[WIP] Peak alignment

.gitignore

@@ -250,3 +250,4 @@ ModelManifest.xml
 # Macintosh files
 **/.DS_Store
 
+/mzLib/TestFlashLFQ/XicTest.cs

mzLib/FlashLFQ/Alex project/Extremum.cs

@@ -0,0 +1,78 @@
+using MzLibUtil;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace FlashLFQ.Alex_project
+{
+
+    public enum ExtremumType { Minimum, Maximum }; //The spectra file the XIC came from
+
+    public class Extremum : IComparable<Extremum>, IEquatable<Extremum>
+    {
+        public readonly double Intensity;     //The aligned intensity of the Extremum point
+        public readonly double RetentionTime; //The interpolated intensity of the Extremum point
+        public readonly ExtremumType Type;    //The type of the Extremum point
+
+        public Extremum(double intensity, double retentionTime, ExtremumType type)
+        {
+            Intensity = intensity;
+            RetentionTime = retentionTime;
+            Type = type;
+        }
+
+
+
+
+        public int CompareTo(Extremum others)
+        {
+            if (others == null)
+            {
+                return 1;
+            }
+
+            if (this - others > 0)
+            {
+                return 1;
+            }
+
+            else if (this - others < 0)
+            {
+                return -1;
+            }
+
+            else 
+            {
+                return 0;
+            }
+
+        }
+
+        public bool Equals(Extremum others)
+        {
+            if (this.Intensity == others.Intensity && Math.Abs(this - others) < 0.006 && this.Type == others.Type)
+            {
+                return true;
+            }
+
+            return false;
+        }
+
+        public override bool Equals(Object obj)
+        {
+            return Equals(this, (Extremum)obj);
+        }
+
+        public static double operator - (Extremum extremun1, Extremum extrenum2)
+        {
+            double rtDiff = extremun1.RetentionTime - extrenum2.RetentionTime;
+            return rtDiff;
+        }
+
+
+
+
+    }
+}

mzLib/FlashLFQ/Alex project/ParallelSearch.cs

@@ -0,0 +1,136 @@
+using Easy.Common.Extensions;
+using SharpLearning.InputOutput.Csv;
+using System;
+using System.Collections.Generic;
+using System.Diagnostics;
+using System.Globalization;
+using System.Linq;
+using System.Runtime.CompilerServices;
+using System.Runtime.ExceptionServices;
+using System.Runtime.InteropServices;
+using System.Text;
+using System.Threading;
+using System.Threading.Tasks;
+using Plotly.NET;
+using Plotly.NET.CSharp;
+using Chart = Plotly.NET.CSharp.Chart;
+using GenericChartExtensions = Plotly.NET.CSharp.GenericChartExtensions;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using Plotly.NET.LayoutObjects;
+using Plotly.NET.TraceObjects;
+using System.ComponentModel;
+using System.Drawing;
+using Color = Plotly.NET.Color;
+
+
+
+namespace FlashLFQ.Alex_project
+{
+    public class ParallelSearch
+    {
+
+        readonly int threadNumber = Environment.ProcessorCount-1;
+        readonly int[] threads;
+        Dictionary<int, XIC> xicDict;
+        XICGroups[] xicGroups;
+
+        public ParallelSearch(Dictionary<int, XIC> xicDict)
+        {
+            threads = Enumerable.Range(0, threadNumber).ToArray();
+            this.xicDict = xicDict;
+            xicGroups = new XICGroups[threadNumber];
+        }
+
+        public void run()
+        {
+            Parallel.ForEach(threads, (currentThread) =>
+            {
+                List<XIC> xics = GroupedXIC(xicDict, currentThread);
+                if (xics.Count() != 0)
+                {
+                    xicGroups[currentThread] = new XICGroups(xics, 0.5, 0.1);
+                    draw(currentThread, xicGroups[currentThread]);
+                }              
+
+            });
+
+            Console.WriteLine("The total sum is ");
+
+        }
+
+        /// <summary>
+        /// Try to group the XICs from a Big XIC data set. If we met the reference XIC, we will build the XICGroups.
+        /// </summary>
+        /// <param name="xicDict"></param>
+        public static List<XIC> GroupedXIC(Dictionary<int, XIC> xicDict, int thread)
+        {
+            Dictionary<int, XIC> xicsToGroup = new Dictionary<int, XIC>();
+
+            lock (xicDict) 
+            {
+                foreach (var xic in xicDict)
+                {
+                    if (xic.Value.Reference == true && xicsToGroup.Where(p => p.Value.Reference).Count() > 0)
+                    {
+                        break;
+                    }
+
+                    else
+                    {
+                        xicsToGroup.Add(xic.Key, xic.Value);
+                        xicDict.Remove(xic.Key);
+                    }
+                }
+            }
+
+            return xicsToGroup.Select(p => p.Value).ToList();
+
+        }
+
+        public static void draw(int currentThread, XICGroups xicGroup)
+        {
+            XIC referenceXIC = xicGroup.reference;
+
+            var plotStack = Chart.Combine(
+                xicGroup.XICs.Select(xic =>
+                    Chart.Scatter<double, double, string>(
+                        xic.Ms1Peaks.Select(p => p.RetentionTime).ToArray(),
+                        xic.Ms1Peaks.Select(p => p.Intensity).ToArray(),
+                        StyleParam.Mode.Lines_Markers,
+                        Name: "No" + currentThread
+                    )
+                ).ToArray()
+
+          )
+          .WithTitle("XIC_differentTime")
+          .WithXAxisStyle<double, double, string>(Title: Title.init("Times"))
+          .WithYAxisStyle<double, double, string>(Title: Title.init("Intensities"))
+          .WithSize(1200, 400);
+
+
+            var plot_extrema = Chart.Combine(new[]
+             {
+                Chart.Scatter<double, double, string>(referenceXIC.Ms1Peaks.Select(P=>P.RetentionTime), referenceXIC.Ms1Peaks.Select(P=>P.Intensity),
+                StyleParam.Mode.Lines_Markers, MarkerSymbol: StyleParam.MarkerSymbol.Circle, Name: "refernece"),
+                Chart.Scatter<double, double, string>(xicGroup.ExtremaInRef.Select(p=> 
+                p.Key), xicGroup.ExtremaInRef.Select(p=> p.Value),
+                StyleParam.Mode.Markers, MarkerSymbol: StyleParam.MarkerSymbol.Star, Name: "shared Extrema").WithMarkerStyle(Size: 15),
+            })
+
+                 .WithTitle("XIC_sharedExtrema")
+                 .WithXAxisStyle<double, double, string>(Title: Title.init("Times"))
+                 .WithYAxisStyle<double, double, string>(Title: Title.init("Intensities"))
+                 .WithSize(1200, 400);
+
+
+            var stack = Chart.Grid(new[] { plotStack, plot_extrema }, 2, 1)
+                .WithSize(1200, 800);
+
+            GenericChartExtensions.Show(stack);
+
+        }
+
+    }
+}