small molecule chromatogram extraction wasn't using spectral library …

…retention times … (#2811)

Small molecule chromatogram extraction wasn't using spectral library retention times (Skyline didn't initially have that capability, and the limitation was never lifted)

Not reported by any user - Brendan noticed the chromatograms weren't being truncated as expected in the context of other work involving spectral libraries and small molecules

pwiz_tools/Skyline/Model/DocSettings/SrmSettings.cs

@@ -1119,9 +1119,6 @@ public bool TryGetRetentionTimes(Target sequence, Adduct adduct, ExplicitMods mo
 
         public double[] GetBestRetentionTimes(PeptideDocNode nodePep, MsDataFileUri filePath)
         {
-            if (!nodePep.IsProteomic)
-                return new double[0]; // No retention time prediction for small molecules
-
             var lookupSequence = nodePep.SourceUnmodifiedTarget;
             var lookupMods = nodePep.SourceExplicitMods;
             if (filePath != null)

pwiz_tools/Skyline/TestTutorial/TargetedMSMSTutorialTest.cs

@@ -93,7 +93,7 @@ public void DoTestTargetedMSMSTutorial(RefinementSettings.ConvertToSmallMolecule
                 return;
             }
 
-            ForceMzml = true;   // 2-3x faster than raw files for this test.
+            ForceMzml = true;   // 2-3x faster than raw files for this test - and audit log expects it.
 
             AsSmallMoleculesTestMode = smallMoleculesTestMode;
 
@@ -468,9 +468,8 @@ private void LowResTest()
 
             const int expectedMoleculeCount = 9;
             const int expectedTransitionGroupCount = 10; // Expect this many with results
-            var expected20TransitionCount = AsSmallMolecules || UseRawFiles ? 87 : 88; // Expect this many with results
-            var expected80TransitionCount = AsSmallMolecules ? 88 : UseRawFiles ? 86 : 87;
-
+            var expected20TransitionCount = AsSmallMoleculeMasses  ? 87 : 88; // Expect this many with results (note no library match possible for "as masses" version)
+            var expected80TransitionCount = AsSmallMoleculeMasses ? 88 : 87;
             AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes20FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expected20TransitionCount, 0);
             AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes80FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expected80TransitionCount, 0);