Mzml writer now rounds to 4 decimal places

mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs

@@ -498,7 +498,7 @@
 
         public byte[] Get64BitXarray()
         {
-            return Get64Bitarray(XArray);
+            return Get64Bitarray(XArray.Select(x => Math.Round(x, 4, MidpointRounding.AwayFromZero)));
         }
 
         public override string ToString()
@@ -782,14 +782,14 @@
             return numerator / denominator;
         }
 
         public bool Equals(MzSpectrum? other)
         {
             if (ReferenceEquals(null, other)) return false;
             if (ReferenceEquals(this, other)) return true;
             return (XArray.SequenceEqual(other.XArray) && YArray.SequenceEqual(other.YArray));
         }
 
         public override bool Equals(object? spectrumToCompare)
         {
             if (ReferenceEquals(null, spectrumToCompare)) return false;
             if (ReferenceEquals(this, spectrumToCompare)) return true;

mzLib/Test/FileReadingTests/TestMsDataFileToResultsAdapter.cs

@@ -3,6 +3,7 @@
 using System.Diagnostics;
 using System.Diagnostics.CodeAnalysis;
 using System.IO;
+using System.Linq;
 using MassSpectrometry;
 using MzLibUtil;
 using NUnit.Framework;
@@ -135,7 +136,8 @@ public void TestWriting(string filePath, string outfile, int loop)
                 Assert.That(readInScan.OneBasedScanNumber.Equals(writtenScan.OneBasedScanNumber));
                 Assert.That(readInScan.MsnOrder.Equals(writtenScan.MsnOrder));
                 Assert.That(readInScan.IsCentroid.Equals(writtenScan.IsCentroid));
-                Assert.That(readInScan.MassSpectrum.Equals(writtenScan.MassSpectrum));
+                Assert.That(readInScan.MassSpectrum.YArray, Is.EquivalentTo(writtenScan.MassSpectrum.YArray));
+                Assert.That(readInScan.MassSpectrum.XArray, Is.EquivalentTo(writtenScan.MassSpectrum.XArray.Select(x => Math.Round(x, 4, MidpointRounding.AwayFromZero))));
             }
 
             File.Delete(outfile);

mzLib/Test/FileReadingTests/TestMzML.cs

@@ -741,7 +741,8 @@ public void WriteMzmlTest()
             Assert.AreEqual(2, reader.GetClosestOneBasedSpectrumNumber(2));
 
             var newFirstValue = reader.GetOneBasedScan(1).MassSpectrum.FirstX;
-            Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);
+            Assert.AreNotEqual(oldFirstValue.Value, newFirstValue.Value);
+            Assert.AreEqual(Math.Round((double)oldFirstValue, 4, MidpointRounding.AwayFromZero), newFirstValue.Value, 1e-6);
 
             var secondScan2 = reader.GetOneBasedScan(2);
 
@@ -1451,6 +1452,32 @@ public void MzmlFindPrecursorReferenceScan()
             Assert.AreEqual(1, fakeMzml1.GetAllScansList().ElementAt(3).OneBasedPrecursorScanNumber);
         }
 
+        [Test]
+        public void TestMzmlWriterRounding()
+        {
+            // This test ensure the CreateAndWriteMzml method only writes m/z values out to 4 decimal places of precision
+            MsDataScan[] scans = new MsDataScan[1];
+
+            double[] intensities0 = new double[] { 1, 1, 1, 1 };
+            double[] mz0 = new double[] { 50.00004, 50.00005, 50.0004, 50.0005 };
+            MzSpectrum massSpec0 = new MzSpectrum(mz0, intensities0, false);
+            scans[0] = new MsDataScan(massSpec0, 1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec0.SumOfAllY, null, null, "1");
+
+            FakeMsDataFile fakeFile = new FakeMsDataFile(scans);
+            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(fakeFile, Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"), false);
+            var fakeMzml =
+                MsDataFileReader.GetDataFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"));
+            fakeMzml.LoadAllStaticData();
+
+            var readSpectrum = fakeMzml.Scans[0].MassSpectrum;
+
+            // Ensure that the spectrum was rounded to the fourth decimal place on write
+            Assert.That(readSpectrum.XArray[0], Is.EqualTo(50).Within(0.000001));
+            Assert.That(readSpectrum.XArray[1], Is.EqualTo(50.0001).Within(0.000001));
+            Assert.That(readSpectrum.XArray[2], Is.EqualTo(50.0004).Within(0.000001));
+            Assert.That(readSpectrum.XArray[3], Is.EqualTo(50.0005).Within(0.000001));
+        }
+
         [Test]
         [TestCase("tester.mzml")]
         [TestCase("SmallCalibratibleYeast.mzml")]

mzLib/Test/FileReadingTests/TestRawFileReader.cs

@@ -171,13 +171,13 @@ public static void TestPeakFilteringRawFileReader(string infile)
 
                 for (int j = 0; j < mzmlScan.MassSpectrum.XArray.Length; j++)
                 {
-                    double roundedMzmlMz = Math.Round(mzmlScan.MassSpectrum.XArray[j], 2);
-                    double roundedRawMz = Math.Round(rawScan.MassSpectrum.XArray[j], 2);
+                    double roundedRawMz = Math.Round(rawScan.MassSpectrum.XArray[j], 4, MidpointRounding.AwayFromZero);
 
-                    Assert.AreEqual(roundedMzmlMz, roundedRawMz);
+                    //  XArray is rounded to the 4th digit during CreateAndWrite
+                    Assert.AreEqual(mzmlScan.MassSpectrum.XArray[j], roundedRawMz);
 
-                    double roundedMzmlIntensity = Math.Round(mzmlScan.MassSpectrum.XArray[j], 0);
-                    double roundedRawIntensity = Math.Round(rawScan.MassSpectrum.XArray[j], 0);
+                    double roundedMzmlIntensity = Math.Round(mzmlScan.MassSpectrum.XArray[j], 0, MidpointRounding.AwayFromZero);
+                    double roundedRawIntensity = Math.Round(rawScan.MassSpectrum.XArray[j], 0, MidpointRounding.AwayFromZero);
 
                     Assert.AreEqual(roundedMzmlIntensity, roundedRawIntensity);
                 }

mzLib/TestFlashLFQ/TestFlashLFQ.cs

@@ -1493,7 +1493,7 @@ public static void ProteoformPeakfindingTest()
 
             Assert.That((int)results.PeptideModifiedSequences[sequence].GetIntensity(file1) == 1386491);
             ChromatographicPeak peak = results.Peaks[file1].First(p => p.Identifications.First().ModifiedSequence == sequence);
-            Assert.That(Math.Round(peak.MassError, 3) == 0);
+            Assert.That(Math.Round(peak.MassError, 3), Is.EqualTo(0.006).Within(0.0001));
             Assert.That(peak.IsotopicEnvelopes.Count == 10);
         }