public override void GenerateTheorFeature(TargetBase mt)
{
Check.Require(mt != null, this.Name + " failed; CurrentMassTag hasn't been declared");
//Check.Require(results.Run.CurrentMassTag.EmpiricalFormula!=null, this.Name + "failed; Problem with EmpiricalFormular of current mass tag.");
//XYData theorXYData = new XYData();
//for (int i = 0; i < mt.IsotopicProfile.Peaklist.Count; i++)
//{
// XYData peakXYData = getTheorPeakData(mt.IsotopicProfile.Peaklist[i], fwhm);
//}
//distributionCreator.MolecularFormula = new MolecularFormula();
//distributionCreator.getIsotopicProfile();
//distributionCreator.OffsetDistribution(result.IsotopicProfile);
//AreaFitter areafitter = new AreaFitter(distributionCreator.Data, result.Run.XYData, 10);
//double fitval = areafitter.getFit();
//if (fitval == double.NaN || fitval > 1) fitval = 1;
//result.IsotopicProfile.Score = fitval;
}
public void HandTarget(TargetBase target)
{
targetGameObject = target.gameObject;
targetBase = target;
targetGameObject.transform.SetParent(targetRoot, false);
targetGameObject.transform.localPosition = Vector3.zero;
}
public override void GenerateTheorFeature(TargetBase mt)
{
Check.Require(mt != null, "FeatureGenerator failed. MassTag not defined.");
Check.Require(!string.IsNullOrEmpty(mt.EmpiricalFormula), "Theoretical feature generator failed. Can't retrieve empirical formula from Mass Tag");
switch (LabelingType)
{
case Globals.LabelingType.NONE:
mt.IsotopicProfile = GetUnlabeledIsotopicProfile(mt);
break;
case Globals.LabelingType.O18:
throw new NotImplementedException();
case Globals.LabelingType.N15:
mt.IsotopicProfileLabeled = _N15IsotopicProfileGenerator.GetN15IsotopicProfile2(mt, LowPeakCutOff);
break;
case Globals.LabelingType.Deuterium:
//mt.IsotopicProfile = GetUnlabeledIsotopicProfile(mt);
//mt.IsotopicProfileLabeled = _DeuteriumIsotopicProfileGenerator.GetDHIsotopicProfile2(mt, LowPeakCutOff, FractionLabeling, MolarMixingFraction);
//swap so we can keep the normal in labeled box and use the D/H for general processing
mt.IsotopicProfile = GetUnlabeledIsotopicProfile(mt);//needed for _DeuteriumIsotopicProfileGenerator
mt.IsotopicProfile = _DeuteriumIsotopicProfileGenerator.GetDHIsotopicProfile2(mt, LowPeakCutOff, FractionLabeling, MolarMixingFraction);
mt.IsotopicProfileLabeled = GetUnlabeledIsotopicProfile(mt);
break;
default:
throw new NotImplementedException();
}
}
public override void GenerateTheorFeature(TargetBase mt)
{
Check.Require(mt != null, "FeatureGenerator failed. MassTag not defined.");
if (mt == null)
{
return;
}
Check.Require(mt.EmpiricalFormula != null, "Theoretical feature generator failed. Can't retrieve empirical formula from Mass Tag");
switch (LabelingType)
{
case Globals.LabelingType.NONE:
mt.IsotopicProfile = GetUnlabeledIsotopicProfile(mt);
break;
case Globals.LabelingType.O18:
throw new NotImplementedException();
case Globals.LabelingType.N15:
mt.IsotopicProfileLabeled = _N15IsotopicProfileGenerator.GetN15IsotopicProfile(mt, LowPeakCutOff);
break;
default:
break;
}
}
private IsotopicProfile GetUnlabelledIsotopicProfile(TargetBase mt)
{
var iso = new IsotopicProfile();
try
{
//empirical formula may contain non-integer values for
iso = _isotopicDistCalculator.GetIsotopePattern(mt.EmpiricalFormula);
}
catch (Exception ex)
{
throw new Exception("Theoretical feature generator failed. Details: " + ex.Message);
}
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
if (iso.ChargeState != 0)
{
calculateMassesForIsotopicProfile(iso, mt.MonoIsotopicMass, mt.ChargeState);
}
return(iso);
}
private void SpawnTargets(List <ShootingGalleryTargetModel> newTargets)
{
List <TargetBase> spawnedTargets = new List <TargetBase>(); //Pass this to whatever will handle the targets
foreach (ShootingGalleryTargetModel target in newTargets)
{
GameObject prefab = null;
foreach (TargetPrefabPair targetPair in potentialTargets)
{
if (targetPair.id.Equals(target.id))
{
prefab = targetPair.prefab;
}
}
if (prefab == null)
{
LSLog.LogError($"Could not find a prefab for target with an ID of {target.id}... will use default");
prefab = defaultTarget;
}
GameObject newTarget = Instantiate(prefab);
TargetBase targetBase = newTarget.GetComponent <TargetBase>();
targetBase.Init(target);
targetObjectsSpawned.Add(targetBase);
spawnedTargets.Add(targetBase);
}
targetHolder.Initialize(spawnedTargets);
targetHolder.Reset();
}
public virtual void Render(TargetBase target)
{
if (!Show)
{
return;
}
if (_effectGraph == null)
{
return;
}
var context2D = target.DeviceManager.ContextDirect2D;
context2D.BeginDraw();
if (EnableClear)
{
context2D.Clear(Color.Black);
}
context2D.Clear(Color.Transparent);
context2D.DrawImage(_effectGraph.Output, InterpolationMode.Linear, CompositeMode.DestinationAtop);
context2D.EndDraw();
}
/// <summary>
/// Renders the model.
/// </summary>
/// <param name="render">The render.</param>
private void Render(TargetBase render)
{
foreach (Element3D e in this.Items)
{
e.Render(render);
}
}
public void Render(TargetBase target)
{
var d3dContext = target.DeviceManager.ContextDirect3D;
var d2dContext = target.DeviceManager.ContextDirect2D;
// Set targets (This is mandatory in the loop)
d3dContext.OutputMerger.SetTargets(target.DepthStencilView, target.RenderTargetView);
// Clear the views
d3dContext.ClearDepthStencilView(target.DepthStencilView, DepthStencilClearFlags.Depth, 1.0f, 0);
if (EnableClear)
{
d3dContext.ClearRenderTargetView(target.RenderTargetView, new Color4(0.0f, 0.0f, 0.0f, 0.0f));
}
spriteBatch.Begin(target);
for (int i = 0; i < 50; i++)
{
spriteBatch.Draw(_textureDot, _currentPointerPosition * new Vector2(1, -1));
}
spriteBatch.End();
}
private clsMassTag convertDeconToolsMassTagToMultialignMassTag(TargetBase mt)
{
var multialignMassTag = new clsMassTag();
multialignMassTag.Id = mt.ID;
multialignMassTag.Charge1FScore = 0;
multialignMassTag.Charge2FScore = 0;
multialignMassTag.Charge3FScore = 0;
multialignMassTag.ChargeState = mt.ChargeState;
multialignMassTag.CleavageState = -1;
multialignMassTag.DiscriminantMax = 0;
//multialignMassTag.DriftTime = 0;
multialignMassTag.HighPeptideProphetProbability = 0;
multialignMassTag.Mass = mt.MonoIsotopicMass;
multialignMassTag.ModCount = -1;
multialignMassTag.Modifications = String.Empty;
multialignMassTag.MSGFSpecProbMax = 0;
multialignMassTag.MSMSObserved = mt.ObsCount;
multialignMassTag.NetAverage = mt.NormalizedElutionTime;
multialignMassTag.NetPredicted = -1;
multialignMassTag.NetStandardDeviation = 0;
multialignMassTag.Peptide = mt.Code;
multialignMassTag.PeptideEx = String.Empty;
multialignMassTag.XCorr = -1;
return(multialignMassTag);
}
public virtual void Render(TargetBase target)
{
if (!Show)
{
return;
}
if (_waveEffect == null)
{
return;
}
UpdateSize(target);
var context2D = target.DeviceManager.ContextDirect2D;
Update();
context2D.BeginDraw();
if (EnableClear)
{
context2D.Clear(Color.CornflowerBlue);
}
context2D.DrawImage(_waveEffect);
context2D.EndDraw();
}
public void Render(TargetBase target)
{
var d3dContext = target.DeviceManager.ContextDirect3D;
float width = (float)target.RenderTargetSize.Width;
float height = (float)target.RenderTargetSize.Height;
// Prepare matrices
var view = Matrix.LookAtLH(new Vector3(0, 0, -5), new Vector3(0, 0, 0), Vector3.UnitY);
var proj = Matrix.PerspectiveFovLH((float)Math.PI / 4.0f, width / (float)height, 0.1f, 100.0f);
var viewProj = Matrix.Multiply(view, proj);
var time = (float)(clock.ElapsedMilliseconds / 1000.0);
// Set targets (This is mandatory in the loop)
d3dContext.OutputMerger.SetTargets(target.DepthStencilView, target.RenderTargetView);
// Clear the views
d3dContext.ClearDepthStencilView(target.DepthStencilView, DepthStencilClearFlags.Depth, 1.0f, 0);
if (EnableClear)
{
d3dContext.ClearRenderTargetView(target.RenderTargetView, new Color4(0.0f, 0.0f, 0.0f, 0.0f));
}
if (ShowCube)
{
// Calculate WorldViewProj
var worldViewProj = Matrix.Scaling(Scale) * Matrix.RotationX(time) * Matrix.RotationY(time * 2.0f) * Matrix.RotationZ(time * .7f) * viewProj;
worldViewProj.Transpose();
// Setup the pipeline
d3dContext.InputAssembler.SetVertexBuffers(0, vertexBufferBinding);
d3dContext.InputAssembler.InputLayout = layout;
d3dContext.InputAssembler.PrimitiveTopology = PrimitiveTopology.TriangleList;
d3dContext.VertexShader.SetConstantBuffer(0, constantBuffer);
d3dContext.VertexShader.Set(vertexShader);
d3dContext.PixelShader.SetShaderResource(0, textureView);
d3dContext.PixelShader.SetSampler(0, sampler);
d3dContext.PixelShader.Set(pixelShader);
// Update Constant Buffer
d3dContext.UpdateSubresource(ref worldViewProj, constantBuffer, 0);
// Draw the cube
d3dContext.Draw(36, 0);
}
}
public override void GenerateTheorFeature(TargetBase mt)
{
Check.Require(mt != null, "FeatureGenerator failed. Target must not be null.");
var iso = IsotopicDistCalculator.GetAveraginePattern(mt.MZ);
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
mt.IsotopicProfile = iso;
}
private void UpdateSize(TargetBase target)
{
var localSize = new Size2((int)target.RenderTargetSize.Width, (int)target.RenderTargetSize.Height);
if (localSize != screenSize)
{
screenSize = localSize;
bitmapSourceEffect.ScaleSource = new Vector2((float)screenSize.Width / imageSize.Width, (float)screenSize.Height / imageSize.Height);
}
}
public void Stop()
{
if (_target != null)
{
_target.Shutdown();
_target = null;
}
_subscriptions.Shutdown();
_subscriptions = new BoardSubscriptionManager();
}
private IsotopicProfile getTheorProfile(TargetBase massTag, Globals.IsotopicProfileType isotopicProfileType)
{
switch (isotopicProfileType)
{
case Globals.IsotopicProfileType.UNLABELED:
return(massTag.IsotopicProfile);
case Globals.IsotopicProfileType.LABELED:
return(massTag.IsotopicProfileLabeled);
default:
return(massTag.IsotopicProfile);
}
}
public override void Render(TargetBase render)
{
base.Render(render);
var context = render.DeviceManager.ContextDirect3D;
var width = render.RenderTargetSize.Width;
var height = render.RenderTargetSize.Height;
// Prepare matrices
var view = global::SharpDX.Matrix.LookAtLH(new global::SharpDX.Vector3(0, 0, -5), new global::SharpDX.Vector3(0, 0, 0), global::SharpDX.Vector3.UnitY);
var proj = global::SharpDX.Matrix.PerspectiveFovLH((float)Math.PI / 4.0f, (float)(width / height), 0.1f, 100.0f);
var viewProj = global::SharpDX.Matrix.Multiply(view, proj);
var time = (float)(this.clock.ElapsedMilliseconds / 1000.0);
// Set targets (This is mandatory in the loop)
context.OutputMerger.SetTargets(render.DepthStencilView, render.RenderTargetView);
// Clear the views
context.ClearDepthStencilView(render.DepthStencilView, global::SharpDX.Direct3D11.DepthStencilClearFlags.Depth, 1.0f, 0);
if (this.EnableClear)
{
context.ClearRenderTargetView(render.RenderTargetView, global::SharpDX.Color.LightGray);
}
if (this.ShowCube)
{
// Calculate WorldViewProj
var worldViewProj = global::SharpDX.Matrix.Scaling((float)this.Scale) * global::SharpDX.Matrix.RotationX((float)this.RotationSpeed * time)
* global::SharpDX.Matrix.RotationY((float)this.RotationSpeed * time * 2.0f) * global::SharpDX.Matrix.RotationZ((float)this.RotationSpeed * time * .7f)
* viewProj;
worldViewProj.Transpose();
context.UpdateSubresource(ref worldViewProj, this.constantBuffer, 0);
// Setup the pipeline
context.InputAssembler.SetVertexBuffers(0, this.vertexBufferBinding);
context.InputAssembler.InputLayout = this.layout;
context.InputAssembler.PrimitiveTopology = global::SharpDX.Direct3D.PrimitiveTopology.TriangleList;
context.VertexShader.Set(this.vertexShader);
context.PixelShader.Set(this.pixelShader);
context.VertexShader.SetConstantBuffer(0, this.constantBuffer);
// Update Constant Buffer
// Draw the cube
context.Draw(36, 0);
}
}
private void calculateMassesForIsotopicProfile(IsotopicProfile iso, TargetBase mt)
{
if (iso?.Peaklist == null)
{
return;
}
for (var i = 0; i < iso.Peaklist.Count; i++)
{
var calcMZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS + i * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / mt.ChargeState;
iso.Peaklist[i].XValue = calcMZ;
}
iso.MonoPeakMZ = iso.Peaklist[0].XValue;
iso.MonoIsotopicMass = (iso.MonoPeakMZ - Globals.PROTON_MASS) * mt.ChargeState;
}
void Shoot()
{
// A simple fire animation using particals.
gunSmoke.Play();
// Raycast for targeting purposes.
RaycastHit rayHit;
// Player Player forward Going out to range
if (Physics.Raycast(transform.position, transform.forward, out rayHit))
{
range = rayHit.distance;
}
{
// Set up target. What the ray hit.
Target target = rayHit.transform.GetComponent <Target>();
TargetEnemy enemyTarget = rayHit.transform.GetComponent <TargetEnemy>();
TargetBase baseTarget = rayHit.transform.GetComponent <TargetBase>();
TargetTank tankTarget = rayHit.transform.GetComponent <TargetTank>();
//GameObject hitHere = Instantiate(hitEffect, transform.position + transform.forward * range, Quaternion.LookRotation(rayHit.point));
GameObject hitHere = Instantiate(hitEffect, rayHit.point, Quaternion.LookRotation(rayHit.normal));
Destroy(hitHere, 0.5f);
Debug.DrawLine(transform.position, transform.position + transform.forward * range, Color.red);
// Show me what the ray hit.
// Debug.Log(rayHit.transform.name);
if (enemyTarget != null)
{ // Target takes damage.
enemyTarget.HitEnemy(damage);
}
// Only if targe is not zero, a valid targe is in range.
if (target != null)
{ // Target takes damage.
target.HitTarget(damage);
}
if (baseTarget != null)
{
baseTarget.HitBase(damage);
}
if (tankTarget != null)
{
tankTarget.HitBase(damage);
}
}
}
void Update ()
{
if( (GameManager.CurrentState == GameManager.GameState.GamePlayer || GameManager.CurrentState == GameManager.GameState.LevelWinOutro) && ((ifEditor() && Input.GetMouseButton(0)) || Input.touchCount > 0) )
{
touching = true;
ray = Camera.main.ScreenPointToRay(Input.mousePosition);
//nextTouchTime <= Time.timeSinceLevelLoad
//Debug.Log(nextTouchTime + " : " + Time.timeSinceLevelLoad);
if (playerTrail != null)
{
playerTrail.transform.position = ray.origin;
}
nextTouchTime = Time.timeSinceLevelLoad;
if (Physics.Raycast(ray, out hit, 100f))
{
// HIT
if (GameManager.CurrentState == GameManager.GameState.GamePlayer)
{
hitBase = hit.collider.gameObject.GetComponent<TargetBase>();
if (hitBase != null)
{
if (GameManager.HandleHitID(hitBase, ref CurrentPlayerHitsID))
{
hitBase.ShowHit();
Debug.Log("HIT: " + CurrentPlayerHitsID);
GameManager.EvaluatePlayerState();
}
}
}
}
}
else
{
touching = false;
}
if (playerTrail != null)
{
playerTrail.SetActive(touching);
}
}
public void Begin(TargetBase render)
{
//var d3dContext = render.DeviceManager.ContextDirect3D;
//var d2dContext = render.DeviceManager.ContextDirect2D;
//m_d3dContext = d3dContext;
m_renderTargetSize = new Vector2((float)render.RenderTargetSize.Width, (float)render.RenderTargetSize.Height);
m_width = (float)render.RenderTargetSize.Width;
m_height = (float)render.RenderTargetSize.Height;
m_dpi = Windows.Graphics.Display.DisplayProperties.LogicalDpi;
m_view = Matrix.LookAtLH(new Vector3(0, 0, -1), new Vector3(0, 0, 0), Vector3.UnitY);
m_projection = Matrix.PerspectiveFovLH((float)Math.PI / 4.0f, m_width / (float)m_height, 0.1f, 2.0f);
m_viewProj = Matrix.Multiply(m_view, m_projection);
}
public IsotopicProfile GetN15IsotopicProfile(TargetBase mt, double lowpeakCutoff)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
var numNitrogens = mt.GetAtomCountForElement("N");
var labeledTheorProfile = _TomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _TomIsotopicPatternGenerator.aafN15Isos);
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheorProfile, numNitrogens, mt.ChargeState);
PeakUtilities.TrimIsotopicProfile(labeledTheorProfile, lowpeakCutoff);
labeledTheorProfile.ChargeState = mt.ChargeState;
return(labeledTheorProfile);
}
public IsotopicProfile GetN15IsotopicProfile2(TargetBase mt, double lowPeakCutoff)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
var nitrogenCount = mt.GetAtomCountForElement("N");
_isotopicDistributionCalculator.SetLabeling("N", N14ISOTOPE_NUMBER, this.N14LabelingAmount, N15ISOTOPE_NUMBER, this.N15LabelingAmount);
var labeledTheorProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheorProfile, nitrogenCount, mt.ChargeState);
_isotopicDistributionCalculator.ResetToUnlabeled();
PeakUtilities.TrimIsotopicProfile(labeledTheorProfile, lowPeakCutoff);
labeledTheorProfile.ChargeState = mt.ChargeState;
return(labeledTheorProfile);
}
private void StartIntegration(IEnumerable <System.Type> types)
{
const string noConfigMessage = "\n\nThis Service has not been configured or the configuration has changed.\n\nUse the Configuration Utility to configure and activate Integrations.\n\n";
var configuration = LoadConfiguration();
// pick correct implementation class for specified target type
if (configuration != null && configuration.Target != null && !string.IsNullOrEmpty(configuration.Target.Type))
{
var targetType = configuration.Target.Type.ToLowerInvariant();
var implementations = types.Where(x => x.IsClass &&
!x.IsAbstract &&
x.IsSubclassOf(typeof(TargetBase))).ToList();
if (!implementations.Any())
{
"No integrations found.".Print();
noConfigMessage.Print();
}
var implementation = implementations.FirstOrDefault(x => x.Name.ToLowerInvariant() == targetType);
if (implementation != null)
{
_target = (TargetBase)Activator.CreateInstance(implementation, _subscriptions);
new Thread(_target.Process).Start();
}
else
{
string.Format("No integration found matching [{0}]. Valid integrations are : {1}", targetType,
string.Join(", ", implementations.Select(x => x.Name).ToList())).Print();
noConfigMessage.Print();
}
}
else
{
noConfigMessage.Print();
}
}
private IsotopicProfile GetUnlabeledIsotopicProfile(TargetBase mt)
{
IsotopicProfile iso;
try
{
iso = _tomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _tomIsotopicPatternGenerator.aafIsos);
}
catch (Exception ex)
{
throw new Exception("Theoretical feature generator failed. Details: " + ex.Message);
}
PeakUtilities.TrimIsotopicProfile(iso, LowPeakCutOff);
iso.ChargeState = mt.ChargeState;
if (iso.ChargeState != 0)
{
calculateMassesForIsotopicProfile(iso, mt);
}
return(iso);
}
private void CalculateEmpiricalFormulas(TargetCollection data)
{
var peptideUtils = new PeptideUtils();
foreach (var targetBase in data.TargetList)
{
var peptide = (PeptideTarget)targetBase;
var baseEmpiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(peptide.Code);
if (peptide.ContainsMods)
{
TargetBase peptide1 = peptide;
var mods = (from n in _massTagModData where n.Item1 == peptide1.ID select n);
foreach (var tuple in mods)
{
baseEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(baseEmpiricalFormula, tuple.Item4);
}
}
peptide.EmpiricalFormula = baseEmpiricalFormula;
}
}
public void DestroyTargetByUID(string uid)
{
TargetBase deadTarget = null;
foreach (TargetBase target in targetObjectsSpawned)
{
if (target.UID.Equals(uid))
{
deadTarget = target;
break;
}
}
if (deadTarget != null)
{
deadTarget.Explode();
targetCount--;
}
else
{
LSLog.LogError($"Could not find a target object with uid {uid}");
}
}
public virtual void Render(TargetBase target)
{
if (!Show)
{
return;
}
IRenderableScreenCopy screenCopy = this.screen.GetScreenCopy();
var context2D = target.DeviceManager.ContextDirect2D;
context2D.BeginDraw();
context2D.Transform = Matrix.Identity;
context2D.Clear(TerminalBackgroundColor);
RectangleF rect = new RectangleF();
var lines = screenCopy.Cells;
for (int y = 0; y < lines.Count(); y++)
{
var cols = lines[y];
rect.Top = y * CellHeight;
rect.Bottom = rect.Top + CellHeight;
for (int x = 0; x < cols.Count(); x++)
{
var cell = cols[x];
rect.Left = x * CellWidth;
rect.Right = rect.Left + CellWidth;
bool isCursor = !screenCopy.CursorHidden && y == screenCopy.CursorRow && x == screenCopy.CursorColumn;
this.DrawCell(target, rect, cell, isCursor, screenCopy.HasFocus);
}
}
context2D.EndDraw();
}
public static bool HandleHitID(TargetBase target, ref string list)
{
if (!list.Contains(target.id.ToString()))
{
list+= target.id;
return true;
}
return false;
}
/// <summary>
/// Renders the element.
/// </summary>
/// <param name="render">The render.</param>
public virtual void Render(TargetBase render)
{
}
private void OutputMassSpectrum(string outputFolder, XYData massSpectrumXYData, TargetBase target, SipperLcmsTargetedResult sipperLcmsTargetedResult)
{
var msGraphGenerator = new MSGraphControl();
msGraphGenerator.SymbolType = SymbolType.None;
if (massSpectrumXYData == null)
{
massSpectrumXYData = new XYData();
massSpectrumXYData.Xvalues = new double[] { 0, 1, 2, 3, 4, 5 };
massSpectrumXYData.Yvalues = new double[] { 0, 1, 2, 3, 4, 5 };
}
msGraphGenerator.GenerateGraph(massSpectrumXYData.Xvalues, massSpectrumXYData.Yvalues, target.MZ - 2,
target.MZ + 6);
var annotation = "fractionC13= " + sipperLcmsTargetedResult.PercentCarbonsLabelled.ToString("0.000") + "\n" +
"populationFraction= " + sipperLcmsTargetedResult.PercentPeptideLabelled.ToString("0.000");
msGraphGenerator.AddAnnotationRelativeAxis(annotation, 0.45, 0.05);
var outputFilename = Path.Combine(outputFolder, target.ID + "_MS.png");
msGraphGenerator.SaveGraph(outputFilename);
}
public IsotopicProfile GetDHIsotopicProfile2(TargetBase mt, double lowpeakCutoff, double fractionLabeling, double molarMixingofH)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
//int numNitrogens = mt.GetAtomCountForElement("N");
var numDeuterium = 0;
//_isotopicDistributionCalculator.SetLabeling("H", H_ISOTOPE_NUMBER, this.HLabelingAmount, D_ISOTOPE_NUMBER, this.DLabelingAmount);
var hydrogenTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
var deuteriumTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
HLabelingAmount = molarMixingofH;
DLabelingAmount = 1 - molarMixingofH;
//convert to floats
var labelingAmountFraction = Convert.ToSingle(fractionLabeling);
var HLabelingAmountMix = Convert.ToSingle(HLabelingAmount);
var DLabelingAmountMix = Convert.ToSingle(DLabelingAmount);
//initialization
float maxHeightForNormalization = 0;
if (hydrogenTheoreticalProfile.Peaklist.Count > 0)
{
maxHeightForNormalization = hydrogenTheoreticalProfile.Peaklist[0].Height * HLabelingAmountMix;
}
//add deuterated peaks as an offset index
for (var i = 0; i < hydrogenTheoreticalProfile.Peaklist.Count; i++)
{
var peakH = hydrogenTheoreticalProfile.Peaklist[i];
MSPeak peakD;
if (i == 0) //initial peak where there is no D contribution
{
peakD = new MSPeak(0);
}
else
{
peakD = deuteriumTheoreticalProfile.Peaklist[i - 1];
}
var contributionH = peakH.Height * HLabelingAmountMix;
var contributionD = (1 - labelingAmountFraction) * peakD.Height * DLabelingAmountMix + labelingAmountFraction * peakD.Height * DLabelingAmountMix;
peakH.Height = contributionH + contributionD;
//peakH.Height = peakH.Height + (1-Convert.ToSingle(fractionLabeling)) * peakD.Height +Convert.ToSingle(fractionLabeling) * peakD.Height;
//find true hightes peak in combined distribusion
if (peakH.Height > maxHeightForNormalization)
{
maxHeightForNormalization = peakH.Height;
}
}
//rename for clarity
var labeledTheoreticalProfile = hydrogenTheoreticalProfile;
//normalize to 1
foreach (var peak in labeledTheoreticalProfile.Peaklist)
{
peak.Height /= maxHeightForNormalization;
}
//should be good up to here
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheoreticalProfile, numDeuterium, mt.ChargeState);//Keep this as the H mass?
//_isotopicDistributionCalculator.ResetToUnlabeled();
PeakUtilities.TrimIsotopicProfile(labeledTheoreticalProfile, lowpeakCutoff);
labeledTheoreticalProfile.ChargeState = mt.ChargeState;
return(labeledTheoreticalProfile);
}
private void SetTarget(TargetBase target)
{
if (target != null)
{
GameManager.HandleHitID(target, ref CurrentTargetsID);
CurrentState = State.Moving;
Vector3 from = transform.position;
Vector3 to = target.transform.position;
Tweener.TweenDelegate[] easings = new Tweener.TweenDelegate[]{ Easing.Linear };
Tweener.TweenDelegate randomEasing = easings[Random.Range(0, easings.Length-1)];
tweener.easeFromTo(from, to, 0.5f, randomEasing, TargetNextTarget);
Debug.Log("AI CurrentTarget: " + target.id);
target.Activate();
}
else
{
CurrentState = State.Waiting;
Debug.Log("AI Waits for: " + CurrentTargetsID);
Invoke("SetAIDoneState", DoneWaitTime);
}
}
