconFile);
}
byte[] packet = pw.ToByteArray();
tbBuildLog.Text += "> Sending packet size: " + packet.Length + Environment.NewLine;
GlobalVariables.SendData(packet);
}
}
IEnumerator CUnpause()
{
yield return(new WaitForSecondsRealtime(1f));
GlobalVariables.UnpauseGame(GlobalVariables.PauseSource.UI);
}
private void Update()
{
RotateShip();
if (Input.GetKeyDown(KeyCode.LeftControl))
{
cursorVisible = !cursorVisible;
SetCursor();
}
float currentSpeed = shipSpeed;
if (Input.GetKey(KeyCode.LeftShift))
{
currentSpeed *= shipBoostMultiplier;
boosterEffect.Play();
rayCam.fieldOfView = Mathf.Lerp(rayCam.fieldOfView, boostFov, Time.deltaTime);
}
else
{
boosterEffect.Stop();
rayCam.fieldOfView = Mathf.Lerp(rayCam.fieldOfView, baseFOV, Time.deltaTime);
}
Vector3 dir = transform.TransformDirection(Vector3.forward);
float forwardMotion = Input.GetAxisRaw("Vertical");
//variables set when hyperspeeding
if (GlobalVariables.isHyperspeed)
{
forwardMotion = 1f;
currentSpeed = hyperdriveSpeed;
rayCam.fieldOfView = Mathf.Lerp(rayCam.fieldOfView, hyperdriveFov, Time.deltaTime);
}
currentSpeed *= forwardMotion;
GlobalVariables.playerSpeed = currentSpeed;
if (GlobalVariables.CurrentPlanet == null)
{
currentSpeed *= Time.deltaTime;
}
Vector3d posDelta = new Vector3d(dir) * currentSpeed;
if (GlobalVariables.CurrentPlanet == null)
{
GlobalVariables.AddPlayerWorldPos(posDelta);
}
else
{
Vector3 gravityUp = (transform.position - GlobalVariables.CurrentPlanet.transform.position).normalized;
rigidbody.velocity = (Vector3)posDelta;
if (rotationContrained)
{
Quaternion targetRot = Quaternion.FromToRotation(transform.up, gravityUp) * transform.rotation;
transform.rotation = Quaternion.Slerp(transform.rotation, targetRot, rotationSmoothness * Time.deltaTime);
float mouseY = Mathf.Abs(Input.GetAxis("Mouse Y"));
if (mouseY > 0.8f)
{
rotationContrained = false;
constraintThreshold = 0;
}
}
else
{
if (Vector3.Dot(transform.up, gravityUp) > 0.95)
{
constraintThreshold += Time.deltaTime;
}
else
{
constraintThreshold = 0;
}
if (constraintThreshold >= 2)
{
rotationContrained = true;
constraintThreshold = 0;
}
}
GlobalVariables.AddPlayerWorldPos(transform.position);
}
if (GlobalVariables.isHyperspeed)
{
if (hyperSpeedTarget.transform.position.magnitude < hyperSpeedTarget.AtmosphereLevel)
{
StopHyperSpeed();
}
}
cameraRay = new Ray(rayCam.transform.position, rayCam.transform.forward);
if (Physics.Raycast(cameraRay, out hit, rayDistance, planetLayer))
{
Planet planet = hit.transform.parent.GetComponent <Planet>();
UiHandler.instance.ShowPlanetPanel(planet);
if (Input.GetKeyDown(KeyCode.F) && GlobalVariables.CurrentPlanet == null)
{
if (!GlobalVariables.isHyperspeed)
{
GlobalVariables.isHyperspeed = true;
hyperSpeedTarget = planet;
hyperDriveEffect.Play();
CameraShake.instance.Shake(x, y, hyperdriveShakeMagnitude, hyperdriveSmoothness);
}
else
{
StopHyperSpeed();
}
}
}
else
{
UiHandler.instance.HidePlanetPanel();
}
}
/// <summary>
/// Initializes a new instance of the <see cref="IVR"/> class.
/// </summary>
/// <param name="client"><see cref="SwitchvoxClient"/> methods will use to communicate with the phone server.</param>
internal IVR(SwitchvoxClient client)
{
this.client = client;
GlobalVariables = new GlobalVariables(client);
}
/// <summary>
///
/// </summary>
/// <param name="e"></param>
/// <param name="ilg"></param>
/// <param name="scope"></param>
/// <param name="args"></param>
/// <exception cref="DynException"></exception>
public void EmitExpression(DynAstNodeExpression e, ILGenerator ilg, Dictionary <string, LocalBuilder> scope, Dictionary <string, int> args)
{
if (e.Operation is null)
{
EmitOperand(e.Left, ilg, scope, args);
return;
}
switch (e.Operation.Token)
{
case DynToken.SymbolEqual:
{
if (e.Left.Lexeme.Token != DynToken.Identifier)
{
throw new DynException($"语法错误，赋值操作只可作用于左值。");
}
// Right
EmitExpression(e.Right, ilg, scope, args);
if (GlobalVariables.Contains(e.Left.Lexeme.Identifier))
{
ilg.Emit(OpCodes.Stfld, e.Left.Lexeme.Identifier);
break;
}
if (!scope.ContainsKey(e.Left.Lexeme.Identifier))
{
LocalBuilder lbt = ilg.DeclareLocal(anyType);
scope.Add(e.Left.Lexeme.Identifier, lbt);
}
LocalBuilder lb = scope[e.Left.Lexeme.Identifier];
ilg.Emit(OpCodes.Stloc, lb.LocalIndex);
break;
}
case DynToken.SymbolPlus:
{
// Left
EmitOperand(e.Left, ilg, scope, args);
// Right
EmitExpression(e.Right, ilg, scope, args);
//ilg.Emit(OpCodes.Add);
ilg.Emit(OpCodes.Call, anyType.GetMethod("add_operator"));
break;
}
case DynToken.SymbolMinus:
{
// Left
EmitOperand(e.Left, ilg, scope, args);
// Right
EmitExpression(e.Right, ilg, scope, args);
ilg.Emit(OpCodes.Sub);
break;
}
case DynToken.SymbolStar:
{
// Left
EmitOperand(e.Left, ilg, scope, args);
// Right
EmitExpression(e.Right, ilg, scope, args);
ilg.Emit(OpCodes.Mul);
break;
}
default:
throw new DynException($"语法错误，未知的表达式 {e.Operation}");
}
}
private void btnSave_Click(object sender, EventArgs e)
{
SaveUsers();
GlobalVariables.Log("Użytkownik dodał nowego użytkownika");
}
public void Quit()
{
GlobalVariables.SoundButton();
Application.Quit();
}
private static int Run(CommandLineSettings settings)
{
int errorCode = 0;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Welcome to MetaMorpheus");
}
if (settings.CustomDataDirectory != null)
{
GlobalVariables.UserSpecifiedDataDir = settings.CustomDataDirectory;
}
GlobalVariables.SetUpGlobalVariables();
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(GlobalVariables.MetaMorpheusVersion);
}
try
{
settings.ValidateCommandLineSettings();
CommandLineSettings = settings;
}
catch (Exception e)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("MetaMorpheus encountered the following error:" + Environment.NewLine + e.Message);
}
errorCode = 2;
return(errorCode);
}
if (settings.GenerateDefaultTomls)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Generating default tomls at location: " + settings.OutputFolder);
}
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
return(errorCode);
}
// set up microvignette
if (settings.RunMicroVignette)
{
// set up the spectra file
settings.Spectra.Clear();
settings.Spectra.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallCalibratible_Yeast.mzML"));
// set up the database
settings.Databases.Clear();
settings.Databases.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallYeast.fasta"));
// set up the tasks (calibration, GPTMD, search)
settings.Tasks.Clear();
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "CalibrationTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "GptmdTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "SearchTask.toml"));
}
MetaMorpheusEngine.WarnHandler += WarnHandler;
MetaMorpheusEngine.OutProgressHandler += MyEngine_outProgressHandler;
MetaMorpheusEngine.StartingSingleEngineHander += MyEngine_startingSingleEngineHander;
MetaMorpheusEngine.FinishedSingleEngineHandler += MyEngine_finishedSingleEngineHandler;
MetaMorpheusTask.WarnHandler += WarnHandler;
MetaMorpheusTask.LogHandler += LogHandler;
MetaMorpheusTask.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
bool containsRawFiles = settings.Spectra.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(v => v == ".raw");
if (containsRawFiles && !GlobalVariables.GlobalSettings.UserHasAgreedToThermoRawFileReaderLicence)
{
// write the Thermo RawFileReader licence agreement
Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
Console.WriteLine("\nIn order to search Thermo .raw files, you must agree to the above terms. Do you agree to the above terms? y/n\n");
string res = Console.ReadLine().ToLowerInvariant();
if (res == "y")
{
var newGlobalSettings = new GlobalSettings
{
UserHasAgreedToThermoRawFileReaderLicence = true,
WriteExcelCompatibleTSVs = GlobalVariables.GlobalSettings.WriteExcelCompatibleTSVs
};
Toml.WriteFile <GlobalSettings>(newGlobalSettings, Path.Combine(GlobalVariables.DataDir, @"settings.toml"));
GlobalVariables.GlobalSettings = newGlobalSettings;
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting MetaMorpheus. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
errorCode = 3;
return(errorCode);
}
}
foreach (var db in settings.Databases)
{
if (!Path.GetExtension(db).Equals(".fasta"))
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(db).OfType <Modification>(), true);
// print any error messages reading the mods to the console
foreach (var error in GlobalVariables.ErrorsReadingMods)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(error);
}
}
GlobalVariables.ErrorsReadingMods.Clear();
}
}
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>();
var tasks = settings.Tasks.ToList();
for (int i = 0; i < tasks.Count; i++)
{
var filePath = tasks[i];
var toml = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (toml.Get <string>("TaskType"))
{
case "Search":
var searchTask = Toml.ReadFile <SearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "SearchTask", searchTask));
break;
case "Calibrate":
var calibrationTask = Toml.ReadFile <CalibrationTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "CalibrationTask", calibrationTask));
break;
case "Gptmd":
var GptmdTask = Toml.ReadFile <GptmdTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GptmdTask", GptmdTask));
break;
case "XLSearch":
var XlTask = Toml.ReadFile <XLSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "XLSearchTask", XlTask));
break;
case "GlycoSearch":
var GlycoTask = Toml.ReadFile <GlycoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GlycoSearchTask", GlycoTask));
break;
default:
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(toml.Get <string>("TaskType") + " is not a known task type! Skipping.");
}
break;
}
}
List <string> startingRawFilenameList = settings.Spectra.Select(b => Path.GetFullPath(b)).ToList();
List <DbForTask> startingXmlDbFilenameList = settings.Databases.Select(b => new DbForTask(Path.GetFullPath(b), IsContaminant(b))).ToList();
// check that experimental design is defined if normalization is enabled
var searchTasks = taskList
.Where(p => p.Item2.TaskType == MyTask.Search)
.Select(p => (SearchTask)p.Item2);
string pathToExperDesign = Directory.GetParent(startingRawFilenameList.First()).FullName;
pathToExperDesign = Path.Combine(pathToExperDesign, GlobalVariables.ExperimentalDesignFileName);
if (!File.Exists(pathToExperDesign))
{
if (searchTasks.Any(p => p.SearchParameters.Normalize))
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Experimental design file was missing! This must be defined to do normalization. Download a template from https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Experimental-Design");
}
return(5);
}
}
else
{
ExperimentalDesign.ReadExperimentalDesign(pathToExperDesign, startingRawFilenameList, out var errors);
if (errors.Any())
{
if (searchTasks.Any(p => p.SearchParameters.Normalize))
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
foreach (var error in errors)
{
Console.WriteLine(error);
}
}
return(5);
}
else
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("An experimental design file was found, but an error " +
"occurred reading it. Do you wish to continue with an empty experimental design? (This will delete your experimental design file) y/n" +
"\nThe error was: " + errors.First());
var result = Console.ReadLine();
if (result.ToLowerInvariant() == "y" || result.ToLowerInvariant() == "yes")
{
File.Delete(pathToExperDesign);
}
else
{
return(5);
}
}
else
{
// just continue on if verbosity is on "none"
File.Delete(pathToExperDesign);
}
}
}
else
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Read ExperimentalDesign.tsv successfully");
}
}
}
EverythingRunnerEngine a = new EverythingRunnerEngine(taskList, startingRawFilenameList, startingXmlDbFilenameList, settings.OutputFolder, settings.OrfCallingTables);
try
{
a.Run();
}
catch (Exception e)
{
while (e.InnerException != null)
{
e = e.InnerException;
}
var message = "Run failed, Exception: " + e.Message;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(message);
}
errorCode = 4;
}
return(errorCode);
}
private void Awake()
{
GV = GameObject.FindGameObjectWithTag("GameController").GetComponent <GlobalVariables>();
buy = GameObject.FindGameObjectWithTag("GameController").GetComponent <PurchaseHandler>();
btn = this.GetComponent <Button>();
}
public HealthSystem(Game1 myGame)
{
EntityManager = myGame.EntityManager;
GlobalVariables = myGame.globalVariables;
Subscribtions = new List <int>();
}
public void DeleteCareer(string id)
{
GlobalVariables.XmlData.Descendants("careers").Elements("career").Where(i => i.Element("id").Value.Equals(id)).Remove();
GlobalVariables.XmlData.Save(HttpContext.Current.Server.MapPath(GlobalVariables.XmlPath));
GlobalVariables.Update();
}
public int GenerateUserID()
{
return(GlobalVariables.GetMaxUserID() + 1);
// return Random.Range(0, 100);
}
public ActionResult ServiceChargeExpenditure(int PropID = 0, string PropName = "")
{
if (Session["CustomerID"] != null || (int)Session["CustomerID"] != 0)
{
Models.ServiceChargeBudgetViewModel mv = new Models.ServiceChargeBudgetViewModel();
if (PropID > 0)
{
Session["SelectedPropertyID"] = PropID;
Session["SelectedProperty"] = PropName;
Session["IsDirector"] = EstateDirectors.EstateDirectorMethods.IsCustomerDirector(GlobalVariables.GetConnection(), PropID).ToString();
}
if (Session["SelectedPropertyID"] == null || (int)Session["SelectedPropertyID"] == 0)
{
//Get Property List
mv.PropertyList = Models.PropertyMethods.GetAllOwnedProperties((int)Session["CustomerID"]);
mv.ViewName = "ServiceChargeExpenditure";
mv.ControllerName = "ServiceCharges";
}
else
{
mv.Estate = Models.EstateMethods.GetEstatedByUnitID((int)Session["SelectedPropertyID"]);
mv.Estate = Models.EstateMethods.GetServiceChargeExpenditure(mv.Estate);
}
return(View("ServiceChargeExpenditure", mv));
}
else
{
return(View("../Home/NotLoggedIn"));
}
}
public void Awake()
{
inst = this;
DontDestroyOnLoad(gameObject);
}
