Version 2.0

3rd Party Licenses.md

@@ -0,0 +1,10 @@
+PeSA uses some 3rd part tools. Corresponding licences are below:
+
+**EPPlus**
+https://github.com/JanKallman/EPPlus
+https://www.nuget.org/packages/EPPlus/4.5.3.3/license
+
+**Newtonsoft.Json**
+https://www.newtonsoft.com/json
+https://licenses.nuget.org/MIT
+

ChangeLog.md

@@ -1,3 +1,6 @@
+__Version 2.0__
+* Migration to .NET Core
+
 __Version 1.11__
 * Save motif to Peptide Array, OPAL and Peptide list forms
 * Direct link from analysis forms to the scorer

PeSA 2.0.sln

@@ -0,0 +1,41 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.1.32328.378
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Folder", "Solution Folder", "{82F43E6D-03E7-4BD7-B720-51A3AA707BC8}"
+	ProjectSection(SolutionItems) = preProject
+		.gitignore = .gitignore
+		3rd Party Licenses.md = 3rd Party Licenses.md
+		ChangeLog.md = ChangeLog.md
+		LICENSE = LICENSE
+		README.md = README.md
+		Todo.txt = Todo.txt
+	EndProjectSection
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "PeSA.Engine", "PeSA.Engine\PeSA.Engine.csproj", "{FA69AFC7-7CCD-4B4B-8EC3-6069AA3FBCD2}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "PeSA.Windows", "PeSA.Windows\PeSA.Windows.csproj", "{90FDDF6C-1CED-4BAE-977D-F6278C544EAF}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{FA69AFC7-7CCD-4B4B-8EC3-6069AA3FBCD2}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{FA69AFC7-7CCD-4B4B-8EC3-6069AA3FBCD2}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{FA69AFC7-7CCD-4B4B-8EC3-6069AA3FBCD2}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{FA69AFC7-7CCD-4B4B-8EC3-6069AA3FBCD2}.Release|Any CPU.Build.0 = Release|Any CPU
+		{90FDDF6C-1CED-4BAE-977D-F6278C544EAF}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{90FDDF6C-1CED-4BAE-977D-F6278C544EAF}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{90FDDF6C-1CED-4BAE-977D-F6278C544EAF}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{90FDDF6C-1CED-4BAE-977D-F6278C544EAF}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {F761AF67-2D69-4BC6-A7F3-F92F89BB29CD}
+	EndGlobalSection
+EndGlobal

PeSA.Engine/Data Structures/Motif.cs

@@ -1,10 +1,5 @@
 using Newtonsoft.Json;
-using System;
-using System.Collections.Generic;
 using System.Drawing;
-using System.IO;
-using System.Linq;
-using System.Windows.Forms.DataVisualization.Charting;
 
 namespace PeSA.Engine
 {
@@ -139,6 +134,8 @@ private void AddColumnValue(Dictionary<int, Dictionary<char, List<double>>> _Col
 
         public Dictionary<int, Dictionary<char, double>> GetScaledColumns(Dictionary<int, Dictionary<char, double>> _Columns)
         {
+            if (_Columns == null || !_Columns.Any())
+                return null;
             Dictionary<int, Dictionary<char, double>> scaled = new Dictionary<int, Dictionary<char, double>>();
             Dictionary<int, double> totalWeightsPerPos = new Dictionary<int, double>();
             foreach (int pos in _Columns.Keys)
@@ -433,6 +430,8 @@ private Bitmap GetLetterImage(Char c, int width, int height, Color color)
             int width, int height, int positionSpacing = 10, int letterSpacing = 3, 
             Color? defColor = null)
         {
+            if (Columns == null || !Columns.Any())
+                return null;
             Settings settings = Settings.Load("default.settings");
 
             int maxAAperCol = settings.MotifMaxAAPerColumn;
@@ -568,7 +567,9 @@ public Bitmap GetFrequencyMotif(int widthImage, int heightImage)
 
         public Bitmap GetBarChart(int width)
         {
-            int pepsize = 0;
+            if (PositiveColumns == null || NegativeColumns == null)
+                return null;
+            int pepsize;
             if (string.IsNullOrEmpty(WildTypePeptide))
                 pepsize = PosCaptions?.Count() ?? PeptideLength;
             else //if (!string.IsNullOrEmpty(WildTypePeptide))

PeSA.Engine/Data Structures/OPALArray.cs

@@ -229,12 +229,13 @@ public static void CheckPermutationAxis(string[,] values, ref bool xPossible, re
             for (int iRow = 1; iRow <= rowCount; iRow++)
             {
                 string s = values[iRow, 0].Trim();
-                if (aaList.Contains(s[0]))
+                char aa = s.Length > 0 ? s[0] : ' ';
+                if (aaList.Contains(aa))
                 {
                     yPossible = false;
                     break;
                 }
-                aaList.Add(s[0]);
+                aaList.Add(aa);
             }
         }
 

PeSA.Engine/Data Structures/Score.cs

@@ -1,12 +1,4 @@
-using Newtonsoft.Json;
-using System;
-using System.Collections.Generic;
-using System.Drawing;
-using System.IO;
-using System.Linq;
-using System.Windows.Forms.DataVisualization.Charting;
-
-namespace PeSA.Engine
+namespace PeSA.Engine
 {
     public class Score
     {

PeSA.Engine/Helpers/MatrixUtil.cs

@@ -1,10 +1,4 @@
-using System;
-using System.Collections.Generic;
-using System.IO;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using System.Windows.Forms;
+using System.Text;
 using System.Xml.Linq;
 
 namespace PeSA.Engine
@@ -83,13 +77,12 @@ public static double GetMaxValue(double[,] matrix, int rowind = -1, int colind =
             return maxval;
         }
 
-        public static string[,] ClipboardToMatrix()
+        public static string[,] ClipboardToMatrix(MemoryStream stream)
         {
             try
             {
-                var dataObject = Clipboard.GetDataObject();
                 string[,] matrix = null;
-                using (var stream = (MemoryStream)dataObject.GetData("XML Spreadsheet"))
+                using (stream)
                 {
                     var xml = Encoding.UTF8.GetString(stream.ToArray());
                     xml = xml.Substring(0, xml.Length - 1);