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stefanks
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Merge pull request #278 from smith-chem-wisc/StefanBranch
Stefan branch
2 parents 54ce55d + 3a1a08f commit 1b1c261

33 files changed

+320
-304
lines changed

‎CMD/CMD.csproj‎

Lines changed: 24 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424
<DefineConstants>DEBUG;TRACE</DefineConstants>
2525
<ErrorReport>prompt</ErrorReport>
2626
<WarningLevel>4</WarningLevel>
27-
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
27+
<CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
2828
<LangVersion>6</LangVersion>
2929
</PropertyGroup>
3030
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
@@ -36,32 +36,33 @@
3636
<ErrorReport>prompt</ErrorReport>
3737
<WarningLevel>4</WarningLevel>
3838
<TreatWarningsAsErrors>true</TreatWarningsAsErrors>
39+
<LangVersion>6</LangVersion>
3940
</PropertyGroup>
4041
<ItemGroup>
41-
<Reference Include="Chemistry, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
42-
<HintPath>..\packages\mzLib.1.0.136\lib\Chemistry.dll</HintPath>
42+
<Reference Include="Chemistry, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
43+
<HintPath>..\packages\mzLib.1.0.138\lib\Chemistry.dll</HintPath>
4344
</Reference>
4445
<Reference Include="FluentCommandLineParser, Version=1.4.3.0, Culture=neutral, processorArchitecture=MSIL">
4546
<HintPath>..\packages\FluentCommandLineParser.1.4.3\lib\net35\FluentCommandLineParser.dll</HintPath>
4647
</Reference>
47-
<Reference Include="ManagedThermoHelperLayer, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
48-
<HintPath>..\packages\mzLib.1.0.136\lib\ManagedThermoHelperLayer.dll</HintPath>
48+
<Reference Include="ManagedThermoHelperLayer, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
49+
<HintPath>..\packages\mzLib.1.0.138\lib\ManagedThermoHelperLayer.dll</HintPath>
4950
</Reference>
50-
<Reference Include="MassSpectrometry, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
51-
<HintPath>..\packages\mzLib.1.0.136\lib\MassSpectrometry.dll</HintPath>
51+
<Reference Include="MassSpectrometry, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
52+
<HintPath>..\packages\mzLib.1.0.138\lib\MassSpectrometry.dll</HintPath>
5253
</Reference>
5354
<Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
5455
<HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
5556
<Private>True</Private>
5657
</Reference>
57-
<Reference Include="mzIdentML, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
58-
<HintPath>..\packages\mzLib.1.0.136\lib\mzIdentML.dll</HintPath>
58+
<Reference Include="mzIdentML, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
59+
<HintPath>..\packages\mzLib.1.0.138\lib\mzIdentML.dll</HintPath>
5960
</Reference>
60-
<Reference Include="MzLibUtil, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
61-
<HintPath>..\packages\mzLib.1.0.136\lib\MzLibUtil.dll</HintPath>
61+
<Reference Include="MzLibUtil, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
62+
<HintPath>..\packages\mzLib.1.0.138\lib\MzLibUtil.dll</HintPath>
6263
</Reference>
63-
<Reference Include="MzML, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
64-
<HintPath>..\packages\mzLib.1.0.136\lib\MzML.dll</HintPath>
64+
<Reference Include="MzML, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
65+
<HintPath>..\packages\mzLib.1.0.138\lib\MzML.dll</HintPath>
6566
</Reference>
6667
<Reference Include="NetSerializer, Version=4.1.0.0, Culture=neutral, processorArchitecture=MSIL">
6768
<HintPath>..\packages\NetSerializer.4.1.0\lib\net45\NetSerializer.dll</HintPath>
@@ -70,11 +71,11 @@
7071
<Reference Include="Nett, Version=0.6.0.0, Culture=neutral, processorArchitecture=MSIL">
7172
<HintPath>..\packages\Nett.0.6.2\lib\Net40\Nett.dll</HintPath>
7273
</Reference>
73-
<Reference Include="Proteomics, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
74-
<HintPath>..\packages\mzLib.1.0.136\lib\Proteomics.dll</HintPath>
74+
<Reference Include="Proteomics, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
75+
<HintPath>..\packages\mzLib.1.0.138\lib\Proteomics.dll</HintPath>
7576
</Reference>
76-
<Reference Include="Spectra, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
77-
<HintPath>..\packages\mzLib.1.0.136\lib\Spectra.dll</HintPath>
77+
<Reference Include="Spectra, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
78+
<HintPath>..\packages\mzLib.1.0.138\lib\Spectra.dll</HintPath>
7879
</Reference>
7980
<Reference Include="System" />
8081
<Reference Include="System.Core" />
@@ -85,11 +86,11 @@
8586
<Reference Include="System.Data" />
8687
<Reference Include="System.Net.Http" />
8788
<Reference Include="System.Xml" />
88-
<Reference Include="Thermo, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
89-
<HintPath>..\packages\mzLib.1.0.136\lib\Thermo.dll</HintPath>
89+
<Reference Include="Thermo, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
90+
<HintPath>..\packages\mzLib.1.0.138\lib\Thermo.dll</HintPath>
9091
</Reference>
91-
<Reference Include="UsefulProteomicsDatabases, Version=1.0.136.0, Culture=neutral, processorArchitecture=AMD64">
92-
<HintPath>..\packages\mzLib.1.0.136\lib\UsefulProteomicsDatabases.dll</HintPath>
92+
<Reference Include="UsefulProteomicsDatabases, Version=1.0.138.0, Culture=neutral, processorArchitecture=AMD64">
93+
<HintPath>..\packages\mzLib.1.0.138\lib\UsefulProteomicsDatabases.dll</HintPath>
9394
</Reference>
9495
<Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
9596
<HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
@@ -138,12 +139,12 @@
138139
<PreBuildEvent>
139140
</PreBuildEvent>
140141
</PropertyGroup>
141-
<Import Project="..\packages\mzLib.1.0.136\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.136\build\mzLib.targets')" />
142+
<Import Project="..\packages\mzLib.1.0.138\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.138\build\mzLib.targets')" />
142143
<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
143144
<PropertyGroup>
144145
<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
145146
</PropertyGroup>
146-
<Error Condition="!Exists('..\packages\mzLib.1.0.136\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.136\build\mzLib.targets'))" />
147+
<Error Condition="!Exists('..\packages\mzLib.1.0.138\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.138\build\mzLib.targets'))" />
147148
</Target>
148149
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
149150
Other similar extension points exist, see Microsoft.Common.targets.

‎CMD/packages.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
<packages>
33
<package id="FluentCommandLineParser" version="1.4.3" targetFramework="net451" />
44
<package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
5-
<package id="mzLib" version="1.0.136" targetFramework="net451" />
5+
<package id="mzLib" version="1.0.138" targetFramework="net451" />
66
<package id="NetSerializer" version="4.1.0" targetFramework="net451" />
77
<package id="Nett" version="0.6.2" targetFramework="net451" />
88
<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />

‎EngineLayer/Analysis/AnalysisEngine.cs‎

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
using MassSpectrometry;
1+
using Chemistry;
2+
using MassSpectrometry;
23
using MzLibUtil;
34
using Proteomics;
4-
using Chemistry;
55
using System;
66
using System.Collections.Concurrent;
77
using System.Collections.Generic;
@@ -114,8 +114,10 @@ public void ApplyProteinParsimony(out List<ProteinGroup> proteinGroups)
114114
{
115115
if (!proteinsWithUniquePeptides.ContainsKey(proteinListHere.First()))
116116
{
117-
var peptides = new HashSet<CompactPeptide>();
118-
peptides.Add(kvp.Key);
117+
var peptides = new HashSet<CompactPeptide>
118+
{
119+
kvp.Key
120+
};
119121
proteinsWithUniquePeptides.Add(proteinListHere.First(), peptides);
120122
}
121123
else
@@ -134,8 +136,10 @@ public void ApplyProteinParsimony(out List<ProteinGroup> proteinGroups)
134136
{
135137
if (!proteinToPeptidesMatching.ContainsKey(peptide.Protein))
136138
{
137-
var peptides = new HashSet<CompactPeptide>();
138-
peptides.Add(kvp.Key);
139+
var peptides = new HashSet<CompactPeptide>
140+
{
141+
kvp.Key
142+
};
139143
proteinToPeptidesMatching.Add(peptide.Protein, peptides);
140144
}
141145
else
@@ -614,7 +618,7 @@ public void RunQuantification(List<NewPsmWithFdr> psms, double rtTolerance, doub
614618

615619
if (isotopeDistributionCheck)
616620
{
617-
for(int i = 0; i < isotopes.Count; i++)
621+
for (int i = 0; i < isotopes.Count; i++)
618622
{
619623
if (isotopes[i].Value < 0.8)
620624
isotopePeaks[i] = null;

‎EngineLayer/Analysis/BinTreeStructure.cs‎

Lines changed: 20 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -59,7 +59,7 @@ internal void GenerateBins(List<NewPsmWithFdr> targetAndDecoyMatches, double dc)
5959
{
6060
// SIGMA IS THE DISTANCE TO THE CLOSEST MASS SHIFT THAT HAS A HIGHER P VALUE THAN ITSELF
6161

62-
sigma[i] = getSigma(thisMassShift, thisP, i, listOfMassShifts, p);
62+
sigma[i] = GetSigma(thisMassShift, thisP, i, listOfMassShifts, p);
6363
}
6464
}
6565

@@ -128,7 +128,7 @@ internal void GenerateBins(List<NewPsmWithFdr> targetAndDecoyMatches, double dc)
128128

129129
#region Private Methods
130130

131-
private static double getSigma(double thisMassShift, int thisP, int i, List<double> listOfMassShifts, int[] p)
131+
private static double GetSigma(double thisMassShift, int thisP, int i, List<double> listOfMassShifts, int[] p)
132132
{
133133
int currentDown = i - 1;
134134
int currentUp = i + 1;
@@ -378,25 +378,24 @@ private void IdentifyAA(double v)
378378

379379
private void IdentifyMine(double v)
380380
{
381-
var myInfos = new List<MyInfo>();
382-
myInfos.Add(new MyInfo(0, "Exact match!"));
383-
myInfos.Add(new MyInfo(-48.128629, "Phosphorylation-Lysine: Probably reverse is the correct match"));
384-
myInfos.Add(new MyInfo(-76.134779, "Phosphorylation-Arginine: Probably reverse is the correct match"));
385-
myInfos.Add(new MyInfo(1.0025, "1 MM"));
386-
myInfos.Add(new MyInfo(2.005, "2 MM"));
387-
myInfos.Add(new MyInfo(3.0075, "3 MM"));
388-
myInfos.Add(new MyInfo(173.051055, "Acetylation + Methionine: Usually on protein N terminus"));
389-
myInfos.Add(new MyInfo(-91.009185, "neg Carbamidomethylation - H2S: Usually on cysteine."));
390-
myInfos.Add(new MyInfo(-32.008456, "oxidation and then loss of oxidized M side chain"));
391-
myInfos.Add(new MyInfo(-79.966331, "neg Phosphorylation."));
392-
myInfos.Add(new MyInfo(189.045969, "Carboxymethylated + Methionine. Usually on protein N terminus"));
393-
myInfos.Add(new MyInfo(356.20596, "Lysine+V+E or Lysine+L+D"));
394-
myInfos.Add(new MyInfo(239.126988, "Lysine+H(5) C(5) N O(2), possibly Nmethylmaleimide"));
395-
myInfos.Add(new MyInfo(-105.02484, "Methionine loss then acetaldehyde"));
396-
myInfos.Add(new MyInfo(52.911464, "Fe[III]"));
397-
398-
399-
381+
var myInfos = new List<MyInfo>
382+
{
383+
new MyInfo(0, "Exact match!"),
384+
new MyInfo(-48.128629, "Phosphorylation-Lysine: Probably reverse is the correct match"),
385+
new MyInfo(-76.134779, "Phosphorylation-Arginine: Probably reverse is the correct match"),
386+
new MyInfo(1.0025, "1 MM"),
387+
new MyInfo(2.005, "2 MM"),
388+
new MyInfo(3.0075, "3 MM"),
389+
new MyInfo(173.051055, "Acetylation + Methionine: Usually on protein N terminus"),
390+
new MyInfo(-91.009185, "neg Carbamidomethylation - H2S: Usually on cysteine."),
391+
new MyInfo(-32.008456, "oxidation and then loss of oxidized M side chain"),
392+
new MyInfo(-79.966331, "neg Phosphorylation."),
393+
new MyInfo(189.045969, "Carboxymethylated + Methionine. Usually on protein N terminus"),
394+
new MyInfo(356.20596, "Lysine+V+E or Lysine+L+D"),
395+
new MyInfo(239.126988, "Lysine+H(5) C(5) N O(2), possibly Nmethylmaleimide"),
396+
new MyInfo(-105.02484, "Methionine loss then acetaldehyde"),
397+
new MyInfo(52.911464, "Fe[III]")
398+
};
400399
foreach (Bin bin in FinalBins)
401400
{
402401
bin.Mine = "";

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