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[proteowizard-commit] SF.net SVN: proteowizard:[4346] branches/skyline_1_4/pwiz/pwiz_tools/ Skyline
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From: <bre...@us...> - 2013-02-19 03:25:49
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Revision: 4346
http://sourceforge.net/p/proteowizard/code/4346
Author: brendanx
Date: 2013-02-19 03:25:46 +0000 (Tue, 19 Feb 2013)
Log Message:
-----------
Skyline (v1.4): Fix Agilent transition list export to differentiate between label types in CompoundName
- Fix export Agilent triggered-MRM to always include a trigger transition, even when an analyte precursor is not present
Modified Paths:
--------------
branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Export.cs
branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Import.cs
branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Test/SrmDocumentTest.cs
branches/skyline_1_4/pwiz/pwiz_tools/Skyline/TestFunctional/ExportMethodDialogTest.zip
Modified: branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Export.cs
===================================================================
--- branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Export.cs 2013-02-17 21:30:21 UTC (rev 4345)
+++ branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Export.cs 2013-02-19 03:25:46 UTC (rev 4346)
@@ -1114,8 +1114,11 @@
writer.Write(nodePepGroup.Name);
writer.Write(FieldSeparator);
// Write modified sequence for the light peptide molecule
- writer.Write(Document.Settings.GetModifiedSequence(nodePep.Peptide.Sequence,
- IsotopeLabelType.light, nodePep.ExplicitMods));
+ string modifiedSequence = Document.Settings.GetModifiedSequence(nodePep.Peptide.Sequence,
+ IsotopeLabelType.light, nodePep.ExplicitMods);
+ string compoundName = string.Format("{0}.{1}", modifiedSequence, nodeTranGroup.TransitionGroup.LabelType);
+ writer.Write(compoundName);
+
writer.Write(FieldSeparator);
var istdTypes = Document.Settings.PeptideSettings.Modifications.InternalStandardTypes;
writer.Write(istdTypes.Contains(nodeTranGroup.TransitionGroup.LabelType) // ISTD?
@@ -1145,7 +1148,7 @@
writer.Write(FieldSeparator);
// Trigger must be rank 1 transition, of analyte type and minimum precursor charge
bool trigger = false;
- if (nodeTranGroup.TransitionGroup.LabelType.IsLight && rank.HasValue && rank.Value == 1)
+ if (IsTriggerType(nodePep, nodeTranGroup, istdTypes) && rank.HasValue && rank.Value == 1)
{
int minCharge = nodePep.TransitionGroups.Select(g => g.TransitionGroup.PrecursorCharge).Min();
if (nodeTranGroup.TransitionGroup.PrecursorCharge == minCharge)
@@ -1191,6 +1194,31 @@
writer.Write(nodeTran.LibInfo.Rank);
writer.WriteLine();
}
+
+ private static bool IsTriggerType(PeptideDocNode nodePep, TransitionGroupDocNode nodeTranGroup, IList<IsotopeLabelType> istdTypes)
+ {
+ // If there is a light precursor, then it is always the trigger
+ if (nodeTranGroup.TransitionGroup.LabelType.IsLight)
+ return true;
+ // Get all precursors with the same charge state and at least 1 transition, including this one
+ var arrayTranGroups = nodePep.TransitionGroups
+ .Where(g => g.TransitionGroup.PrecursorCharge == nodeTranGroup.TransitionGroup.PrecursorCharge &&
+ g.TransitionCount > 0).ToArray();
+ // If it is the only precursor of this charge state, then it must be the trigger
+ if (arrayTranGroups.Length == 1)
+ return true;
+ // If there is no light precursor
+ var firstGroup = arrayTranGroups.First();
+ if (!firstGroup.TransitionGroup.LabelType.IsLight)
+ {
+ // See if there is a precursor not of an internal standard type, and use the first such precursor
+ var analyteGroup = arrayTranGroups.FirstOrDefault(g => !istdTypes.Contains(g.TransitionGroup.LabelType));
+ if (analyteGroup != null)
+ return ReferenceEquals(analyteGroup, nodeTranGroup);
+ }
+ // Otherwise, the first precursor in the list is the trigger.
+ return ReferenceEquals(firstGroup, nodeTranGroup);
+ }
}
public class AgilentMethodExporter : AgilentMassListExporter
@@ -1397,7 +1425,7 @@
protected override void WriteHeaders(TextWriter writer)
{
- // TODO: L1ON?
+ // Not L10N
writer.Write("protein.name");
writer.Write(FieldSeparator);
writer.Write("peptide.seq"); // modified sequence to support 1:1 requirement with precursor m/z
Modified: branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Import.cs
===================================================================
--- branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Import.cs 2013-02-17 21:30:21 UTC (rev 4345)
+++ branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Model/Import.cs 2013-02-19 03:25:46 UTC (rev 4346)
@@ -745,7 +745,7 @@
private static string RemoveSequenceNotes(string seq)
{
- if (seq.IndexOf('[') == -1) // Not L10N
+ if (seq.IndexOf('[') == -1 && seq.IndexOf('.') == -1) // Not L10N
return seq;
StringBuilder seqBuild = new StringBuilder(seq.Length);
bool inNote = false;
@@ -763,7 +763,11 @@
inNote = false;
}
}
- return seqBuild.ToString();
+ string seqClean = seqBuild.ToString();
+ int dotIndex = seqClean.IndexOf('.'); // Not L10N
+ if (dotIndex != -1)
+ seqClean = seqClean.Substring(0, dotIndex);
+ return seqClean;
}
private static readonly string[] EXCLUDE_PROTEIN_VALUES = new[] { "true", "false", "heavy", "light", "unit" }; // Not L10N
Modified: branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Test/SrmDocumentTest.cs
===================================================================
--- branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Test/SrmDocumentTest.cs 2013-02-17 21:30:21 UTC (rev 4345)
+++ branches/skyline_1_4/pwiz/pwiz_tools/Skyline/Test/SrmDocumentTest.cs 2013-02-19 03:25:46 UTC (rev 4346)
@@ -195,12 +195,29 @@
count = EqualCsvs(DOC_0_1_BOVINE, 4, ThermoExporters, ExportStrategy.Single, 1, null,
ExportMethodType.Standard);
Assert.AreEqual(1, count);
+ count = ExportAll(DOC_0_1_PEPTIDES_NO_EMPTY, 4, CreateWatersExporter, ExportStrategy.Single, 2, null,
+ ExportMethodType.Standard);
+ Assert.AreEqual(1, count);
count = EqualCsvs(DOC_0_1_PEPTIDES_NO_EMPTY, 0, CreateAbiExporters, ExportStrategy.Buckets, 1, 6,
ExportMethodType.Standard);
// TODO: Test scheduled runs
Assert.AreEqual(3, count);
}
+ /// <summary>
+ /// Test export and reimport of Waters and Agilent transition list formats
+ /// </summary>
+ [TestMethod]
+ public void DocumentExportImportTest()
+ {
+ int count = ExportAll(DOC_0_1_PEPTIDES_NO_EMPTY, 4, CreateWatersExporter, ExportStrategy.Single, 2, null,
+ ExportMethodType.Standard);
+ Assert.AreEqual(1, count);
+ count = ExportAll(DOC_0_1_PEPTIDES_NO_EMPTY, 4, CreateAgilentExporter, ExportStrategy.Single, 2, null,
+ ExportMethodType.Standard);
+ Assert.AreEqual(1, count);
+ }
+
private static int EqualCsvs(string xml, int countFields, CreateExporters exporters,
ExportStrategy strategy, int minTransition, int? maxTransition, ExportMethodType methodType)
{
@@ -210,7 +227,7 @@
return EqualCsvs(target, actual, countFields, exporters, strategy, minTransition, maxTransition, methodType);
}
- private static int EqualCsvs(XmlSrmDocument target, SrmDocument actual, int coundFields, CreateExporters exporters,
+ private static int EqualCsvs(XmlSrmDocument target, SrmDocument actual, int countFields, CreateExporters exporters,
ExportStrategy strategy, int minTransition, int? maxTransition, ExportMethodType methodType)
{
XmlMassListExporter exporterTarget;
@@ -240,8 +257,8 @@
string actualList = exportedActual[key].ToString();
Assert.AreNotEqual(0, targetList.Length);
- if (coundFields > 0)
- AssertEx.FieldsEqual(targetList, actualList, coundFields);
+ if (countFields > 0)
+ AssertEx.FieldsEqual(targetList, actualList, countFields);
else
AssertEx.NoDiff(targetList, actualList);
@@ -260,6 +277,41 @@
return exportedTarget.Count;
}
+ private static int ExportAll(string xml, int countFields, CreateExporter exporters,
+ ExportStrategy strategy, int minTransition, int? maxTransition,
+ ExportMethodType methodType)
+ {
+ SrmDocument actual = AssertEx.Deserialize<SrmDocument>(xml);
+
+ return ExportAll(actual, countFields, exporters, strategy, minTransition, maxTransition, methodType);
+ }
+
+ private static int ExportAll(SrmDocument actual, int countFields, CreateExporter exporter,
+ ExportStrategy strategy, int minTransition, int? maxTransition,
+ ExportMethodType methodType)
+ {
+ AbstractMassListExporter exporterActual;
+ exporter(actual, out exporterActual);
+ exporterActual.Export(null);
+ var exportedActual = exporterActual.MemoryOutput;
+
+ // Make sure the resulting output can be imported
+ SrmDocument docImport = new SrmDocument(actual.Settings);
+ foreach (string key in exportedActual.Keys)
+ {
+ string actualList = exportedActual[key].ToString();
+
+ // Import the exported list
+ using (var readerImport = new StringReader(actualList))
+ {
+ IdentityPath pathAdded;
+ IFormatProvider provider = CultureInfo.InvariantCulture;
+ docImport = docImport.ImportMassList(readerImport, provider, ',', IdentityPath.ROOT, out pathAdded);
+ }
+ }
+ return exportedActual.Count;
+ }
+
private delegate void CreateExporters(XmlSrmDocument target, out XmlMassListExporter exporterTarget,
SrmDocument actual, out AbstractMassListExporter exporterActual);
@@ -277,6 +329,18 @@
exporterActual = new AbiMassListExporter(actual);
}
+ private delegate void CreateExporter(SrmDocument actual, out AbstractMassListExporter exporterActual);
+
+ private static void CreateWatersExporter(SrmDocument actual, out AbstractMassListExporter exporterActual)
+ {
+ exporterActual = new WatersMassListExporter(actual);
+ }
+
+ private static void CreateAgilentExporter(SrmDocument actual, out AbstractMassListExporter exporterActual)
+ {
+ exporterActual = new AgilentMassListExporter(actual);
+ }
+
private static void CheckImportSimilarity(SrmDocument document, SrmDocument docImport)
{
CheckImportSimilarity(document.PeptideGroups, docImport.PeptideGroups,
Modified: branches/skyline_1_4/pwiz/pwiz_tools/Skyline/TestFunctional/ExportMethodDialogTest.zip
===================================================================
(Binary files differ)
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