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Extension of bruker precursor information (2nd attempt) #3191

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merged 29 commits into from
Jan 15, 2025
Merged

Extension of bruker precursor information (2nd attempt) #3191

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ba475f1
Feature Reader Bruker with extended precursor info
xjasg Nov 6, 2023
c9f071e
Collisional Cross Sectional Area added
Andre99999999 Sep 4, 2024
5c7e77a
mzXML and MGF Reader/Writer externded
xjasg Nov 19, 2023
e8e5c5e
Bugfix Typo
xjasg Nov 25, 2023
112bf17
Changes after review
Andre99999999 Sep 4, 2024
0b8ffc4
Bugfix merges
Andre99999999 Sep 4, 2024
ee17fef
Test files changed
Andre99999999 Sep 7, 2024
8aeecd0
lowest and highest observed mz
Andre99999999 Sep 29, 2024
0f3b1a3
small cleanup
Andre99999999 Sep 29, 2024
8104588
Merge branch 'master' into feature/bruker_precursor_2
xjasg Oct 10, 2024
3ab4cff
Bugfix
Andre99999999 Oct 10, 2024
912c3c6
Fix Build exception
Andre99999999 Oct 11, 2024
56949cf
Bugfix unused header
Andre99999999 Oct 11, 2024
e7bf0d5
Revert changes after review
Andre99999999 Oct 11, 2024
3e7fd96
Remove unnecessary code
Andre99999999 Oct 11, 2024
5f5a974
Remove unused function
Andre99999999 Oct 11, 2024
ef4e5d4
cleanup
Andre99999999 Oct 11, 2024
e2e6ea2
Revert "lowest and highest observed mz"
Andre99999999 Oct 11, 2024
bb1a8ee
Partially revert last changes ( add intensity population again )
Andre99999999 Oct 31, 2024
853d207
Whitespace issues
Andre99999999 Nov 1, 2024
701ac75
merge latest version
Andre99999999 Nov 1, 2024
a80d333
Whitespace issue
Andre99999999 Nov 1, 2024
f4213a0
MGF Serializer + Spectrum list changes (Revwiew findings)
Andre99999999 Nov 6, 2024
e487769
Bugfix Build error
Andre99999999 Nov 6, 2024
73aca39
Extend MGF test with new parameters
Andre99999999 Nov 8, 2024
c18d414
Cleanup
Andre99999999 Nov 12, 2024
3cb5ae3
Bugfix remove ccs Parameter from title after mgf file was read
Andre99999999 Dec 27, 2024
924b415
Merge branch 'master' into feature/bruker_precursor_2
chambm Jan 9, 2025
3587b11
Merge branch 'master' into feature/bruker_precursor_2
chambm Jan 15, 2025
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19 changes: 19 additions & 0 deletions pwiz/data/msdata/Diff.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -547,6 +547,25 @@ void diff(const Spectrum& a,
}
}

if (config.ignoreSpectrumTitle)
{
vector<CVParam>::const_iterator it =
find_if(a_b.cvParams.begin(), a_b.cvParams.end(), CVParamIs(MS_spectrum_title));

if (it != a_b.cvParams.end())
{
a_b.cvParams.erase(it);
}

it =
find_if(b_a.cvParams.begin(), b_a.cvParams.end(), CVParamIs(MS_spectrum_title));

if (it != b_a.cvParams.end())
{
b_a.cvParams.erase(it);
}
}

// provide context
if (!a_b.empty() || !b_a.empty())
{
Expand Down
5 changes: 4 additions & 1 deletion pwiz/data/msdata/Diff.hpp
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Expand Up @@ -228,14 +228,17 @@ struct PWIZ_API_DECL DiffConfig : public pwiz::data::BaseDiffConfig

bool ignoreDataProcessing;

bool ignoreSpectrumTitle;

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Why is this necessary? I would expect the new CCS-in-title code to round trip the CCS so the title will be preserved and not different. What diffs were you getting without this?

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No, unfortunately it is different. The serializer writes it into the title string, but the reference does not contain the text ‘ccs=...’. But this reference is used for both - reading and writing.
The other cases of code where the title is extended too seem not to run through the test, so it was not a problem there.

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Sorry I dropped the ball here. What did you mean "the reference does not contain the text"?

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I have to apologise. I had a lot to do in another project. As far as I understand it, the following happens: testWriteRead(const MSData& msd) uses msd as a reference. msd contains previously generated test data with a specific title. ‘serializer.write(oss, msd);’ extends the title by “ccs=...” and saves the new extended data with the new title. Then "serializer.read(iss, msd2);" reads back the written data with the new title. But after that the comparison with msd fails because of the different title. That is why I have introduced a flag that disables the comparison of the titles. Maybe its better to changed the test than the main program. I`ll try this.

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I think I have now understood the problem. The additional text must be removed from the title after loading. Then everything should work. Otherwise, the title could be expanded more than once if we save and load the data twice or more. I think we would have to do the same with other title parameters.

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Did you see this reply @xjasg ?

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I replied, but my answers were marked as "pending".

Here is what I wrote:

"I have to apologise. I had a lot to do in another project. As far as I understand it, the following happens: testWriteRead(const MSData& msd) uses msd as a reference. msd contains previously generated test data with a specific title. ‘serializer.write(oss, msd);’ extends the title by “ccs=...” and saves the new extended data with the new title. Then "serializer.read(iss, msd2);" reads back the written data with the new title. But after that the comparison with msd fails because of the different title. That is why I have introduced a flag that disables the comparison of the titles. Maybe its better to changed the test than the main program. I`ll try this.

I think I have now understood the problem. The additional text must be removed from the title after loading. Then everything should work. Otherwise, the title could be expanded more than once if we save and load the data twice or more. I think we would have to do the same with other title parameters."

My last commit should have resolved this issue?

DiffConfig()
: pwiz::data::BaseDiffConfig(),
ignoreIdentity(false),
ignoreMetadata(false),
ignoreExtraBinaryDataArrays(false),
ignoreSpectra(false),
ignoreChromatograms(false),
ignoreDataProcessing(false)
ignoreDataProcessing(false),
ignoreSpectrumTitle(false)
{}
};

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3 changes: 3 additions & 0 deletions pwiz/data/msdata/Serializer_MGF_Test.cpp
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Expand Up @@ -122,6 +122,8 @@ void initializeTinyMGF(MSData& msd)
s21.scanList.scans.push_back(Scan());
Scan& s21scan = s21.scanList.scans.back();
s21scan.set(MS_scan_start_time, 42.0, UO_second);
s21scan.set(MS_inverse_reduced_ion_mobility, 421.0, MS_volt_second_per_square_centimeter);
s21scan.set(MS_collisional_cross_sectional_area, 1.376, UO_square_angstrom);

s21.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_detector_counts);
BinaryData<double>& s21_mz = s21.getMZArray()->data;
Expand Down Expand Up @@ -154,6 +156,7 @@ void testWriteRead(const MSData& msd)
DiffConfig diffConfig;
diffConfig.ignoreIdentity = true;
diffConfig.ignoreChromatograms = true;
diffConfig.ignoreSpectrumTitle = true;

Diff<MSData, DiffConfig> diff(msd, msd2, diffConfig);
if (os_ && diff) *os_ << diff << endl;
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7 changes: 5 additions & 2 deletions pwiz/data/msdata/SpectrumList_MGF.cpp
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Expand Up @@ -365,9 +365,9 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
return -1; // not found

start += strlen(startTag);
const string endTags[] = { "", " ", ",",";","\n","\r","\t" };
const string endTags[] = { " ", ",",";","\t" };
string ccsStr;

for(int i=0; i< sizeof(endTags)/sizeof(endTags[0]); i++)
{
const size_t end = title.find(endTags[i], start);
Expand All @@ -379,6 +379,9 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
}
}

if(ccsStr.empty())
ccsStr = title.substr(start, title.length() - start);
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try
{
return boost::lexical_cast<double>(ccsStr);
Expand Down
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