From 74ae37dbc6810e48ea01d137793d2297ed3d39bf Mon Sep 17 00:00:00 2001
From: stefanks <solntsev@gmail.com>
Date: Tue, 17 Oct 2017 14:38:36 -0500
Subject: [PATCH] Fix decon (#260)

* Ordinal

* noice

* Aaha

* fix
---
 MS2decon/Program.cs                                |  3 ++-
 .../DeconvolutionFeatureWithMassesAndScans.cs      | 14 +++++++++-----
 MassSpectrometry/MsDataFile.cs                     |  3 ++-
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/MS2decon/Program.cs b/MS2decon/Program.cs
index c1ff8e9b4..5bfdf2768 100644
--- a/MS2decon/Program.cs
+++ b/MS2decon/Program.cs
@@ -2,6 +2,7 @@
 using IO.MzML;
 using IO.Thermo;
 using MassSpectrometry;
+using MzLibUtil;
 using System;
 using System.Collections.Generic;
 using System.Globalization;
@@ -62,7 +63,7 @@ private static void Main(string[] args)
                     {
                         if ((!p.Object.MinScan.HasValue || ok.OneBasedScanNumber >= p.Object.MinScan) && (!p.Object.MaxScan.HasValue || ok.OneBasedScanNumber <= p.Object.MaxScan))
                         {
-                            var hmm = ok.MassSpectrum.Deconvolute(ok.ScanWindowRange, p.Object.MaxAssumedChargeState, p.Object.DeconvolutionTolerancePpm, p.Object.IntensityRatioLimit).ToList();
+                            var hmm = ok.MassSpectrum.Deconvolute(new MzRange(0, double.PositiveInfinity), p.Object.MaxAssumedChargeState, p.Object.DeconvolutionTolerancePpm, p.Object.IntensityRatioLimit).ToList();
 
                             List<DeconvolutionFeatureWithMassesAndScans> currentListOfGroups = new List<DeconvolutionFeatureWithMassesAndScans>();
 
diff --git a/MassSpectrometry/DeconvolutionFeatureWithMassesAndScans.cs b/MassSpectrometry/DeconvolutionFeatureWithMassesAndScans.cs
index 81f27b96c..c3c86271b 100644
--- a/MassSpectrometry/DeconvolutionFeatureWithMassesAndScans.cs
+++ b/MassSpectrometry/DeconvolutionFeatureWithMassesAndScans.cs
@@ -80,18 +80,22 @@ public void AddEnvelope(IsotopicEnvelope isotopicEnvelope, int scanIndex, double
             MaxScanIndex = Math.Max(scanIndex, MaxScanIndex);
             MinElutionTime = Math.Min(elutionTime, MinElutionTime);
             MaxElutionTime = Math.Max(elutionTime, MaxElutionTime);
+            bool added = false;
             foreach (var massGroup in groups)
             {
                 if (Math.Abs(massGroup.Mass - isotopicEnvelope.monoisotopicMass) < 0.5)
                 {
                     massGroup.AddEnvelope(isotopicEnvelope);
-                    Mass = groups.OrderBy(b => -b.NumPeaks).First().Mass;
-                    return;
+                    added = true;
+                    break;
                 }
             }
-            var newMassGroup = new DeconvolutionFeature();
-            newMassGroup.AddEnvelope(isotopicEnvelope);
-            groups.Add(newMassGroup);
+            if (!added)
+            {
+                var newMassGroup = new DeconvolutionFeature();
+                newMassGroup.AddEnvelope(isotopicEnvelope);
+                groups.Add(newMassGroup);
+            }
 
             Mass = groups.OrderBy(b => -b.NumPeaks).First().Mass;
             TotalIntensity += isotopicEnvelope.peaks.Sum(b => b.Item2);
diff --git a/MassSpectrometry/MsDataFile.cs b/MassSpectrometry/MsDataFile.cs
index 1170ab041..eae022593 100644
--- a/MassSpectrometry/MsDataFile.cs
+++ b/MassSpectrometry/MsDataFile.cs
@@ -16,6 +16,7 @@
 // You should have received a copy of the GNU Lesser General Public
 // License along with MassSpectrometry. If not, see <http://www.gnu.org/licenses/>.
 
+using MzLibUtil;
 using System;
 using System.Collections;
 using System.Collections.Concurrent;
@@ -141,7 +142,7 @@ public IEnumerable<DeconvolutionFeatureWithMassesAndScans> Deconvolute(int? minS
                 {
                     var theScan = GetOneBasedScan(scanIndex);
                     if (scanFilterFunc(theScan))
-                        allAggregateGroups[scanIndex - minScan.Value] = theScan.MassSpectrum.Deconvolute(theScan.ScanWindowRange, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatioLimit).ToList();
+                        allAggregateGroups[scanIndex - minScan.Value] = theScan.MassSpectrum.Deconvolute(new MzRange(0, double.PositiveInfinity), maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatioLimit).ToList();
                 }
             });