Merge pull request #223 from smith-chem-wisc/StefanBranch

stefanks · web-flow · commit c6e8598b99ae · 2017-02-16T09:44:09.000-06:00
calib and other
diff --git a/EngineLayer/Indexing/IndexingResults.cs b/EngineLayer/Indexing/IndexingResults.cs
@@ -5,6 +5,7 @@ namespace EngineLayer.Indexing
 {
     public class IndexingResults : MyResults
     {
+
         #region Public Constructors
 
         public IndexingResults(List<CompactPeptide> peptideIndex, Dictionary<float, List<int>> fragmentIndexDict, IndexingEngine indexParams) : base(indexParams)
@@ -22,17 +23,18 @@ public IndexingResults(List<CompactPeptide> peptideIndex, Dictionary<float, List
 
         #endregion Public Properties
 
-        #region Protected Properties
+        #region Public Methods
 
         public override string ToString()
         {
             var sb = new StringBuilder();
-            sb.AppendLine(base.ToString());
+            sb.Append(base.ToString());
             sb.AppendLine("\t\tfragmentIndexDict.Count: " + FragmentIndexDict.Count);
-            sb.Append("\t\tpeptideIndex.Count: " + PeptideIndex.Count);
+            sb.AppendLine("\t\tpeptideIndex.Count: " + PeptideIndex.Count);
             return sb.ToString();
         }
 
-        #endregion Protected Properties
+        #endregion Public Methods
+
     }
 }
diff --git a/EngineLayer/ModernSearch/ModernSearchResults.cs b/EngineLayer/ModernSearch/ModernSearchResults.cs
@@ -21,15 +21,16 @@ public ModernSearchResults(List<PsmModern>[] newPsms, ModernSearchEngine s) : ba
 
         #endregion Public Properties
 
-        #region Protected Properties
+        #region Public Methods
 
         public override string ToString()
         {
             var sb = new StringBuilder();
-            sb.AppendLine(base.ToString());
+            sb.Append(base.ToString());
             return sb.ToString();
         }
-        #endregion Protected Properties
+
+        #endregion Public Methods
 
     }
 }
diff --git a/EngineLayer/MyEngine.cs b/EngineLayer/MyEngine.cs
@@ -134,6 +134,59 @@ private static IEnumerable<SearchMode> LoadSearchModesFromFile()
             yield return new OpenSearchMode();
             yield return new IntervalSearchMode(new List<DoubleRange> { new DoubleRange(-0.005, 0.005), new DoubleRange(21.981943 - 0.005, 21.981943 + 0.005) });
             yield return new IntervalSearchMode(new List<DoubleRange> { new DoubleRange(-187, double.PositiveInfinity) });
+            foreach (var sm in GetResidueInclusionExclusionSearchModes(new DoubleRange(-187, double.PositiveInfinity), 0.0075))
+                yield return sm;
+        }
+
+        /// <summary>
+        /// Ideally v is less than 0.00168565165, so no overlaps happen
+        /// </summary>
+        /// <param name="doubleRange"></param>
+        /// <param name="v"></param>
+        /// <returns></returns>
+        private static IEnumerable<SearchMode> GetResidueInclusionExclusionSearchModes(DoubleRange doubleRange, double v)
+        {
+            List<double> massesToExclude = new List<double>();
+            for (char c = 'A'; c <= 'Z'; c++)
+            {
+                Residue residue;
+                if (Residue.TryGetResidue(c, out residue))
+                {
+                    massesToExclude.Add(residue.MonoisotopicMass);
+                    massesToExclude.Add(-residue.MonoisotopicMass);
+                    for (char cc = 'A'; cc <= 'Z'; cc++)
+                    {
+                        Residue residueCC;
+                        if (Residue.TryGetResidue(cc, out residueCC))
+                        {
+                            massesToExclude.Add(residue.MonoisotopicMass + residueCC.MonoisotopicMass);
+                            massesToExclude.Add(residue.MonoisotopicMass - residueCC.MonoisotopicMass);
+                            massesToExclude.Add(-residue.MonoisotopicMass + residueCC.MonoisotopicMass);
+                            massesToExclude.Add(-residue.MonoisotopicMass - residueCC.MonoisotopicMass);
+                        }
+                    }
+                }
+            }
+            List<double> filteredMasses = massesToExclude.GroupBy(b => Math.Round(b, 6)).Select(b => b.FirstOrDefault()).OrderBy(b => b).ToList();
+
+            yield return new DotSearchMode("Only AAs", filteredMasses, new Tolerance(ToleranceUnit.Absolute, v));
+
+            List<DoubleRange> doubleRanges = new List<DoubleRange>();
+
+            var prevGoodMin = double.NegativeInfinity;
+
+            for (int i = 0; i < filteredMasses.Count; i++)
+            {
+                if (Math.Round(filteredMasses[i], 6) == 0)
+                    continue;
+                doubleRanges.Add(new DoubleRange(prevGoodMin, filteredMasses[i] - v));
+                prevGoodMin = filteredMasses[i] + v;
+            }
+            doubleRanges.Add(new DoubleRange(prevGoodMin, double.PositiveInfinity));
+
+            doubleRanges = doubleRanges.Where(b => b.Minimum <= doubleRange.Maximum && b.Maximum >= doubleRange.Minimum).Select(b => new DoubleRange(Math.Max(doubleRange.Minimum, b.Minimum), Math.Min(doubleRange.Maximum, b.Maximum))).ToList();
+
+            yield return new IntervalSearchMode("Exclude AAs", doubleRanges);
         }
 
         private static int GuessCharge(List<IMzPeak> mzPeaks)
diff --git a/EngineLayer/SearchModes/DotSearchMode.cs b/EngineLayer/SearchModes/DotSearchMode.cs
@@ -1,5 +1,4 @@
 ﻿using MzLibUtil;
-using Spectra;
 using System;
 using System.Collections.Generic;
 using System.Globalization;
@@ -25,8 +24,7 @@ public DotSearchMode(IEnumerable<double> acceptableMassShifts, Tolerance tol) :
 
         public DotSearchMode(string FileNameAddition, IEnumerable<double> acceptableMassShifts, Tolerance tol) : base(FileNameAddition)
         {
-            HashSet<double> hs = new HashSet<double>(acceptableMassShifts.Select(b => Math.Round(b, 5)));
-            this.acceptableSortedMassShifts = hs.OrderBy(b => b).ToList();
+            this.acceptableSortedMassShifts = acceptableMassShifts.OrderBy(b => b).ToList();
             this.tol = tol;
             this.NumNotches = acceptableSortedMassShifts.Count;
         }
diff --git a/EngineLayer/SearchModes/IntervalSearchMode.cs b/EngineLayer/SearchModes/IntervalSearchMode.cs
@@ -18,9 +18,9 @@ public class IntervalSearchMode : SearchMode
 
         #region Public Constructors
 
-        public IntervalSearchMode(string fileNameAddition, IEnumerable<DoubleRange> nonOverlappingDoubleRanges) : base(fileNameAddition)
+        public IntervalSearchMode(string fileNameAddition, IEnumerable<DoubleRange> doubleRanges) : base(fileNameAddition)
         {
-            intervals = nonOverlappingDoubleRanges.OrderBy(b => b.Mean).ToList();
+            intervals = doubleRanges.OrderBy(b => b.Mean).ToList();
             means = intervals.Select(b => b.Mean).ToArray();
         }
 
diff --git a/GUI/CalibrateTaskWindow.xaml b/GUI/CalibrateTaskWindow.xaml
@@ -13,6 +13,10 @@
             <TextBox x:Name="precursorMassToleranceTextBox" HorizontalAlignment="Left"  TextWrapping="Wrap" Width="45" />
             <ComboBox x:Name="precursorMassToleranceComboBox" HorizontalAlignment="Left" />
         </StackPanel>
+        <StackPanel Orientation="Horizontal" Margin="5">
+            <Label x:Name="ff" Content="Max Degrees Of Parallelism" />
+            <TextBox x:Name="maxDegreesOfParallelism" Width="45" Text="-1"/>
+        </StackPanel>
         <Grid>
             <Grid.ColumnDefinitions>
                 <ColumnDefinition Width="1*" />
diff --git a/GUI/CalibrateTaskWindow.xaml.cs b/GUI/CalibrateTaskWindow.xaml.cs
@@ -1,6 +1,5 @@
 ﻿using EngineLayer;
 using MzLibUtil;
-using Spectra;
 using System;
 using System.Collections.ObjectModel;
 using System.Globalization;
@@ -71,6 +70,7 @@ private void UpdateFieldsFromTask(CalibrationTask task)
 
             bCheckBox.IsChecked = task.BIons;
             yCheckBox.IsChecked = task.YIons;
+            maxDegreesOfParallelism.Text = task.MaxDegreeOfParallelism.ToString(CultureInfo.InvariantCulture);
 
             foreach (var modList in task.ListOfModListsFixed)
                 ModFileListInWindow.First(b => b.FileName.Equals(modList.FileName)).Fixed = true;
@@ -128,6 +128,8 @@ private void saveButton_Click(object sender, RoutedEventArgs e)
             TheTask.PrecursorMassTolerance.Value = double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture);
             TheTask.PrecursorMassTolerance.Unit = (ToleranceUnit)precursorMassToleranceComboBox.SelectedIndex;
 
+            TheTask.MaxDegreeOfParallelism = int.Parse(maxDegreesOfParallelism.Text);
+
             DialogResult = true;
         }
 
diff --git a/GUI/ForDisplayingInDataGrids/MetaMorpheusTaskForDataGrid.cs b/GUI/ForDisplayingInDataGrids/MetaMorpheusTaskForDataGrid.cs
@@ -4,13 +4,28 @@ namespace MetaMorpheusGUI
 {
     internal class MetaMorpheusTaskForDataGrid
     {
-        public string Task { get { return metaMorpheusTask.GetType().Name; } }
-        public bool IsMySelected { get; set; }
+
+        #region Public Fields
+
         public readonly MetaMorpheusTask metaMorpheusTask;
 
+        #endregion Public Fields
+
+        #region Public Constructors
+
         public MetaMorpheusTaskForDataGrid(MetaMorpheusTask theTask)
         {
             this.metaMorpheusTask = theTask;
         }
+
+        #endregion Public Constructors
+
+        #region Public Properties
+
+        public string Task { get { return metaMorpheusTask.GetType().Name; } }
+        public bool InProgress { get; set; }
+
+        #endregion Public Properties
+
     }
 }
diff --git a/GUI/MainWindow.xaml b/GUI/MainWindow.xaml
@@ -148,7 +148,7 @@
                                                 <Setter Property="BorderBrush" Value="Transparent" />
                                                 <Setter Property="Foreground" Value="Black" />
                                             </Trigger>
-                                            <DataTrigger Binding="{Binding IsMySelected}" Value="True">
+                                            <DataTrigger Binding="{Binding InProgress}" Value="True">
                                                 <Setter Property="Foreground" Value="Blue" />
                                                 <Setter Property="FontWeight" Value="Bold" />
                                             </DataTrigger>
@@ -164,7 +164,7 @@
                                                 <Setter Property="BorderBrush" Value="Transparent" />
                                                 <Setter Property="Foreground" Value="Black" />
                                             </Trigger>
-                                            <DataTrigger Binding="{Binding IsMySelected}" Value="True">
+                                            <DataTrigger Binding="{Binding InProgress}" Value="True">
                                                 <Setter Property="Foreground" Value="Blue" />
                                                 <Setter Property="FontWeight" Value="Bold" />
                                             </DataTrigger>
diff --git a/GUI/MainWindow.xaml.cs b/GUI/MainWindow.xaml.cs
@@ -162,7 +162,7 @@ private void Po_startingSingleTaskHander(object sender, SingleTaskEventArgs s)
             }
             else
             {
-                taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).IsMySelected = true;
+                taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).InProgress = true;
                 statusLabel.Content = "Running " + s.TheTask.TaskType + " task";
                 outProgressBar.IsIndeterminate = true;
 
@@ -180,7 +180,7 @@ private void Po_finishedSingleTaskHandler(object sender, SingleTaskEventArgs s)
             }
             else
             {
-                taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).IsMySelected = false;
+                taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).InProgress = false;
                 statusLabel.Content = "Finished " + s.TheTask.TaskType + " task";
                 outProgressBar.Value = 100;
 
diff --git a/TaskLayer/CalibrationTask/CalibrationTask.cs b/TaskLayer/CalibrationTask/CalibrationTask.cs
@@ -39,6 +39,8 @@ public CalibrationTask()
 
             TaskType = MyTask.Calibrate;
             MaxNumPeaksPerScan = 400;
+
+            MaxDegreeOfParallelism = -1;
         }
 
         #endregion Public Constructors
@@ -50,6 +52,7 @@ public CalibrationTask()
         public List<ModList> ListOfModListsLocalize { get; set; }
         public Tolerance ProductMassTolerance { get; set; }
         public Tolerance PrecursorMassTolerance { get; set; }
+        public int MaxDegreeOfParallelism { get; set; }
 
         #endregion Public Properties
 
@@ -112,13 +115,17 @@ protected override MyResults RunSpecific()
                 lp.Add(ProductType.Y);
             }
 
-            Parallel.For(0, currentRawFileList.Count, spectraFileIndex =>
+            object lock1 = new object();
+            object lock2 = new object();
+            ParallelOptions parallelOptions = new ParallelOptions();
+            parallelOptions.MaxDegreeOfParallelism = MaxDegreeOfParallelism;
+            Parallel.For(0, currentRawFileList.Count, parallelOptions, spectraFileIndex =>
             {
                 var compactPeptideToProteinPeptideMatching = new Dictionary<CompactPeptide, HashSet<PeptideWithSetModifications>>();
                 var origDataFileName = currentRawFileList[spectraFileIndex];
                 LocalMS2Scan[] listOfSortedms2Scans;
                 IMsDataFile<IMsDataScan<IMzSpectrum<IMzPeak>>> myMsDataFile;
-                lock (myTaskResults)
+                lock (lock1) // Lock because reading is sequential
                 {
                     StartingDataFile(origDataFileName);
                     Status("Loading spectra file " + origDataFileName + "...");
@@ -183,7 +190,7 @@ protected override MyResults RunSpecific()
                 {
                     Status("Creating _indexedmzMLConnection, putting data in it, and writing!");
                     var path = Path.Combine(OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + "-Calibrated.mzML");
-                    lock (myTaskResults)
+                    lock (lock2) // Lock because writing is sequential
                     {
                         MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(((CalibrationResults)result).MyMSDataFile, path);
 
diff --git a/TaskLayer/GPTMDTask/GPTMDTask.cs b/TaskLayer/GPTMDTask/GPTMDTask.cs
@@ -208,7 +208,7 @@ protected override MyResults RunSpecific()
             IEnumerable<Tuple<double, double>> combos = LoadCombos().ToList();
 
             // Do not remove the zero!!! It's needed here
-            SearchMode searchMode = new DotSearchMode("", gptmdModifications.SelectMany(b => b.massesObserved).Concat(combos.Select(b => b.Item1 + b.Item2)).Concat(new List<double> { 0 }).OrderBy(b => b), PrecursorMassTolerance);
+            SearchMode searchMode = new DotSearchMode("", gptmdModifications.SelectMany(b => b.massesObserved).Concat(combos.Select(b => b.Item1 + b.Item2)).Concat(new List<double> { 0 }).GroupBy(b => Math.Round(b, 6)).Select(b => b.FirstOrDefault()).OrderBy(b => b), PrecursorMassTolerance);
             var searchModes = new List<SearchMode> { searchMode };
 
             List<PsmParent>[] allPsms = new List<PsmParent>[1];

Original file line number	Diff line number	Diff line change
`@@ -5,6 +5,7 @@ namespace EngineLayer.Indexing`
`5`	`5`	`{`
`6`	`6`	`public class IndexingResults : MyResults`
`7`	`7`	`{`
	`8`	`+`
`8`	`9`	`#region Public Constructors`
`9`	`10`
`10`	`11`	`public IndexingResults(List<CompactPeptide> peptideIndex, Dictionary<float, List<int>> fragmentIndexDict, IndexingEngine indexParams) : base(indexParams)`
`@@ -22,17 +23,18 @@ public IndexingResults(List<CompactPeptide> peptideIndex, Dictionary<float, List`
`22`	`23`
`23`	`24`	`#endregion Public Properties`
`24`	`25`
`25`		`- #region Protected Properties`
	`26`	`+ #region Public Methods`
`26`	`27`
`27`	`28`	`public override string ToString()`
`28`	`29`	`{`
`29`	`30`	`var sb = new StringBuilder();`
`30`		`- sb.AppendLine(base.ToString());`
	`31`	`+ sb.Append(base.ToString());`
`31`	`32`	`sb.AppendLine("\t\tfragmentIndexDict.Count: " + FragmentIndexDict.Count);`
`32`		`- sb.Append("\t\tpeptideIndex.Count: " + PeptideIndex.Count);`
	`33`	`+ sb.AppendLine("\t\tpeptideIndex.Count: " + PeptideIndex.Count);`
`33`	`34`	`return sb.ToString();`
`34`	`35`	`}`
`35`	`36`
`36`		`- #endregion Protected Properties`
	`37`	`+ #endregion Public Methods`
	`38`	`+`
`37`	`39`	`}`
`38`	`40`	`}`
Original file line number	Diff line number	Diff line change
`@@ -21,15 +21,16 @@ public ModernSearchResults(List<PsmModern>[] newPsms, ModernSearchEngine s) : ba`
`21`	`21`
`22`	`22`	`#endregion Public Properties`
`23`	`23`
`24`		`- #region Protected Properties`
	`24`	`+ #region Public Methods`
`25`	`25`
`26`	`26`	`public override string ToString()`
`27`	`27`	`{`
`28`	`28`	`var sb = new StringBuilder();`
`29`		`- sb.AppendLine(base.ToString());`
	`29`	`+ sb.Append(base.ToString());`
`30`	`30`	`return sb.ToString();`
`31`	`31`	`}`
`32`		`- #endregion Protected Properties`
	`32`	`+`
	`33`	`+ #endregion Public Methods`
`33`	`34`
`34`	`35`	`}`
`35`	`36`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`using MzLibUtil;`
`2`		`-using Spectra;`
`3`	`2`	`using System;`
`4`	`3`	`using System.Collections.Generic;`
`5`	`4`	`using System.Globalization;`
`@@ -25,8 +24,7 @@ public DotSearchMode(IEnumerable<double> acceptableMassShifts, Tolerance tol) :`
`25`	`24`
`26`	`25`	`public DotSearchMode(string FileNameAddition, IEnumerable<double> acceptableMassShifts, Tolerance tol) : base(FileNameAddition)`
`27`	`26`	`{`
`28`		`- HashSet<double> hs = new HashSet<double>(acceptableMassShifts.Select(b => Math.Round(b, 5)));`
`29`		`- this.acceptableSortedMassShifts = hs.OrderBy(b => b).ToList();`
	`27`	`+ this.acceptableSortedMassShifts = acceptableMassShifts.OrderBy(b => b).ToList();`
`30`	`28`	`this.tol = tol;`
`31`	`29`	`this.NumNotches = acceptableSortedMassShifts.Count;`
`32`	`30`	`}`
Original file line number	Diff line number	Diff line change
`@@ -18,9 +18,9 @@ public class IntervalSearchMode : SearchMode`
`18`	`18`
`19`	`19`	`#region Public Constructors`
`20`	`20`
`21`		`- public IntervalSearchMode(string fileNameAddition, IEnumerable<DoubleRange> nonOverlappingDoubleRanges) : base(fileNameAddition)`
	`21`	`+ public IntervalSearchMode(string fileNameAddition, IEnumerable<DoubleRange> doubleRanges) : base(fileNameAddition)`
`22`	`22`	`{`
`23`		`- intervals = nonOverlappingDoubleRanges.OrderBy(b => b.Mean).ToList();`
	`23`	`+ intervals = doubleRanges.OrderBy(b => b.Mean).ToList();`
`24`	`24`	`means = intervals.Select(b => b.Mean).ToArray();`
`25`	`25`	`}`
`26`	`26`
Original file line number	Diff line number	Diff line change
`@@ -4,13 +4,28 @@ namespace MetaMorpheusGUI`
`4`	`4`	`{`
`5`	`5`	`internal class MetaMorpheusTaskForDataGrid`
`6`	`6`	`{`
`7`		`- public string Task { get { return metaMorpheusTask.GetType().Name; } }`
`8`		`- public bool IsMySelected { get; set; }`
	`7`	`+`
	`8`	`+ #region Public Fields`
	`9`	`+`
`9`	`10`	`public readonly MetaMorpheusTask metaMorpheusTask;`
`10`	`11`
	`12`	`+ #endregion Public Fields`
	`13`	`+`
	`14`	`+ #region Public Constructors`
	`15`	`+`
`11`	`16`	`public MetaMorpheusTaskForDataGrid(MetaMorpheusTask theTask)`
`12`	`17`	`{`
`13`	`18`	`this.metaMorpheusTask = theTask;`
`14`	`19`	`}`
	`20`	`+`
	`21`	`+ #endregion Public Constructors`
	`22`	`+`
	`23`	`+ #region Public Properties`
	`24`	`+`
	`25`	`+ public string Task { get { return metaMorpheusTask.GetType().Name; } }`
	`26`	`+ public bool InProgress { get; set; }`
	`27`	`+`
	`28`	`+ #endregion Public Properties`
	`29`	`+`
`15`	`30`	`}`
`16`	`31`	`}`
Original file line number	Diff line number	Diff line change
`@@ -162,7 +162,7 @@ private void Po_startingSingleTaskHander(object sender, SingleTaskEventArgs s)`
`162`	`162`	`}`
`163`	`163`	`else`
`164`	`164`	`{`
`165`		`- taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).IsMySelected = true;`
	`165`	`+ taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).InProgress = true;`
`166`	`166`	`statusLabel.Content = "Running " + s.TheTask.TaskType + " task";`
`167`	`167`	`outProgressBar.IsIndeterminate = true;`
`168`	`168`
`@@ -180,7 +180,7 @@ private void Po_finishedSingleTaskHandler(object sender, SingleTaskEventArgs s)`
`180`	`180`	`}`
`181`	`181`	`else`
`182`	`182`	`{`
`183`		`- taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).IsMySelected = false;`
	`183`	`+ taskEngineObservableCollection.First(b => b.metaMorpheusTask.Equals(s.TheTask)).InProgress = false;`
`184`	`184`	`statusLabel.Content = "Finished " + s.TheTask.TaskType + " task";`
`185`	`185`	`outProgressBar.Value = 100;`
`186`	`186`