Merge branch 'ypriverol-master'

Author: nielshulstaert

ThermoRawFileParser.csproj

@@ -124,6 +124,7 @@
     <Compile Include="MainClass.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="RawFileParser.cs" />
+    <Compile Include="Util\LimitedSizeDictionary.cs" />
     <Compile Include="Writer\ISpectrumWriter.cs" />
     <Compile Include="Writer\Metadata.cs" />
     <Compile Include="Writer\MetadataWriter.cs" />

ThermoRawFileParserTest/ThermoRawFileParserTest.csproj

@@ -142,7 +142,8 @@
     </Reference>
   </ItemGroup>
   <ItemGroup>
-    <Compile Include="Tests.cs" />
+    <Compile Include="UtilTests.cs" />
+    <Compile Include="WriterTests.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
   </ItemGroup>
   <ItemGroup>

ThermoRawFileParserTest/UtilTests.cs

@@ -0,0 +1,26 @@
+using System.Text.RegularExpressions;
+using NUnit.Framework;
+
+namespace ThermoRawFileParserTest
+{
+    [TestFixture]
+    public class UtilTests
+    {
+        [Test]
+        public void TestRegex()
+        {
+            const string filterString = "ITMS + c NSI r d Full ms2 961.8803@cid35.00 [259.0000-1934.0000]";
+            const string pattern = @"ms2 (.*?)@";
+            
+            Match result = Regex.Match(filterString, pattern);
+            if (result.Success)
+            {
+                Assert.AreEqual("961.8803", result.Groups[1].Value);
+            }
+            else
+            {
+                Assert.Fail();
+            }
+        }
+    }
+}

ThermoRawFileParserTest/Tests.cs ThermoRawFileParserTest/WriterTests.csThermoRawFileParserTest/Tests.cs renamed to ThermoRawFileParserTest/WriterTests.cs

@@ -10,7 +10,7 @@
 namespace ThermoRawFileParserTest
 {
     [TestFixture]
-    public class Tests
+    public class WriterTests
     {
         [Test]
         public void TestMgf()

Util/LimitedSizeDictionary.cs

@@ -0,0 +1,102 @@
+using System.Collections;
+using System.Collections.Generic;
+
+namespace ThermoRawFileParser.Util
+{
+    //https://social.msdn.microsoft.com/Forums/vstudio/en-US/789c37ea-b9bf-4512-a418-f4f9532c59bf/dictionary-with-limited-size?forum=csharpgeneral
+    public class LimitedSizeDictionary<TKey, TValue> : IDictionary<TKey, TValue>
+    {
+        private readonly Dictionary<TKey, TValue> _dict;
+        private Queue<TKey> _queue;
+        private readonly int _size;
+
+        public LimitedSizeDictionary(int size)
+        {
+            _size = size;
+            _dict = new Dictionary<TKey, TValue>(size + 1);
+            _queue = new Queue<TKey>(size);
+        }
+
+        public void Add(TKey key, TValue value)
+        {
+            _dict.Add(key, value);
+            if (_queue.Count == _size)
+                _dict.Remove(_queue.Dequeue());
+            _queue.Enqueue(key);
+        }
+
+        public bool ContainsKey(TKey key)
+        {
+            return _dict.ContainsKey(key);
+        }
+
+        public bool Remove(TKey key)
+        {
+            if (_dict.Remove(key))
+            {
+                var newQueue = new Queue<TKey>(_size);
+                foreach (var item in _queue)
+                    if (!_dict.Comparer.Equals(item, key))
+                        newQueue.Enqueue(item);
+                _queue = newQueue;
+                return true;
+            }
+            else
+                return false;
+        }
+
+        public bool TryGetValue(TKey key, out TValue value)
+        {
+            return _dict.TryGetValue(key, out value);
+        }
+
+        public TValue this[TKey key]
+        {
+            get => _dict[key];
+            set => _dict[key] = value;
+        }
+
+        public ICollection<TKey> Keys => _dict.Keys;
+
+        public ICollection<TValue> Values => _dict.Values;
+
+        public IEnumerator<KeyValuePair<TKey, TValue>> GetEnumerator()
+        {
+            return _dict.GetEnumerator();
+        }
+
+        IEnumerator IEnumerable.GetEnumerator()
+        {
+            return ((IEnumerable) _dict).GetEnumerator();
+        }
+
+        public void Add(KeyValuePair<TKey, TValue> item)
+        {
+            ((IDictionary<TKey, TValue>) _dict).Add(item);
+        }
+
+        public void Clear()
+        {
+            _dict.Clear();
+        }
+
+        public bool Contains(KeyValuePair<TKey, TValue> item)
+        {
+            return ((IDictionary<TKey, TValue>) _dict).Contains(item);
+        }
+
+        public void CopyTo(KeyValuePair<TKey, TValue>[] array, int arrayIndex)
+        {
+            ((IDictionary<TKey, TValue>) _dict).CopyTo(array, arrayIndex);
+        }
+
+        public bool Remove(KeyValuePair<TKey, TValue> item)
+        {
+            return ((IDictionary<TKey, TValue>) _dict).Remove(item);
+        }
+
+        public int Count => _dict.Count;
+
+        public bool IsReadOnly => ((IDictionary<TKey, TValue>) _dict).IsReadOnly;
+    }
+}

Writer/MgfSpectrumWriter.cs

@@ -55,7 +55,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                             {
                                 Writer.WriteLine("BEGIN IONS");
                                 Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
-                                Writer.WriteLine($"SCAN={scanNumber}");
+                                Writer.WriteLine($"SCANS={scanNumber}");
                                 Writer.WriteLine($"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");
                                 // Get the reaction information for the first precursor
                                 try