Version 1.11

ChangeLog.md

@@ -1,3 +1,7 @@
+__Version 1.11__
+* Save motif to Peptide Array, OPAL and Peptide list forms
+* Direct link from analysis forms to the scorer
+
 __Version 1.10__
 * Amino acid letter images are saved as resource for better resolution and optimization
 * Improve visual color matrix

PeSA.Engine/Data Structures/Motif.cs

@@ -570,8 +570,8 @@ public Bitmap GetBarChart(int width)
         {
             int pepsize = 0;
             if (string.IsNullOrEmpty(WildTypePeptide))
-                pepsize = PosCaptions?.Count() ?? 0;
-            else
+                pepsize = PosCaptions?.Count() ?? PeptideLength;
+            else //if (!string.IsNullOrEmpty(WildTypePeptide))
                 pepsize = WildTypePeptide.Length;
 
             //Calculate size for each position
@@ -661,5 +661,31 @@ public Bitmap GetBarChart(int width)
             return bmp;
         }
 
+        /// <summary>
+        /// returns the key AA based on the key position
+        /// if WildTYpePeptide is set, it returns the aa of wildtype corresponding to that position
+        /// Otherwise it brings the most frequenet amino acid in the positive columns or frequencies
+        /// </summary>
+        /// <param name="keyPosition"></param>
+        /// 0-indexed
+        /// <returns></returns>
+        public char GetKeyChar(int keyPosition)
+        {
+            char keyAA = ' ';
+            if (keyPosition >= 0)
+            {
+                if (string.IsNullOrEmpty(WildTypePeptide))
+                {
+                    if (PositiveColumns != null && keyPosition < PositiveColumns.Count())//OPAL - wieght based motif with no wildtypepeptide
+                        keyAA = PositiveColumns[keyPosition].
+                            OrderByDescending(kv => kv.Value).Select(kv => kv.Key).FirstOrDefault();
+                    else if (Frequencies != null && keyPosition < Frequencies.Count())//frequency based peptide array, peptide list
+                        keyAA = Frequencies[keyPosition].OrderByDescending(kv => kv.Value).Select(kv => kv.Key).FirstOrDefault();
+                }
+                else if (keyPosition < WildTypePeptide.Length)
+                    keyAA = WildTypePeptide[keyPosition];
+            }
+            return keyAA;
+        }
     }
 }

PeSA.Engine/Data Structures/OPALArray.cs

@@ -27,6 +27,7 @@ public class OPALArray: BaseArray
         /// </summary>
         public string WildTypePeptide { get; set; }
 
+        public Motif Motif { get; set; }
         override protected void Upgrade(string mode)
         {
             base.Upgrade(mode);

PeSA.Engine/Properties/AssemblyInfo.cs

@@ -32,5 +32,5 @@
 // You can specify all the values or you can default the Build and Revision Numbers
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.10.*")]
-[assembly: AssemblyFileVersion("1.10.0.0")]
+[assembly: AssemblyVersion("1.11.*")]
+[assembly: AssemblyFileVersion("1.11.0.0")]

PeSA.Engine/Scorer.cs

@@ -8,8 +8,7 @@
 namespace PeSA.Engine
 {
     public class Scorer
-    {
-        public Motif Motif { get; set; }
+    {        public Motif Motif { get; set; }
         public List<Protein> ProteinList { get; set; }
         public List<string> PeptideList { get; set; }
         public List<Score> ScoreList { get; set; }
@@ -24,16 +23,17 @@ public class Scorer
         private int keyPosition = -1;
         /// <summary>
         /// Key position and character used in scoring
+        /// O-indexed
         /// </summary>
         public int KeyPosition
         {
             get { return keyPosition; }
             set
             {
-                if (value >= 0 && value < Motif.WildTypePeptide.Length)
+                if (value >= 0 && value < Motif.PeptideLength)
                 {
                     keyPosition = value;
-                    KeyChar = Motif.WildTypePeptide[keyPosition];
+                    KeyChar = Motif.GetKeyChar(keyPosition);
                 }
                 else
                 {
@@ -54,8 +54,8 @@ private Score GetScore(string peptide, string inputSegment, int startpos = 0)
                 {
                     char aa = inputSegment[pos - startpos];
                     if (aa == 'x' || aa == 'X') continue;
-                    Dictionary<char, double> posWeights = Motif.PositiveColumns[pos];
-                    Dictionary<char, double> negWeights = Motif.NegativeColumns[pos];
+                    Dictionary<char, double> posWeights = Motif.PositiveColumns?[pos]?? Motif.Frequencies[pos];
+                    Dictionary<char, double> negWeights = Motif.NegativeColumns?[pos];
                     if (posWeights.ContainsKey(aa))
                     {
                         if (UserEnteredPosThreshold != null && posWeights[aa] < UserEnteredPosThreshold)
@@ -64,7 +64,7 @@ private Score GetScore(string peptide, string inputSegment, int startpos = 0)
                         s.weightedMatch += posWeights[aa];
                         s.priorityMatch += posWeights[aa] / posWeights.Count;
                     }
-                    else if (negWeights.ContainsKey(aa))
+                    else if (negWeights!=null && negWeights.ContainsKey(aa))
                     {
                         if (UserEnteredNegThreshold != null && negWeights[aa] < UserEnteredNegThreshold)
                             continue;