Special ions annotations. #2114
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…/github.com/ProteoWizard/pwiz into Skyline/work/20220505_specialIonAnnotations
…/github.com/ProteoWizard/pwiz into Skyline/work/20220505_specialIonAnnotations
| @@ -193,7 +193,9 @@ protected override void DoTest() | |||
| Assert.AreEqual(testRange, SkylineWindow.GraphFullScan.Range); | |||
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| RunUI(() => SkylineWindow.SynchMzScale(SkylineWindow.GraphSpectrum, false)); // Sync from the library match to the full scan viewer | |||
| TestSpecialIonsAnnotations(); | |||
| //annotations are not shown in the offscreen mode | |||
| if (!Skyline.Program.SkylineOffscreen) | |||
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This seems overly drastic. If it is a painting issue, then you should add a method that tells what would be annotated during a paint, and use that to make sure the graph understands what it is supposed to do. We use this approach a lot with our graphs.
| @@ -1,513 +1,520 @@ | |||
| /* | |||
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Avoid diffs like this of the entire file. Likely a change in line endings.
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I'm not sure it's a real issue. I cannot identify a commit that introduced this whole file change. When I look at the changes in each individual commit in this PR they all show only individual line-by-line changes. When I checkout the original file and compare with it I do not see any global differences either. Both files have CR/LF line endings. How do we debug such things?
| moleculeMasses = new MoleculeMasses( | ||
| SequenceMassCalc.GetMZ(calcMatchPre.GetPrecursorMass(Sequence), PrecursorAdduct), | ||
| new IonMasses(calcMatch.GetPrecursorFragmentMass(Sequence), | ||
| calcMatch.GetFragmentIonMasses(Sequence))); | ||
| new IonMasses(calcMatch.GetPrecursorFragmentMass(Sequence), ionTypes) .ChangeKnownFragments(specialIons) |
| @@ -701,6 +719,10 @@ private RankedMI CalculateRank(RankingState rankingState, RankedMI rankedMI) | |||
| continue; | |||
| } | |||
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| //custom ions have been already matched above. No need to do anything. | |||
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Your comment style is at odds with the project. Put a space after the // and capitalize the first letter.
| @@ -1,2821 +1,2831 @@ | |||
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Avoid whole file diffs, likely the result of line endings changing.
pwiz_tools/Skyline/SkylineGraphs.cs
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| @@ -914,7 +918,7 @@ public void ShowLosses(IEnumerable<string> losses) | |||
| private void IonTypeSelector_IonTypeChanges(IonType type, bool show) | |||
| { | |||
| switch (type) | |||
| { | |||
| { | |||
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This brace indenting change seems unnecessary and incorrect.
pwiz_tools/Skyline/SkylineGraphs.cs
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| { | ||
| ShowSpecialIons(!_graphSpectrumSettings.ShowSpecialIons); | ||
| } | ||
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| public void SynchMzScaleToolStripMenuItemClick(IMzScalePlot source = null) | ||
| { | ||
| if(ListMzScaleCopyables().Count() < 2) |
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If statements get spaces between if and (. They are not function calls.
pwiz_tools/Skyline/SkylineGraphs.cs
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| @@ -984,9 +993,9 @@ private void synchMzScaleToolStripMenuItem_Click(object sender, EventArgs e) | |||
| } | |||
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| //Testing support | |||
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Again put a space between // and the next character.
pwiz_tools/Skyline/SkylineGraphs.cs
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| @@ -995,7 +1004,7 @@ public void chargesMenuItem_DropDownOpening(object sender, EventArgs e) | |||
| if (chargesContextMenuItem.DropDownItems.Count > 0 && chargesContextMenuItem.DropDownItems[0] is MenuControl<ChargeSelectionPanel> chargeSelector) | |||
| { | |||
| chargeSelector.Update(_graphSpectrumSettings, DocumentUI.Settings.PeptideSettings); | |||
| } | |||
| } | |||
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This indenting change seems incorrect.
…/github.com/ProteoWizard/pwiz into Skyline/work/20220505_specialIonAnnotations
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