public static bool CheckSettings(string filepath, ISettingsData currentSettings)
{
if (string.IsNullOrWhiteSpace(filepath) || !File.Exists(filepath))
{
return(false);
}
var fileSettings = new SettingsData();
using (var streamReader = new StreamReader(new FileStream(filepath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)))
{
var line = streamReader.ReadLine();
if (line != null && !line.StartsWith("#"))
{
// Later versions: comment line is the second line (after the headers)
line = streamReader.ReadLine();
}
if (string.IsNullOrWhiteSpace(line) || !line.StartsWith("#"))
{
return(false);
}
fileSettings.PopulateFromTsvComment(line);
}
return(currentSettings.SettingsEquals(fileSettings));
}
private void Init()
{
if (isUsingActualConfig)
{
// Load configurations
GameConfiguration.Load();
settingsData = GameConfiguration.Settings;
}
else
{
settingsData = new SettingsData();
var a = settingsData.AddTabData(new SettingsTab("A", "icon-arrow-left"));
a.AddEntry(new SettingsEntryBool("a-a", testDataAA = new BindableBool(false)));
a.AddEntry(new SettingsEntryBool("a-b", testDataAB = new BindableBool(true)));
a.AddEntry(new SettingsEntryEnum <TestType>("a-c", testDataAC = new Bindable <TestType>(TestType.TypeB)));
var b = settingsData.AddTabData(new SettingsTab("B", "icon-backward"));
b.AddEntry(new SettingsEntryFloat("b-a", testDataBA = new BindableFloat(0f, -10f, 10f)));
b.AddEntry(new SettingsEntryFloat("b-b", testDataBB = new BindableFloat(5f, 10f, 20f)));
b.AddEntry(new SettingsEntryInt("b-c", testDataBC = new BindableInt(0, -20, 5)));
}
// Create nav bar.
navBar = RootMain.CreateChild <NavBar>("nav-bar");
{
navBar.Size = new Vector2(64f, 400f);
navBar.SetSettingsData(settingsData);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="WallboxClient"/> class.
/// </summary>
/// <param name="settings"></param>
/// <param name="logger"></param>
public WallboxClient(ISettingsData settings,
ILogger <WallboxClient> logger) : base(logger)
{
HostName = settings.HostName;
Port = settings.Port;
Timeout = settings.Timeout;
}
/// <summary>
/// Sets the settings data to build nav tabs based on.
/// </summary>
public void SetSettingsData(ISettingsData data)
{
if (data == null)
{
Cleanup();
return;
}
if (this.settingsData == data)
{
return;
}
Cleanup();
this.settingsData = data;
InvokeAfterTransformed(1, () =>
{
CellSize = new Vector2(Width, Height / data.TabCount);
foreach (var tabData in data.GetTabs())
{
var tabButton = CreateChild <NavTab>("tab-" + tabData.Name, tabs.Count);
tabButton.SetTabData(tabData);
tabs.Add(tabButton);
tabButton.OnTriggered += () =>
{
OnTabFocused?.Invoke(tabData);
};
}
});
}
public static void SetDefaultThresholds(this ISettingsData settings)
{
settings.DefaultIntensityThreshold = 10000;
settings.EdgeNETThresholdMinutes = 0.5;
settings.ElutionConcurrenceThresholdMinutes = 0.5;
settings.SignalToNoiseHeuristicThreshold = 10;
settings.CheckAllCompounds = false;
}
public SettingsProcess(ISettingsData settingsData,
IFieldofwaterData fieldOfWater,
IIdeaStatusData ideaStatusData)
{
this.settingsData = settingsData;
this.fieldOfWater = fieldOfWater;
this.ideaStatusData = ideaStatusData;
}
public IdeaProcess(IFieldofwaterData fieldOfWaterData,
ISettingsData settingsData,
IIdeasData ideaData,
IFileProcess fileProcess)
{
this.fieldOfWaterData = fieldOfWaterData;
this.settingsData = settingsData;
this.ideaData = ideaData;
this.fileProcess = fileProcess;
}
public static bool SettingsEquals(this ISettingsData settings1, ISettingsData settings2)
{
if (settings1 == null || settings2 == null)
{
return(false);
}
if (!settings1.DefaultIntensityThreshold.Equals(settings2.DefaultIntensityThreshold) ||
!settings1.EdgeNETThresholdMinutes.Equals(settings2.EdgeNETThresholdMinutes) ||
!settings1.ElutionConcurrenceThresholdMinutes.Equals(settings2.ElutionConcurrenceThresholdMinutes) ||
!settings1.SignalToNoiseHeuristicThreshold.Equals(settings2.SignalToNoiseHeuristicThreshold))
{
return(false);
}
if (string.IsNullOrWhiteSpace(settings1.CompoundThresholdFileSha1Hash) &&
string.IsNullOrWhiteSpace(settings1.CompoundThresholdFileSha1Hash) &&
string.IsNullOrWhiteSpace(settings1.CompoundThresholdFilePath) &&
string.IsNullOrWhiteSpace(settings1.CompoundThresholdFilePath))
{
return(true);
}
if (string.IsNullOrWhiteSpace(settings1.CompoundThresholdFileSha1Hash) ||
string.IsNullOrWhiteSpace(settings1.CompoundThresholdFileSha1Hash))
{
return(false);
}
if (!settings1.CompoundThresholdFileSha1Hash.Equals(settings2.CompoundThresholdFileSha1Hash))
{
return(false);
}
if (string.IsNullOrWhiteSpace(settings1.CompoundThresholdFilePath) ||
string.IsNullOrWhiteSpace(settings1.CompoundThresholdFilePath))
{
return(false);
}
if (settings1.CompoundThresholdFilePath.Equals(settings2.CompoundThresholdFilePath))
{
return(true);
}
// If direct equality was false, try again, comparing only the file names
if (!Path.GetFileName(settings1.CompoundThresholdFilePath).Equals(Path.GetFileName(settings2.CompoundThresholdFilePath)))
{
return(false);
}
return(true);
}
/// <summary>
/// Sets the settings data to display content for.
/// </summary>
public void SetSettingsData(ISettingsData settingsData)
{
if (settingsData == null)
{
Cleanup();
return;
}
else if (this.settingsData == settingsData)
{
return;
}
Cleanup();
this.settingsData = settingsData;
InvokeAfterTransformed(1, () =>
{
scrollviewHeight = Height;
// Create content groups.
ResetPosition();
container.Height = containerHeight = 0f;
foreach (var tab in settingsData.GetTabs())
{
var group = container.CreateChild <ContentGroup>(tab.Name);
{
group.Anchor = AnchorType.TopStretch;
group.Pivot = PivotType.Top;
group.Y = -container.Height;
group.SetOffsetHorizontal(0f);
}
group.SetTabData(tab);
groups.Add(group);
container.Height = (containerHeight += group.Height);
}
maxScrollPos = Math.Max(containerHeight - scrollviewHeight, 0f);
// Cache position progress of each group for tab focus feature.
if (maxScrollPos > 0f)
{
foreach (var group in groups)
{
group.PositionProgress = -group.Y / containerHeight;
}
}
});
}
/// <summary>
/// Removes previous states and child components for a new settings data.
/// </summary>
public void Cleanup()
{
for (int i = 0; i < groups.Count; i++)
{
groups[i].Destroy();
}
groups.Clear();
settingsData = null;
focusedTab = null;
scrollviewHeight = 0f;
containerHeight = 0f;
maxScrollPos = 0f;
}
public static void ComputeSha1(this ISettingsData settings)
{
if (string.IsNullOrWhiteSpace(settings.CompoundThresholdFilePath) || !File.Exists(settings.CompoundThresholdFilePath))
{
settings.CompoundThresholdFileSha1Hash = "";
return;
}
using (var stream = new FileStream(settings.CompoundThresholdFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite))
using (var sha1 = new SHA1Managed())
{
var hash = sha1.ComputeHash(stream);
settings.CompoundThresholdFileSha1Hash = string.Join("", hash.Select(x => x.ToString("x2")));
}
}
public static string ConvertToTsvComment(this ISettingsData settings)
{
var formatted = $"DefaultIntensityThreshold: {settings.DefaultIntensityThreshold:0.###}; NET time threshold (min): {settings.EdgeNETThresholdMinutes:0.###}";
formatted += $"; Elution Concurrence threshold (min): {settings.ElutionConcurrenceThresholdMinutes:0.###}; S/N Heuristic threshold: {settings.SignalToNoiseHeuristicThreshold:0.###}";
if (!string.IsNullOrWhiteSpace(settings.CompoundThresholdFilePath))
{
if (string.IsNullOrWhiteSpace(settings.CompoundThresholdFileSha1Hash))
{
settings.ComputeSha1();
}
formatted += $"; CompoundThresholdsFile: \"{settings.CompoundThresholdFilePath}\"; SHA1Hash {settings.CompoundThresholdFileSha1Hash}";
}
return(formatted);
}
public static List <CompoundData> ReadMethodData(this IMethodReader reader, ISettingsData settings)
{
var transitions = reader.GetAllTransitions();
if (!settings.CheckAllCompounds)
{
transitions = transitions.GetHeavyTransitions();
}
//Console.WriteLine($"File \"{reader.DatasetPath}\": {transitions.Count} heavy transitions in instrument method.");
if (transitions.Count == 0)
{
var heavy = settings.CheckAllCompounds ? "" : " heavy";
Console.WriteLine($"ERROR: Could not read instrument methods or find{heavy} transitions for file \"{reader.DatasetPath}\"");
return(null);
}
// TODO: Could determine heavy peptides by checking names vs. precursor m/z?
return(transitions.JoinTransitions(settings));
}
public MainWindowViewModel(
IWindowManager windowManager,
IArgipApiData argipApiData,
ISettingsData settingsData,
AccessTokenService accessTokenService,
CartHolder cartHolder)
{
this.windowManager = windowManager;
this.argipApiData = argipApiData;
this.settingsData = settingsData;
this.accessTokenService = accessTokenService;
this.cartHolder = cartHolder;
ProductList = new BindableCollection <Product>();
ProductCustomIndex = new BindableCollection <Product>();
// read settings from store
var settings = settingsData.ReadSettings();
BaseApiAddress = settings.BaseApiAddress;
TokenEndpoint = settings.TokenEndpoint;
ClientId = settings.ClientId;
ClientSecret = settings.ClientSecret;
}
public static void PopulateFromTsvComment(this ISettingsData settings, string tsvCommentLine)
{
var match = TsvCommentSettingsRegex.Match(tsvCommentLine);
var defaultThreshold = match.Groups["defaultThreshold"].Value;
if (!string.IsNullOrWhiteSpace(defaultThreshold))
{
settings.DefaultIntensityThreshold = double.Parse(defaultThreshold);
}
var netTimeThreshold = match.Groups["netTimeThreshold"].Value;
if (!string.IsNullOrWhiteSpace(netTimeThreshold))
{
settings.EdgeNETThresholdMinutes = double.Parse(netTimeThreshold);
}
var elutionConcurrenceThreshold = match.Groups["elutionConcurrenceThreshold"].Value;
if (!string.IsNullOrWhiteSpace(elutionConcurrenceThreshold))
{
settings.ElutionConcurrenceThresholdMinutes = double.Parse(elutionConcurrenceThreshold);
}
var snHeuristicThreshold = match.Groups["snHeuristicThreshold"].Value;
if (!string.IsNullOrWhiteSpace(snHeuristicThreshold))
{
settings.SignalToNoiseHeuristicThreshold = double.Parse(snHeuristicThreshold);
}
// if not match, the value is string.Empty. (also .Success will be false)
settings.CompoundThresholdFilePath = match.Groups["filepath"].Value.Trim().Trim('"', '\'');
settings.CompoundThresholdFileSha1Hash = match.Groups["fileHash"].Value.Trim();
}
public static void WriteCombinedResultsToFile(string filepath, List <CompoundData> results, ISettingsData settings)
{
foreach (var compound in results)
{
if (compound.Transitions.Count >= 10)
{
System.Console.WriteLine(@"Warning: Will not output additional transition for compound ""{0}"": it already has 10 transitions.", compound.CompoundName);
}
compound.CalculateSummaryData();
}
var maxTrans = results.Max(x => x.Transitions.Count);
using (var csv = new CsvWriter(new StreamWriter(new FileStream(filepath, FileMode.Create, FileAccess.Write, FileShare.ReadWrite))))
{
csv.Configuration.RegisterClassMap(new CompoundResultMap(maxTrans));
csv.Configuration.Delimiter = "\t";
csv.Configuration.Comment = '#';
csv.Configuration.AllowComments = true;
// write the header first
csv.WriteHeader <CompoundData>();
csv.NextRecord();
// Write the settings comment
csv.WriteComment(" Settings: " + settings.ConvertToTsvComment());
// Make sure to finish the line
csv.NextRecord();
// Write everything else (which shouldn't include the headers).
csv.WriteRecords(results);
}
}
public static Dictionary <string, CompoundThresholdData> LoadCompoundThresholds(this ISettingsData settings)
{
if (string.IsNullOrWhiteSpace(settings.CompoundThresholdFilePath) || !File.Exists(settings.CompoundThresholdFilePath))
{
return(null);
}
var thresholds = CompoundThresholdData.ReadFromFile(settings.CompoundThresholdFilePath).ToList();
return(CompoundThresholdData.ConvertToSearchMap(thresholds));
}
//Client program that connect to the server.
void OpenPipeClient()
{
try
{
NetNamedPipeBinding binding = new NetNamedPipeBinding();
binding.MaxBufferPoolSize = 100000000;
binding.MaxBufferSize = 100000000;
binding.MaxReceivedMessageSize = 100000000;
binding.SendTimeout = TimeSpan.MaxValue;
binding.ReceiveTimeout = TimeSpan.MaxValue;
binding.ReaderQuotas.MaxArrayLength = 100000000;
binding.ReaderQuotas.MaxBytesPerRead = 100000000;
binding.ReaderQuotas.MaxDepth = 100000000;
binding.ReaderQuotas.MaxNameTableCharCount = 100000000;
binding.ReaderQuotas.MaxStringContentLength = 100000000;
EndpointAddress endpoint = new EndpointAddress("net.pipe://localhost/ISettingsData");
LockerChannel = new ChannelFactory<ISettingsData>(binding, endpoint);
LockerAccess = LockerChannel.CreateChannel();
LockerChannel.Faulted += LockerChannel_Faulted;
LockerChannel.Closed += LockerChannel_Closed;
nVenTory = new StoredInventoryWrapper(LockerAccess);
cHarActors = new ServerCharStatsWrapper(LockerAccess);
}catch(Exception ex){LogError(ex);}
}
internal StoredInventoryWrapper(ISettingsData PipeAccess)
{
LockerAccess = PipeAccess;
}
public void WritePdf(List <CompoundData> results, ISettingsData settings, bool useNonVectorImages = false)
{
if (useNonVectorImages && Thread.CurrentThread.GetApartmentState() != ApartmentState.STA)
{
var thread = new Thread(() => WritePdf(results, settings, useNonVectorImages));
thread.SetApartmentState(ApartmentState.STA);
thread.Start();
thread.Join();
return;
}
Func <List <CompoundData>, int, int, int, XImage> summaryPlotCreateMethod = CreatePlot;
Func <CompoundData, int, int, int, XImage> plotCreateMethod = CreatePlot;
var plotSizeMultiplier = 3d;
if (useNonVectorImages)
{
summaryPlotCreateMethod = CreatePlotBitmapWpf;
plotCreateMethod = CreatePlotBitmapWpf;
// Plot text is naturally larger in OxyPlot.WPF-rendered images, so increase the size multiplier
plotSizeMultiplier = 4;
}
// Guarantee that the plots will be backed at 300+ DPI
var desiredResolution = 300;
var resolution = 96;
// Add a header: Dataset name
currentPageY += AddText(DatasetName, fontHeader, 0.75, position: XStringFormats.BaseLineCenter);
// Add the analysis settings
currentPageY += AddText("Q4SRM Analysis settings:", fontHeader2);
currentPageY += AddText($"Input file path: {DatasetPath}", fontDefault);
currentPageY += AddText($"Compound minimum summed intensity threshold: {settings.DefaultIntensityThreshold:F0}", fontDefault);
currentPageY += AddText($"Compound peak elution concurrence threshold (minutes): {settings.ElutionConcurrenceThresholdMinutes:F2}", fontDefault);
currentPageY += AddText($"Transition minimum peak distance from elution window edge (minutes): {settings.ElutionConcurrenceThresholdMinutes:F2}", fontDefault);
currentPageY += AddText($"Transition minimum signal to noise heuristic (max intensity / median intensity): {settings.SignalToNoiseHeuristicThreshold:F2}", fontDefault);
if (!string.IsNullOrWhiteSpace(settings.CompoundThresholdFilePath))
{
currentPageY += AddText($"Per-compound intensity threshold file path: {settings.CompoundThresholdFilePath}", fontDefault);
currentPageY += AddText($"Per-compound intensity threshold file SHA1: {settings.CompoundThresholdFileSha1Hash}", fontDefault);
}
// Add the summary plot
var summaryPlotAspectRatio = 4.0 / 3.0;
var summaryPlotWidth = currentPage.Width - DoublePageMargin;
var summaryPlotHeight = summaryPlotWidth / summaryPlotAspectRatio;
var summaryPlotWidthWpf = (int)(summaryPlotWidth * plotSizeMultiplier);
var summaryPlotHeightWpf = (int)(summaryPlotHeight * plotSizeMultiplier);
var summaryPlotImage = summaryPlotCreateMethod(results, summaryPlotWidthWpf, summaryPlotHeightWpf, resolution);
AddPlot(summaryPlotImage, PageMargin, summaryPlotWidth, summaryPlotHeight, null);
currentPageY += summaryPlotHeight + 25;
AddPage();
// Add the error plots
currentPageY += AddText("Errors:", fontHeader2);
currentPageY += AddText("Key: int=intensity, pp=peak position, ec=elution concurrence, sn=S/N heuristic", fontDefault);
var plotSize = (currentPage.Width - DoublePageMargin - 10) / 3;
var wpfRenderSize = (int)(plotSize * plotSizeMultiplier);
// Check the resolution vs. pdf render size
if (wpfRenderSize < desiredResolution / (double)resolution * plotSize)
{
wpfRenderSize = (int)(desiredResolution / (double)resolution * plotSize);
}
var counter = 0;
var xOffset = PageMargin;
var textHeight = GetTextHeight("int", currentPageGraphics, fontDefault);
foreach (var result in results.Where(x => !x.PassesAllThresholds).OrderBy(x => x.CompoundName))
{
if (counter % 3 == 0 && counter > 0)
{
xOffset = PageMargin;
currentPageY += textHeight + plotSize + 25;
if (currentPageY + textHeight + plotSize > currentPage.Height - PageMargin)
{
AddPage();
}
}
counter++;
var plotImage = plotCreateMethod(result, wpfRenderSize, wpfRenderSize, resolution);
AddPlot(plotImage, xOffset, plotSize, plotSize, $"{counter}: {GetCompoundDataHeader(result)}");
xOffset += plotSize + 5;
}
currentPageY += textHeight + plotSize + 25;
if (currentPageY + textHeight + plotSize > currentPage.Height - PageMargin)
{
AddPage();
}
// Add the passing plots
currentPageY += AddText("Passes:", fontHeader2);
counter = 0;
xOffset = PageMargin;
foreach (var result in results.Where(x => x.PassesAllThresholds).OrderBy(x => x.CompoundName))
{
if (counter % 3 == 0 && counter > 0)
{
xOffset = PageMargin;
currentPageY += plotSize;
if (currentPageY + plotSize > currentPage.Height - PageMargin)
{
AddPage();
}
}
counter++;
var plotImage = plotCreateMethod(result, wpfRenderSize, wpfRenderSize, resolution);
AddPlot(plotImage, xOffset, plotSize, plotSize, null);
xOffset += plotSize;
}
currentPageY += plotSize + 25;
//if (currentPageY + plotSize > currentPage.Height - PageMargin)
//{
// AddPage();
//}
document.Save(SavePath);
}
internal ServerCharStatsWrapper(ISettingsData PipeAccess)
{
LockerAccess = PipeAccess;
}
/// <summary>
/// Event called when the settings data has changed.
/// </summary>
private void OnSettingsDataChange(ISettingsData data)
{
navBar.SetSettingsData(data);
contentHolder.SetSettingsData(data);
}
/// <summary>
/// Sets the settings data to visually represent.
/// </summary>
public void SetSettingsData(ISettingsData settings)
{
currentSettings.Value = settings;
}
public static List <CompoundData> JoinTransitions(this List <TransitionData> transitions, ISettingsData settings)
{
var compoundThresholds = settings.LoadCompoundThresholds();
if (compoundThresholds == null)
{
compoundThresholds = new Dictionary <string, CompoundThresholdData>();
}
var combined = new Dictionary <string, CompoundData>();
foreach (var item in transitions)
{
if (!combined.TryGetValue(item.CompoundName, out var group))
{
group = new CompoundData(item)
{
IntensityThreshold = settings.DefaultIntensityThreshold,
EdgeNETThresholdMinutes = settings.EdgeNETThresholdMinutes,
ElutionConcurrenceThresholdMinutes = settings.ElutionConcurrenceThresholdMinutes,
SignalToNoiseHeuristicThreshold = settings.SignalToNoiseHeuristicThreshold
};
// Look for and handle custom thresholds
if (compoundThresholds.TryGetValue(item.CompoundName, out var cThreshold))
{
group.IntensityThreshold = cThreshold.Threshold;
}
combined.Add(group.CompoundName, group);
}
group.Transitions.Add(item);
}
return(combined.Values.ToList());
}
public void InjectMetod(ISettingsData settingsData)
{
this.settingsData = settingsData;
}
