private void AddTransitionRecord(ITransition transitionRecord)
{
TransitionRecord record = new TransitionRecord();
record.transition = transitionRecord;
record.time = Time.time;
record.gameObject = stateMachine.Component.gameObject;
record.stackTrace = new System.Diagnostics.StackTrace(true);
record.index = g_nextTransitionIndex;
g_nextTransitionIndex++;
transitionHistory.Add(record);
if (transitionHistory.Count > transitionHistorySize)
{
transitionHistory.RemoveAt(0);
}
// add to global history
g_transitionHistory.Add(record);
if (g_transitionHistory.Count > g_transitionHistorySize)
{
g_transitionHistory.RemoveAt(0);
}
}
private static Dictionary <string, List <TransitionRecord> > GetTransitions(string reportLocation)
{
var csv = new CsvReader(File.OpenText(reportLocation),
new CsvConfiguration {
CultureInfo = CultureInfo.InvariantCulture
});
// loops through each row as csv.CurrentRecord
var peptideTransitions = new Dictionary <string, List <TransitionRecord> >();
// creates dictionary from Skyline report of peptides -> precursors
while (csv.Read())
{
try
{
var proteinName = csv.GetField <string>(0);
var peptideModifiedSequence = csv.GetField <string>(1);
var isotopeLabelType = csv.GetField <string>(2);
var modifiedSequence = csv.GetField <string>(3);
// ReSharper disable InconsistentNaming
var TFExport_IntegrationStrategy = csv.GetField <string>(4);
var TFExport_WindowType = csv.GetField <string>(5);
var TFExport_WorkFlow = csv.GetField <string>(6);
// ReSharper restore InconsistentNaming
var precursorMz = csv.GetField <double>(7);
var productMz = csv.GetField <double>(8);
var productCharge = csv.GetField <int>(9);
var bestRetentionTime = csv.GetField <string>(10);
var fragmentIon = csv.GetField <string>(11);
var fragmentIonType = csv.GetField <string>(12);
var standardType = csv.GetField <string>(13);
var collisionEnergy = csv.GetField <string>(14);
var retentionTime = csv.GetField <string>(15);
var fileName = csv.GetField <string>(16);
var area = csv.GetField <string>(17);
var precursorCharge = csv.GetField <int>(18);
double.TryParse(area, out var areaInt);
var record = new TransitionRecord(proteinName, peptideModifiedSequence, isotopeLabelType,
modifiedSequence,
TFExport_IntegrationStrategy, TFExport_WindowType, TFExport_WorkFlow, precursorMz, productMz,
productCharge,
bestRetentionTime, fragmentIon, fragmentIonType, standardType,
collisionEnergy, fileName, retentionTime, areaInt, precursorCharge);
var key = record.ProteinName + "-" + record.PeptideModifiedSequence;
if (!peptideTransitions.ContainsKey(key))
{
peptideTransitions.Add(key, new List <TransitionRecord>());
}
peptideTransitions[key].Add(record);
}
catch (Exception)
{
throw new IOException("There was an issue processing the Skyline report. Ensure that the tool is using the TFExport report in Skyline.");
}
}
return(peptideTransitions);
}
private static string GetKey(TransitionRecord tr)
{
var key = tr.ModifiedSequence + KEY_SEP +
tr.PrecursorMz.ToString(CultureInfo.InstalledUICulture) + KEY_SEP +
tr.FragmentIon + KEY_SEP +
tr.IsotopeLabelType + KEY_SEP +
tr.ProductMz.ToString(CultureInfo.InvariantCulture);
return(key);
}
/// <param name="transition"></param>
/// <param name="lNum">レイヤー番号</param>
/// <param name="smNum">ステートマシン番号</param>
/// <param name="sNum">ステート番号</param>
/// <param name="tNum">トランジション番号</param>
/// <returns></returns>
public override bool OnTransition(AnimatorStateTransition transition, int lNum, int smNum, int sNum, int tNum)
{
TransitionRecord transitionRecord = new TransitionRecord(
lNum,
smNum,
sNum,
tNum,
transition, "");
AconDocument.transitions.Add(transitionRecord); return(true);
}
private string GetTransitionKey(TransitionRecord transitionRecord)
{
return("@" + transitionRecord.SourceActivityRecord.Id + "_" + transitionRecord.SourceEndpoint);
}
private static void WriteToCsv(string saveLocation, Dictionary <string, List <TransitionRecord> > peptideTransitions)
{
int startRow = 6;
int rowCount = 0;
foreach (var peptide in peptideTransitions.Values)
{
rowCount += peptide.Count;
}
// Auto Fill Transition Workflow information
AutoFillTransitions(peptideTransitions);
// Validate rows : No longer used
// Ensure necessary data exists to export a TF formatted file
// ValidateTransitions(peptideTransitions);
const string emptyLine = ",,,,,,,,,,,,,,,,,,,,,,,,";
var csvLines = new List <string>
{
"TraceFinder Compound Database Mass List Export,,,,,,,,,,,,,,,,,,,,,,,,",
emptyLine,
"Schema Version,Peak Header Line Number,Peak Last Row Line Number,Compound Header Line Number,,,,,,,,,,,,,,,,,,,,,",
string.Format("1,{0},{1},{2},,,,,,,,,,,,,,,,,,,,,", startRow, rowCount + startRow, rowCount + startRow + 2),
",,,,,,,,,,,,,,,,,,,,,,,,",
"Protein Name,Compound Name,Workflow,Associated Target Peak,MS Order,Precursor m/z,Product m/z,m/z,Height Threshold,Area Threshold,Collision Energy,Modification,Lens,Energy Ramp,Ion Coelution,Ratio Window,Target Ratio,Window Type,Ion Type,PeakPolarity,Adduct,Charge State,Retention Time,Retention Time Window,Integration Strategy"
}; // each object is a line that will be outputted when the result csv file is saved
// Header row/version info
// line1
// line2
// line3
// line4
// line5
// First section column headers
// line6 - column headers
// First section data rows
Dictionary <string, List <TransitionRecord> > peptideAnalytes = new Dictionary <string, List <TransitionRecord> >();
foreach (var pt in peptideTransitions)
{
var transitions = pt.Value;
foreach (var transitionRecord in transitions)
{
var newKey = pt.Key + transitionRecord.IsotopeLabelType;
if (!peptideAnalytes.ContainsKey(newKey))
{
peptideAnalytes.Add(newKey, new List <TransitionRecord>());
}
peptideAnalytes[newKey].Add(transitionRecord);
}
}
foreach (var transitions in peptideAnalytes.Values)
{
// find transition with highest product mz, this will be the target peak
TransitionRecord highestTransitionMz = null;
var highestTransitionIndex = 0;
for (var i = 0; i < transitions.Count; i++)
{
TransitionRecord transition = transitions[i];
if (highestTransitionMz == null && transition.TFExport_WorkFlow.Equals(TARGET_PEAK))
{
highestTransitionMz = transition;
highestTransitionIndex = i + 1; // index starts at 1 instead of 0
}
if (highestTransitionMz != null && transition.ProductMz > highestTransitionMz.ProductMz &&
transition.TFExport_WorkFlow.Equals(TARGET_PEAK))
{
highestTransitionIndex = i + 1; // index starts at 1 instead of 0
highestTransitionMz = transition;
}
}
foreach (TransitionRecord transition in transitions)
{
var proteinName = transition.ProteinName;
var compoundName = transition.PeptideModifiedSequence;
if (transition.IsotopeLabelType.Equals("heavy"))
{
if (_internalStandardType == InternalStandardType.heavy)
{
compoundName += "[heavyIS]";
}
else if (_internalStandardType == InternalStandardType.none)
{
compoundName += "[heavy]";
}
}
else if (transition.IsotopeLabelType.Equals("light"))
{
if (_internalStandardType == InternalStandardType.light)
{
compoundName += "[lightIS]";
}
else if (_internalStandardType == InternalStandardType.none)
{
compoundName += "[light]";
}
}
var workflow = transition.TFExport_WorkFlow;
var associatedTargetPeak = string.Empty;
var msOrder = "ms2";
if (transition.FragmentIonType.Equals("precursor"))
{
msOrder = "ms1";
}
var precursorMz = transition.PrecursorMz;
var productMz = transition.ProductMz.ToString(CultureInfo.InvariantCulture);
if (msOrder.Equals("ms1"))
{
productMz = string.Empty;
}
var mz = transition.PrecursorMz;
var heightThreshold = string.Empty;
var areaThreshold = string.Empty;
var collisionEnergy = transition.CollisionEnergy;
var modification = transition.IsotopeLabelType;
var lens = 0;
var energyRamp = 0;
var ionCoelution = string.Empty;
var ratioWindow = string.Empty;
var targetRatio = string.Empty;
var windowType = transition.TFExport_WindowType;
var ionType = transition.FragmentIon;
var peakPolarity = string.Empty;
var adduct = string.Empty;
if (transition.TFExport_WorkFlow.Equals(CONFIRMING) ||
transition.TFExport_WorkFlow.Equals(FRAGMENT))
{
associatedTargetPeak = highestTransitionIndex.ToString();
}
if (transition.ProductCharge > 0) // should never never be 0 or less
{
peakPolarity = "Positive";
adduct = "M+";
}
var chargeState = transition.ProductCharge;
if (chargeState < 0) // should never happen
{
chargeState = 0;
}
var retentionTime = transition.RetentionTime;
if (_useAvgRt)
{
retentionTime = transition.BestRetentionTime;
}
if (retentionTime.Equals("#N/A"))
{
retentionTime = string.Empty;
}
var retentionTimeWindow = _rtWindow;
var integrationStrategy = transition.TFExport_IntegrationStrategy;
csvLines.Add(string.Format(CultureInfo.InvariantCulture, "{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11},{12},{13},{14},{15},{16},{17}," +
"{18},{19},{20},{21},{22},{23},{24}",
proteinName, compoundName, workflow, associatedTargetPeak, msOrder, precursorMz, productMz, mz, heightThreshold,
areaThreshold, collisionEnergy, modification, lens, energyRamp, ionCoelution, ratioWindow, targetRatio, windowType, ionType,
peakPolarity, adduct, chargeState, retentionTime, retentionTimeWindow, integrationStrategy));
}
}
csvLines.Add(emptyLine); // add empty line to break for second section
// Second section column headers
csvLines.Add("Protein Name,Compound Name,Peptide Sequence,Cas Number,Category,Compound Type,Internal Standard Concentration,ISTD Protein Name,ISTD Compound Name,Ionization Field,Compound Group,,,,,,,,,,,,,,");
// Second section data rows
foreach (var transitions in peptideTransitions.Values)
{
transitions.Sort((a, b) => a.PrecursorMz.CompareTo(b.PrecursorMz));
bool heavyUsed = false;
bool lightUsed = false;
foreach (TransitionRecord transition in transitions)
{
if (!heavyUsed && transition.IsotopeLabelType.Equals("heavy"))
{
heavyUsed = true;
var proteinName = transition.ProteinName;
var compoundName = transition.PeptideModifiedSequence;
if (_internalStandardType == InternalStandardType.heavy)
{
compoundName += "[heavyIS]";
}
else
{
compoundName += "[heavy]";
}
var peptideSequence = transition.PeptideModifiedSequence;
var casNumber = string.Empty;
var category = string.Empty;
var compoundType = string.Empty;
var internalStandardConcentration = string.Empty;
var iStdProteinName = string.Empty;
var iStdCompoundName = string.Empty;
var ionizationField = "None";
var compoundGroup = string.Empty;
csvLines.Add(
string.Format(CultureInfo.InvariantCulture,
"{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},,,,,,,,,,,,,,", proteinName, compoundName,
peptideSequence, casNumber, category, compoundType, internalStandardConcentration, iStdProteinName,
iStdCompoundName, ionizationField, compoundGroup));
}
if (!lightUsed && transition.IsotopeLabelType.Equals("light"))
{
lightUsed = true;
var proteinName = transition.ProteinName;
var compoundName = transition.PeptideModifiedSequence;
if (_internalStandardType == InternalStandardType.light)
{
compoundName += "[lightIS]";
}
else
{
compoundName += "[light]";
}
var peptideSequence = transition.PeptideModifiedSequence;
var casNumber = string.Empty;
var category = string.Empty;
var compoundType = string.Empty;
var internalStandardConcentration = string.Empty;
var iStdProteinName = string.Empty;
var iStdCompoundName = string.Empty;
var ionizationField = "None";
var compoundGroup = string.Empty;
csvLines.Add(
string.Format(CultureInfo.InvariantCulture,
"{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},,,,,,,,,,,,,,", proteinName, compoundName,
peptideSequence, casNumber, category, compoundType, internalStandardConcentration, iStdProteinName,
iStdCompoundName, ionizationField, compoundGroup));
}
}
}
using (var outfile = new StreamWriter(saveLocation))
{
foreach (var line in csvLines)
{
outfile.WriteLine(line);
}
}
}
public void CreateSendEmailToFollowersWorkflow()
{
WorkflowDefinitionRecord workflow = new WorkflowDefinitionRecord {
Name = this.SendEmailToFollowersTicket, Enabled = true
};
this.workflowDefinitionRepository.Create(workflow);
var emailTemplate = this.emailTemplatesRepository.Table.FirstOrDefault(c => c.TypeId == (int)EmailTemplateType.FollowersNotification);
if (emailTemplate == null)
{
throw new NullReferenceException();
}
ActivityRecord itemPublishRecord = new ActivityRecord
{
WorkflowDefinitionRecord = workflow,
Start = true,
X = 552,
Y = 227,
State = "{}",
Name = NewActivityStreamActivity.ActivityStreamActivityName
};
this.activityRepository.Create(itemPublishRecord);
ActivityRecord timerActivity = new ActivityRecord
{
WorkflowDefinitionRecord = workflow,
Start = false,
X = 552,
Y = 388,
State = "{\"Amount\":\"1\",\"Unity\":\"Minute\"}",
Name = OrchardCollaborationTimerActivity.ActionName
};
this.activityRepository.Create(timerActivity);
ActivityRecord sendEmailActivityRecord = new ActivityRecord
{
State = string.Format(
CultureInfo.InvariantCulture,
"{{\"{0}\":\"{1}\"}}",
EmailTemplateActivityForm.EmailTemplateIdFieldName,
emailTemplate.Id.ToString(CultureInfo.InvariantCulture)),
Name = "SendEmailToFollowersActivity",
WorkflowDefinitionRecord = workflow,
X = 494,
Y = 588,
Start = false
};
this.activityRepository.Create(sendEmailActivityRecord);
TransitionRecord timerTransitionRecord = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = timerActivity,
SourceActivityRecord = itemPublishRecord,
DestinationEndpoint = "",
SourceEndpoint = "Done"
};
this.transitionRepository.Create(timerTransitionRecord);
TransitionRecord sendEmailTransitionRecord = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = sendEmailActivityRecord,
SourceActivityRecord = timerActivity,
DestinationEndpoint = "",
SourceEndpoint = "Done"
};
this.transitionRepository.Create(sendEmailTransitionRecord);
this.workflowDefinitionRepository.Flush();
this.activityRepository.Flush();
this.transitionRepository.Flush();
}
private void CreateCRMCommentWorkflow()
{
WorkflowDefinitionRecord workflow = new WorkflowDefinitionRecord {
Name = this.CreateTicketCommentsWorkflowName, Enabled = true
};
this.workflowDefinitionRepository.Create(workflow);
var emailTemplate = this.emailTemplatesRepository.Table.FirstOrDefault(c => c.TypeId == (int)EmailTemplateType.NewMessage);
if (emailTemplate == null)
{
throw new NullReferenceException();
}
ActivityRecord crmCommentPublishRecord = new ActivityRecord
{
WorkflowDefinitionRecord = workflow,
Start = true,
X = 552,
Y = 227,
State = "{\"ContentTypes\":\"CRMComment\"}",
Name = "ContentPublished"
};
this.activityRepository.Create(crmCommentPublishRecord);
ActivityRecord timerActivity = new ActivityRecord
{
WorkflowDefinitionRecord = workflow,
Start = false,
X = 552,
Y = 388,
State = "{\"Amount\":\"1\",\"Unity\":\"Minute\"}",
Name = OrchardCollaborationTimerActivity.ActionName
};
this.activityRepository.Create(timerActivity);
ActivityRecord sendEmailCRMCommentActivity = new ActivityRecord
{
State = string.Format(
CultureInfo.InvariantCulture,
"{{\"{0}\":\"{1}\",\"{2}\":\"true\",\"{3}\":\"true\"}}",
EmailTemplateActivityForm.EmailTemplateIdFieldName,
emailTemplate.Id.ToString(CultureInfo.InvariantCulture),
EmailTemplateActivityForm.SentToRequestingUserFieldName,
EmailTemplateActivityForm.SentToOwnerFieldName
),
Name = "SendTicketEmailActivity",
WorkflowDefinitionRecord = workflow,
X = 494,
Y = 588,
Start = false
};
this.activityRepository.Create(sendEmailCRMCommentActivity);
TransitionRecord timerTransitionRecord = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = timerActivity,
SourceActivityRecord = crmCommentPublishRecord,
DestinationEndpoint = "",
SourceEndpoint = "Done"
};
this.transitionRepository.Create(timerTransitionRecord);
TransitionRecord sendEmailCRMCommentTransitionRecord = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = sendEmailCRMCommentActivity,
SourceActivityRecord = timerActivity,
DestinationEndpoint = "",
SourceEndpoint = "Done"
};
this.transitionRepository.Create(sendEmailCRMCommentTransitionRecord);
this.workflowDefinitionRepository.Flush();
this.activityRepository.Flush();
this.transitionRepository.Flush();
}
private void CreateTicketForReceivedEmailsWorkflow()
{
WorkflowDefinitionRecord workflow = new WorkflowDefinitionRecord {
Name = this.CreateTicketForRecievedEmailWorkflowName, Enabled = true
};
this.workflowDefinitionRepository.Create(workflow);
ActivityRecord emailReceivedRecord = new ActivityRecord
{
WorkflowDefinitionRecord = workflow,
Start = true,
State = "{}",
X = 552,
Y = 227,
Name = IMapEmailReceivedActivity.ActivityName
};
this.activityRepository.Create(emailReceivedRecord);
ActivityRecord checkEmailBelongToUserActivityRecord = new ActivityRecord
{
State = "{}",
Name = "CheckEmailBelongToUser",
WorkflowDefinitionRecord = workflow,
X = 494,
Y = 538,
Start = false
};
this.activityRepository.Create(checkEmailBelongToUserActivityRecord);
TransitionRecord transitionRecord1 = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = checkEmailBelongToUserActivityRecord,
SourceActivityRecord = emailReceivedRecord,
DestinationEndpoint = "",
SourceEndpoint = "Done"
};
this.transitionRepository.Create(transitionRecord1);
ActivityRecord createTicketActivityRecord = new ActivityRecord
{
State = "{\"EditableBy\":\"{EEmail.UserName}\",\"Title\":\"{EEmail.Subject}\",\"Description\":\"{EEmail.Body}\",\"DownloadEmailAttachments\":\"true\"}",
Name = CreateTicketActivity.ActivityName,
WorkflowDefinitionRecord = workflow,
X = 494,
Y = 688,
Start = false
};
this.activityRepository.Create(createTicketActivityRecord);
TransitionRecord transitionRecord2 = new TransitionRecord
{
WorkflowDefinitionRecord = workflow,
DestinationActivityRecord = createTicketActivityRecord,
SourceActivityRecord = checkEmailBelongToUserActivityRecord,
DestinationEndpoint = "",
SourceEndpoint = "Yes"
};
this.transitionRepository.Create(transitionRecord2);
this.workflowDefinitionRepository.Flush();
this.activityRepository.Flush();
this.transitionRepository.Flush();
}