public override string GetHTML(int deep = 0)
{
if (autofocus)
{
SetAttribute("autofocus", null);
}
if (disabled)
{
SetAttribute("disabled", null);
}
if (multiple)
{
SetAttribute("multiple", null);
}
if (required)
{
SetAttribute("required", null);
}
if (size > 0)
{
SetAttribute("size", size);
}
Childs.Clear();
Childs.AddRange(Options);
return(base.GetHTML(deep));
}
public void AddProperties(IEnumerable <NodeViewModel> properties)
{
foreach (var property in properties)
{
Childs.ElementAt(0).Childs.Add(property);
}
}
/// ///////////////////////////////////////
public override bool AddChild(I2iObjetGraphique child)
{
if (child is C2iWndDataGridColumn)
{
return(base.AddChild(child));
}
else
{
C2iWnd wnd = child as C2iWnd;
if (wnd != null)
{
if (wnd is IWndIncluableDansDataGrid)
{
wnd.AutoBackColor = false;
C2iWndDataGridColumn col = new C2iWndDataGridColumn();
col.Text = "col " + (Childs.Count() + 1);
col.Control = wnd;
base.AddChild(col);
col.ForeColor = DefaultColumnHeaderForeColor;
col.BackColor = DefaultColumnHeaderBackColor;
col.Parent = this;
return(true);
}
}
}
return(false);
}
public void Offset(float dx, float dy)
{
foreach (var f in Childs.OfType <IMoveable>())
{
f.Offset(dx, dy);
}
}
public Color4VM(string Name, Color4 Color) : base(Name, true)
{
var red = new JMXAttribute("Red", Color.Red);
var green = new JMXAttribute("Green", Color.Green);
var blue = new JMXAttribute("Blue", Color.Blue);
// Add nodes
Childs.Add(red);
Childs.Add(green);
Childs.Add(blue);
Childs.Add(new JMXAttribute("Alpha", Color.Alpha));
// Add handlers to update color brush
void OnColorChange(object s, PropertyChangedEventArgs e)
{
DemoBrush = new SolidColorBrush(new Color()
{
R = (byte)((float)red.Value * 255),
G = (byte)((float)green.Value * 255),
B = (byte)((float)blue.Value * 255),
A = 255
});
;
OnPropertyChanged(nameof(DemoBrush));
};
red.PropertyChanged += OnColorChange;
green.PropertyChanged += OnColorChange;
blue.PropertyChanged += OnColorChange;
// Update it
OnColorChange(null, null);
}
public ADLElement this[string key]
{
get
{
return(Childs.FirstOrDefault(row => row.Name == key));
}
}
public void Insert(LPOperator op)
{
op.Parent = this;
op.Function = Function;
op.Module = Module;
Childs.Add(op);
}
public TemplateNodeInfo CloneNotSavedTree(
Dictionary <TemplateNodeInfo, TemplateNodeInfo> originalsAndClones,
ConnectionData connectionData,
TemplateNodeInfo parent = null
)
{
TemplateNodeInfo clone = (TemplateNodeInfo)MemberwiseClone();
clone._templateNodeId = null;
clone.Parent = parent;
clone.Connection = connectionData;
clone.Childs = new List <TemplateNodeInfo>(
Childs.Select(
ch => ch.CloneNotSavedTree(
originalsAndClones,
connectionData,
clone
)
)
);
originalsAndClones.Add(this, clone);
return(clone);
}
public void UpdateChildren(NodeUpdatingSource mode, CancellationTokenSource cancellationSource)
{
if (IsDisabled)
{
mode = NodeUpdatingSource.LocallyOnly;
}
Debug.Assert(this.IsInstance);
IStorageManager vault = this._model.GetVaultProcessor(Connection.ConnectionGroup);
bool updated = false;
if (mode == NodeUpdatingSource.FromServerIfNotSavedLocally || mode == NodeUpdatingSource.LocallyOnly)
{
updated = vault.CurrentStorage.NodeInstances.TryLoadChildren(this);
}
if (updated || mode == NodeUpdatingSource.LocallyOnly)
{
return;
}
Childs.Clear();
Childs.AddRange(InstantiateStaticNodes(this.Template.Childs, Connection, this));
vault.CurrentStorage.NodeInstances.SaveChildren(this);
if (MayHaveDynamicChildren && Connection.IsLiveConnection)
{
UpdateDynamicChildren(cancellationSource.Token);
}
}
public ModDataSetVM(string Name, ModDataSet DataSet) : base(Name, true)
{
// Add new format
m_SupportedFormats.Add(typeof(IModData), (s, e) => {
e.Childs.Add(new ModDataVM("[" + e.Childs.Count + "]",
JMXAbstract.GetTypes(
typeof(ModDataMtrl),
typeof(ModDataTexAni),
typeof(ModDataMultiTex),
typeof(ModDataMultiTexRev),
typeof(ModDataParticle),
typeof(ModDataEnvMap),
typeof(ModDataBumpEnv),
typeof(ModDataSound),
typeof(ModDataDyVertex),
typeof(ModDataDyJoint),
typeof(ModDataDyLattice),
typeof(ModDataProgEquipPow)),
e.Obj?.GetType(), e.Obj));
});
// Create nodes
Childs.Add(new JMXAttribute("Type", DataSet.Type));
Childs.Add(new JMXOption("AnimationType", DataSet.AnimationType, JMXOption.GetValues <object>(typeof(PrimAnimationType))));
Childs.Add(new JMXAttribute("Name", DataSet.Name));
AddChildArray("ModsData", DataSet.ModData.ToArray(), true, true);
}
public FuncNode(string name, IList <MathFuncNode> args)
{
var lowercasename = name.ToLower();
if (args.Count >= 2)
{
KnownFuncType functionType;
if (KnownFunc.BinaryNamesFuncs.TryGetValue(lowercasename, out functionType))
{
FunctionType = functionType;
}
}
else if (args.Count == 1)
{
KnownFuncType functionType;
if (KnownFunc.UnaryNamesFuncs.TryGetValue(lowercasename, out functionType))
{
FunctionType = functionType;
}
else if (KnownFunc.BinaryNamesFuncs.TryGetValue(lowercasename, out functionType))
{
FunctionType = functionType;
}
}
Name = lowercasename;
foreach (var arg in args)
{
Childs.Add(arg);
}
if (FunctionType == KnownFuncType.Sqrt)
{
FunctionType = KnownFuncType.Pow;
Childs.Add(new ValueNode(new Rational <long>(1, 2)));
}
}
/// <summary>
/// This Methods is used to Generate the complete tree
/// </summary>
/// <param name="root"></param>
/// <returns></returns>
public ObjectTreeItem CreateTree(ObjectTreeItem root = null)
{
//if (treeItem == null)
//{
// return null;
//}
if (root == null)
{
root = this;
}
foreach (var child in CreateChildLayer())
{
if (child == null)
{
throw new NullReferenceException();
}
Childs.Add(child);
if (ReferenceEquals(child.Item, root.Item))
{
root.RecursionObjectTreeItems.Add(child);
}
else
{
child.CreateTree(root);
}
}
return(root);
}
/// <summary>
/// Child <see cref="IPanel.Closed"/> event handler.
/// </summary>
/// <param name="sender">Event sender.</param>
/// <param name="e">Event params.</param>
private void OnChildClose(object sender, EventArgs e)
{
var panel = sender as IPanel;
if (Childs.Contains(panel))
{
int panelIndex = Childs.IndexOf(panel);
Childs.Remove(panel);
if (Active == panel && Childs.Count > 0)
{
// Todo: Make this configurable - after child panel is closed, make next OR prev child panel active.
int newActiveIndex = panelIndex < Childs.Count
? panelIndex
: Childs.Count - 1;
Active = Childs[newActiveIndex];
}
}
if (Childs.Count == 0 && !isClosing)
{
active = null;
RequestClose();
}
}
/// <summary>
/// Add a (projected) Field
/// </summary>
/// <returns>Fluent <see cref="ProjectedFields"/></returns>
public ProjectedFields AddField(string name, string type, string list, string showField)
{
var field = new ProjectedField(name, type, list, showField);
Childs.Add(field);
return(this);
}
/// <summary>
/// Add a RowLimit to this View
/// </summary>
/// <param name="rowLimit"></param>
/// <returns></returns>
public View RowLimit(int rowLimit)
{
var child = new RowLimit(rowLimit);
Childs.Add(child);
return(this);
}
public override string GetHTML(int deep = 0)
{
if (string.IsNullOrEmpty(Select.Id_DOM))
{
if (!string.IsNullOrEmpty(Select.Name))
{
Select.Id_DOM = Select.Name;
}
else
{
Select.Id_DOM = Guid.NewGuid().ToString().Replace("-", "");
Select.Name_DOM = Select.Id_DOM;
}
}
Childs.Clear();
if (!(LabelSelectMenu is null))
{
LabelSelectMenu.@for = Select.Id_DOM;
Childs.Add(LabelSelectMenu);
}
if (!(SizeSelect is null))
{
Select.AddCSS("form-control-" + SizeSelect?.ToString("g"));
}
if (isCustomBootstrapSelect)
{
Select.AddCSS("custom-select");
}
Childs.Add(Select);
return(base.GetHTML(deep));
}
public override string GetHTML(int deep = 0)
{
/// <summary>
/// Вложеные элементы могут быть только source
/// </summary>
Childs = Childs.Where(x => x is source).ToList();
if (Childs.Count == 0)
{
SetAttribute("src", src);
}
if (autoplay)
{
SetAttribute("autoplay", "autoplay");
}
else
{
SetAttribute("preload", preload.ToString("g"));
}
if (controls)
{
SetAttribute("controls", "controls");
}
if (loop)
{
SetAttribute("loop", "loop");
}
return(base.GetHTML(deep));
}
/// <summary>
/// Add a <Where>-Tag
/// </summary>
/// <returns><see cref="Query"/></returns>
public Query Where(Action <Where> action)
{
var where = new Where();
action(where);
Childs.Add(where);
return(this);
}
public override string ToString()
{
StringBuilder sb = new StringBuilder("{");
sb.AppendFormat("Id={0}", Id ?? string.Empty);
if (Name != null)
{
sb.AppendFormat(", Name={0}", Name);
}
if (Parent != null)
{
sb.AppendFormat(", Parent={0}", Parent.Id);
}
if (Childs.Count != 0)
{
sb.AppendFormat(", Childs={0}", Childs.Select(x => x.Id).Sketch());
}
if (Countries.Count != 0)
{
sb.AppendFormat(", Countries={0}", Countries.Select(x => x.Id).Sketch());
}
if (RowVersion != null)
{
sb.AppendFormat(", RowVersion={0}", RowVersion.Sketch());
}
sb.Append("}"); return(sb.ToString());
}
public void RemoveDescendant(GroupInfo group)
{
if (group != null && Childs.Remove(group))
{
group.Parent = null;
}
}
public ImageBuilder DefineImage(string image = null)
{
var builder = new ImageBuilder(this).AsImageName(image);
Childs.Add(builder);
return(builder);
}
public ContainerBuilder UseContainer()
{
var builder = new ContainerBuilder(this);
Childs.Add(builder);
return(builder);
}
public CompositeBuilder UseCompose()
{
var builder = new CompositeBuilder(this);
Childs.Add(builder);
return(builder);
}
public override string GetHTML(int deep = 0)
{
////////////////////////////
// Вложеные элементы не предусмотрены
Childs.Clear();
return(base.GetHTML(deep));
}
public override void OnEnter()
{
PriorityIndex.Clear();
Children.Clear();
Children.AddRange(Childs.ToArray());
RandList.Clear();
PriorityList = new List <int>();
RepeatIntFieldDesigner repeatIntField = Node["Priority"].Field as RepeatIntFieldDesigner;
List <int> tempList = repeatIntField.Value;
if (Childs.Count == 1)
{
Status = DebugNodeStatus.Error;
return;
}
if (tempList.Count != Childs.Count)
{
Status = DebugNodeStatus.Error;
return;
}
PriorityList.AddRange(tempList.ToArray());
RateSortChildren();
}
public void AddNode <T>(T node) where T : INode
{
if (Childs != null)
{
Childs.Add(node);
}
}
public VolumeBuilder UseVolume(string name = null)
{
var builder = new VolumeBuilder(this, name);
Childs.Add(builder);
return(builder);
}
public NetworkBuilder UseNetwork(string name = null)
{
var builder = new NetworkBuilder(this, name);
Childs.Add(builder);
return(builder);
}
public RemoteSshHostBuilder UseSsh(string ipAddress = null)
{
var builder = new RemoteSshHostBuilder(this, ipAddress);
Childs.Add(builder);
return(builder);
}
public override string GetHTML(int deep = 0)
{
AddCSS("form-group " + ClassInputGroup, true);
if (!(LabelInput is null))
{
Childs.Add(LabelInput);
}
Childs.Add(Input);
if (Input.required)
{
Childs.AddRange(GetValidationAlerts(Input.Name));
}
if (!string.IsNullOrEmpty(InputInfoFooter))
{
string input_info_id = Input.Name + "Help";
using (small info_text = new small(InputInfoFooter)
{
inline = true, Id_DOM = input_info_id
})
{
info_text.AddCSS("form-text text-muted", true);
Childs.Add(info_text);
}
Input.SetAttribute("aria-describedby", input_info_id);
}
return(base.GetHTML(deep));
}
static int Main(string[] args)
{
//Параметры соответствуют вводу в форму RawtoMGF
//args[0] - имя Raw-файла
//args[1] - имя MGF-файла
//args[2] - minimal MZ
//args[3] - maximal MZ
//args[4] - minimal RT
//args[5] - maximal RT
//args[6] - minimal Charge
//args[7] - maximal Charge
//args[8] - number of top peaks
//args[9] - CleanETD:yes / CleanETD:no
//args[10] - Instrument:yes / Instrument:no
//дополнительно (к версии 2.0.6)
//args[11] - CheckSpectra:yes / CheckSpectra:no
try{
Console.ReadLine();
//Thread.Sleep(30000);
string InFileName = args[0];
string OutFileName = args[1];
double MinMZ = Convert.ToDouble(args[2]);
double MaxMZ = Convert.ToDouble(args[3]);
double MinRT = Convert.ToDouble(args[4]);
double MaxRT = Convert.ToDouble(args[5]);
int MinCharge = Convert.ToInt32(args[6]);
int MaxCharge = Convert.ToInt32(args[7]);
int MaxPeakNumber = Convert.ToInt32(args[8]);
bool CleanETD = args[9].Contains("CleanETD:yes");
bool MarkInstrtument = args[10].Contains("Instrument:yes");
bool CheckSpectra = args[11].Contains("CheckSpectra:yes");
bool RTApex = args[12].Contains("RTApex:yes");
string[] Refs = {"@cid","@hcd","@etd","@ecd","FTMS","ITMS"};
MSFileReader_XRawfile RawFile;
int Spectra,LocalCount = 0;
string Filter;
MGFFile MGF;
MGFSpectrum ms;
Childs ch;
ChildbyIntensity ci = new ChildbyIntensity();
ChildbyMass cm = new ChildbyMass();
int ArraySize = 0;
Object MassList, EmptyRef;
Object Labels,Values;
double temp=0.0;
int Progress = 0;
int MSCount = 0;
int MSMSCount = 0;
if (RTApex){
MSFileBox = new RawFileBox();
MSFileBox.LoadIndex(InFileName);
RawFileBox.RepProgress = RepProgress;
RawFile = MSFileBox.RawFile;
}else{
RawFile = new MSFileReader_XRawfile();
RawFile.Open(InFileName);
RawFile.SetCurrentController(0, 1);
}
Spectra = 0;
RawFile.GetNumSpectra(ref Spectra);
if (Spectra == 0) {
throw new Exception("Cannot get spectra from the file "+InFileName+", File is invalid, broken or empty");
}
MGF = new MGFFile();
for (int j=1 ; j<=Spectra ; j++){
Filter = null;
RawFile.GetFilterForScanNum(j, ref Filter);
if (Filter.IndexOf("ms2") == -1) {
MSCount++;
if (!CheckSpectra){
continue;
}else{
ArraySize = 0;
MassList = null;
EmptyRef=null;
temp=0.0;
try {
RawFile.GetMassListFromScanNum(ref j, null, 0, 0, 0, 0,
ref temp, ref MassList, ref EmptyRef, ref ArraySize);
continue;
}catch{
Exception e = new Exception(string.Format("Scan #{0} cannot be loaded, probably RAW file is corrupted!",j));
throw e;
}
}
}
MSMSCount++;
ms = new MGFSpectrum();
//определяем родительскую массу, заряд и RT
Labels = null;
Values = null;
ArraySize = 0;
LocalCount++;
RawFile.GetTrailerExtraForScanNum(j, ref Labels, ref Values, ref ArraySize);
for (int k = 0 ; k < ArraySize ; k++ ){
if ((Labels as Array).GetValue(k).ToString().Contains("Mono")){
ms.mz = Convert.ToDouble((Values as Array).GetValue(k).ToString());
}
if ((Labels as Array).GetValue(k).ToString().Contains("Charge State")){
ms.Charge = Convert.ToInt32((Values as Array).GetValue(k).ToString());
}
}
//Если не нашли в labels - берем из фильтра
if (ms.mz == 0.0) {
string part= Filter.Substring(0,Filter.IndexOf('@'));
ms.mz = Convert.ToDouble(part.Substring(part.LastIndexOf(' ')));
}
Labels = null;
Values = null;
ArraySize = 0;
double RT = 0;
RawFile.GetStatusLogForScanNum(j,ref RT, ref Labels, ref Values, ref ArraySize);
RawFile.RTFromScanNum(j,ref ms.RT);
ms.ScanNumber = j;
//Фильтры
if (ms.Charge < MinCharge) continue;
if (ms.Charge > MaxCharge) continue;
if (ms.RT < MinRT) continue;
if (MaxRT != 0.0 && ms.RT > MaxRT) continue;
if (ms.mz < MinMZ) continue;
if (MaxMZ != 0.0 && ms.mz > MaxMZ) continue;
//забираем сам спектр
MassList = null;
EmptyRef=null;
ArraySize = 0;
temp=0.0;
try{
if (Filter.IndexOf("FTMS") != -1){
//извлекаем FTMS данные
(RawFile as IXRawfile2).GetLabelData(ref MassList, ref EmptyRef, ref j);
ArraySize = (MassList as Array).GetLength(1);
for (int k = 0 ; k<ArraySize ; k++ ){
ch = new Childs();
ch.Mass = (double)(MassList as Array).GetValue(0, k);
ch.Intensity = (double)(MassList as Array).GetValue(1, k);
ms.Data.Add(ch);
}
}else{
//извлекаем ITMS данные
RawFile.GetMassListFromScanNum(ref j, null, 0, 0, 0, 1, ref temp, ref MassList, ref EmptyRef, ref ArraySize);
ArraySize = (MassList as Array).GetLength(1);
for ( int k = 0 ; k<ArraySize ; k++){
ch = new Childs();
ch.Mass = (double)(MassList as Array).GetValue(0, k);
ch.Intensity = (double)(MassList as Array).GetValue(1, k);
ms.Data.Add(ch);
}
}
}catch{
Exception e = new Exception(string.Format("Scan #{0} cannot be loaded, probably RAW file is corrupted!",j));
throw e;
}
if (RTApex){
ms.RTApex = CheckRTApex(ms.RT, ms.mz);
}
if (MarkInstrtument){
if (Filter.Contains("ecd") || Filter.Contains("etd")){
ms.Instrument = "ETD-TRAP";
}else{
ms.Instrument= "ESI-FTICR";
}
}
//очистить ETD если был такой запрос
if ( CleanETD ){
if (Filter.Contains("ecd") || Filter.Contains("etd")){
FilterETD(ref ms, Filter.Contains("FTMS"));
}
}
//сбросить лишние сигналы
if (MaxPeakNumber > 0 && ms.Data.Count > MaxPeakNumber){
ms.Data.Sort(ci);
ms.Data.RemoveRange(0,ms.Data.Count-MaxPeakNumber);
ms.Data.Sort(cm);
}
//сформировать TITLE
if (RTApex){
ms.Title = String.Format("Elution from: {0:f4} to {0:f4} RT Apex: {1:f2} FinneganScanNumber: {2}",
ms.RT, ms.RTApex, ms.ScanNumber);
}else{
ms.Title = String.Format("Elution from: {0:f4} to {0:f4} FinneganScanNumber: {1}",
ms.RT,ms.ScanNumber);
}
MGF.Spectra.Add(ms);
// рапортовать прогресс
GC.Collect(2);
if ((int)(((double)j/(double)Spectra)*100.0) > Progress){
Progress = (int)(((double)j/(double)Spectra)*100.0);
Console.WriteLine("{0}%... {1} {2}",Progress,MSCount,MSMSCount);
}
//backgroundWorker1.ReportProgress((int)(((double)LocalCount/(double)SpCount)*100.0));
}
MGF.MGFComments.Add(String.Format("Created by RawToMGF 2.1.3; Spectra obtained from {0}",InFileName));
MGF.MGFComments.Add(String.Format("Filters: Parent m/z from {0} Th to {1} Th;",MinMZ,MaxMZ));
MGF.MGFComments.Add(String.Format(" RT from {0} min. to {1} min.;",MinRT,MaxRT));
MGF.MGFComments.Add(String.Format(" Charge state of parent ions minimum {0}, maximum {1};",MinCharge,MaxCharge));
MGF.MGFComments.Add(String.Format(" Max number of peaks in MS/MS spectra - {0}",MaxPeakNumber));
if ( CleanETD ) {
MGF.MGFComments.Add(" ETD spectra cleaned from precursors and neutral losses");
}
MGF.MGFWrite(OutFileName,true);
}catch(Exception e){
Console.Write("Error:");
Console.Write(e.Message);
Console.WriteLine("STACKINFO:"+e.StackTrace);
//Console.ReadKey();
return 1;
}
Console.WriteLine("Completed");
Console.ReadLine();
return 0;
}
