From 4d02c66710f63c6793dc891689f5220ce7575a49 Mon Sep 17 00:00:00 2001
From: RACHEL M MILLER <rmmiller22@wisc.edu>
Date: Mon, 16 Nov 2020 17:44:30 -0600
Subject: [PATCH 1/5] Include proteins that have no peptides based on
 proteolytic digestion

---
 Tasks/DigestionTask.cs | 6 +++++-
 Tasks/MyTaskResults.cs | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/Tasks/DigestionTask.cs b/Tasks/DigestionTask.cs
index 38926d9..dda1ee5 100644
--- a/Tasks/DigestionTask.cs
+++ b/Tasks/DigestionTask.cs
@@ -131,7 +131,7 @@ protected Dictionary<Protein, List<PeptideWithSetModifications>> DigestDatabase(
             Dictionary<Protein, List<PeptideWithSetModifications>> peptidesForProtein = new Dictionary<Protein, List<PeptideWithSetModifications>>(proteinsFromDatabase.Count);
             foreach (var protein in proteinsFromDatabase)
             {
-                List<PeptideWithSetModifications> peptides = protein.Digest(dp, new List<Modification> { }, new List<Modification> { }).ToList();
+                List<PeptideWithSetModifications> peptides = protein.Digest(dp, new List<Modification> { }, new List<Modification> { }).ToList();                
                 peptidesForProtein.Add(protein, peptides);
             }
             return peptidesForProtein;
@@ -228,6 +228,10 @@ Dictionary<Protein, List<InSilicoPep>> DeterminePeptideStatus(string databaseNam
                     }
                 }
             }
+            foreach (var protein in databasePeptides.Keys.Where(p => inSilicoPeptides.ContainsKey(p) == false))
+            {
+                inSilicoPeptides.Add(protein, new List<InSilicoPep>());
+            }
             databasePeptides = null;
             return inSilicoPeptides;
         }
diff --git a/Tasks/MyTaskResults.cs b/Tasks/MyTaskResults.cs
index be0e27a..39c7f2e 100644
--- a/Tasks/MyTaskResults.cs
+++ b/Tasks/MyTaskResults.cs
@@ -118,7 +118,7 @@ private List<string> writeSummary(Dictionary<string, Dictionary<string, Dictiona
                     {
                         string prot = protease.Key;
                        summary.Add("    "+prot + " Results:");
-                        var allPeptides = protease.Value.SelectMany(p => p.Value);
+                        var allPeptides = protease.Value.SelectMany(p => p.Value);                        
                         if (parameters.TreatModifiedPeptidesAsDifferent)
                         {
                             summary.Add("       Number of Peptides: " + allPeptides.Count());

From 229f45d76b74a2f1a7f7306e5040d2b4e1e1933f Mon Sep 17 00:00:00 2001
From: RACHEL M MILLER <rmmiller22@wisc.edu>
Date: Mon, 16 Nov 2020 17:49:18 -0600
Subject: [PATCH 2/5] version update

---
 Engine/GlobalVariables.cs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Engine/GlobalVariables.cs b/Engine/GlobalVariables.cs
index e29aa66..5de7ee5 100644
--- a/Engine/GlobalVariables.cs
+++ b/Engine/GlobalVariables.cs
@@ -32,7 +32,7 @@ static GlobalVariables()
 #if DEBUG
                 ProteaseGuruVersion = "Not a release version. DEBUG.";
 #else
-                ProteaseGuruVersion = "0.0.14";
+                ProteaseGuruVersion = "0.0.15";
 #endif
             }
             else

From a30b7f7ba2233f772c8505e126025610d047ec4d Mon Sep 17 00:00:00 2001
From: RACHEL M MILLER <rmmiller22@wisc.edu>
Date: Mon, 16 Nov 2020 18:02:04 -0600
Subject: [PATCH 3/5] json file appveyor issue

---
 global.json | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 global.json

diff --git a/global.json b/global.json
new file mode 100644
index 0000000..6156170
--- /dev/null
+++ b/global.json
@@ -0,0 +1,6 @@
+{
+  "sdk": {
+    "version": "3.1.102",
+    "rollForward": "latestFeature"
+  }
+}
\ No newline at end of file

From 10ebfd83e32345f5ec92b6aead279ceb1ca818fc Mon Sep 17 00:00:00 2001
From: rmmiller22 <30324061+rmmiller22@users.noreply.github.com>
Date: Mon, 16 Nov 2020 18:04:48 -0600
Subject: [PATCH 4/5] Delete global.json

---
 global.json | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 global.json

diff --git a/global.json b/global.json
deleted file mode 100644
index 6156170..0000000
--- a/global.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "sdk": {
-    "version": "3.1.102",
-    "rollForward": "latestFeature"
-  }
-}
\ No newline at end of file

From 97a1e5b7fa92f9a902114ed2cc1ec1a0e4467137 Mon Sep 17 00:00:00 2001
From: rmmiller22 <30324061+rmmiller22@users.noreply.github.com>
Date: Mon, 16 Nov 2020 18:06:44 -0600
Subject: [PATCH 5/5] Reload global.json

---
 global.json | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 global.json

diff --git a/global.json b/global.json
new file mode 100644
index 0000000..1e16307
--- /dev/null
+++ b/global.json
@@ -0,0 +1,6 @@
+{
+  "sdk": {
+    "version": "3.1.102",
+    "rollForward": "latestFeature"
+  }
+}
\ No newline at end of file