[proteowizard-commit] SF.net SVN: proteowizard:[1848] trunk/pwiz/pwiz_tools/Skyline/Model

[<bre...@us...>]

Revision: 1848
          http://proteowizard.svn.sourceforge.net/proteowizard/?rev=1848&view=rev
Author:   brendanx
Date:     2010-02-28 06:35:45 +0000 (Sun, 28 Feb 2010)

Log Message:
-----------
Transition list export fixes for Skyline:
- Reduce precision of CE, DP and Cone Voltage
- Modify column headers for Waters transition lists to be recognized by VerifyE

Modified Paths:
--------------
    trunk/pwiz/pwiz_tools/Skyline/Model/Export.cs
    trunk/pwiz/pwiz_tools/Skyline/Model/V01/XmlExport.cs

Modified: trunk/pwiz/pwiz_tools/Skyline/Model/Export.cs
===================================================================
--- trunk/pwiz/pwiz_tools/Skyline/Model/Export.cs	2010-02-27 14:03:23 UTC (rev 1847)
+++ trunk/pwiz/pwiz_tools/Skyline/Model/Export.cs	2010-02-28 06:35:45 UTC (rev 1848)
@@ -926,7 +926,7 @@
             writer.Write(FieldSeparator);
             writer.Write(GetProductMz(SequenceMassCalc.PersistentMZ(nodeTran.Mz), step));
             writer.Write(FieldSeparator);
-            writer.Write(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step));
+            writer.Write(Math.Round(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step), 1));
             writer.Write(FieldSeparator);
             if (MethodType == ExportMethodType.Scheduled)
             {
@@ -1142,9 +1142,9 @@
             writer.Write(nodeTranGroup.TransitionGroup.LabelType == IsotopeLabelType.light ? "light" : "heavy");
             writer.Write(FieldSeparator);
 
-            writer.Write(GetDeclusteringPotential(nodePep, nodeTranGroup, nodeTran, step));
+            writer.Write(Math.Round(GetDeclusteringPotential(nodePep, nodeTranGroup, nodeTran, step), 1));
             writer.Write(FieldSeparator);
-            writer.Write(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step));
+            writer.Write(Math.Round(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step), 1));
             writer.WriteLine();
         }
     }
@@ -1237,10 +1237,9 @@
                 writer.Write(FieldSeparator);                
             }
 
-
             writer.Write(Fragmentor);
             writer.Write(FieldSeparator);
-            writer.Write(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step));
+            writer.Write(Math.Round(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step), 1));
             writer.Write(FieldSeparator);
 
             if (MethodType != ExportMethodType.Standard)
@@ -1301,28 +1300,28 @@
 
         protected override void WriteHeaders(TextWriter writer)
         {
-            writer.Write("Protein");
+            writer.Write("protein.name");
             writer.Write(FieldSeparator);
-            writer.Write("Sequence");
+            writer.Write("peptide.seq");
             writer.Write(FieldSeparator);
-            writer.Write("Precursor M/Z");
+            writer.Write("precursor.mz");
             writer.Write(FieldSeparator);
-            writer.Write("Precursor Retention Time");
+            writer.Write("precursor.retT");
             writer.Write(FieldSeparator);
-            writer.Write("Product M/Z");
+            writer.Write("product.m_z");
             writer.Write(FieldSeparator);
-            writer.Write("Collision Energy");
+            writer.Write("collision_energy");
             writer.Write(FieldSeparator);
-            writer.Write("Cone Voltage");
+            writer.Write("cone_voltage");
             // Informational columns
             writer.Write(FieldSeparator);
-            writer.Write("Ion Name");
+            writer.Write("ion_name");
             writer.Write(FieldSeparator);
-            writer.Write("Library Rank");
+            writer.Write("library_rank");
             if (Document.Settings.PeptideSettings.Modifications.HasHeavyModifications)
             {
                 writer.Write(FieldSeparator);
-                writer.Write("Label Type");                
+                writer.Write("label_type");                
             }
             writer.WriteLine();
         }
@@ -1361,10 +1360,11 @@
             writer.Write(GetProductMz(SequenceMassCalc.PersistentMZ(nodeTran.Mz), step));
             writer.Write(FieldSeparator);
 
-            writer.Write(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step));
+            // Waters only excepts integers for CE and CV
+            writer.Write((int)Math.Round(GetCollisionEnergy(nodePep, nodeTranGroup, nodeTran, step)));
             writer.Write(FieldSeparator);
 
-            writer.Write(ConeVoltage);
+            writer.Write((int)Math.Round(ConeVoltage));
             writer.Write(FieldSeparator);
 
             // Extra information not used by instrument

Modified: trunk/pwiz/pwiz_tools/Skyline/Model/V01/XmlExport.cs
===================================================================
--- trunk/pwiz/pwiz_tools/Skyline/Model/V01/XmlExport.cs	2010-02-27 14:03:23 UTC (rev 1847)
+++ trunk/pwiz/pwiz_tools/Skyline/Model/V01/XmlExport.cs	2010-02-28 06:35:45 UTC (rev 1848)
@@ -192,7 +192,7 @@
             writer.Write(',');
             writer.Write(transition.ProductMz);
             writer.Write(',');
-            writer.Write(transition.CollisionEnergy);
+            writer.Write(Math.Round(transition.CollisionEnergy, 1));
             writer.Write(',');
             if (MethodType == ExportMethodType.Scheduled)
             {
@@ -252,12 +252,12 @@
             writer.Write("light");
             writer.Write(',');
 
-            writer.Write(transition.DeclusteringPotential ?? 0);
+            writer.Write(Math.Round(transition.DeclusteringPotential ?? 0, 1));
 //            Removed in v0.2 for test compatibility
 //            writer.Write(',');
             // EP : not used by Paulovich Lab
             writer.Write(',');
-            writer.Write(transition.CollisionEnergy);
+            writer.Write(Math.Round(transition.CollisionEnergy, 1));
 //            Removed in v0.2 for test compatibility
 //            writer.Write(',');
             // CXP : not used by Paulovich Lab


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