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Merged
sander-willems-bruker merged 3 commits into from
Aug 18, 2026
Merged

feat: added patched path and spectrumreader #60

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c5917e0
feat: added patched path and spectrumreader
sander-willems-bruker Aug 17, 2026
2ae9fa6
Potential fix for pull request finding
sander-willems-bruker Aug 18, 2026
1a916c5
Potential fix for pull request finding
sander-willems-bruker Aug 18, 2026
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44 changes: 28 additions & 16 deletions crates/timsrust/src/converters.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -21,28 +21,32 @@ impl MzConverter {
let timstof = TimsTofPath::new(path.as_ref()).ok()?;
#[allow(unreachable_code)]
match timstof.file_type() {
#[cfg(feature = "patched")]
TimsTofFileType::Patched(_) => {
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tdf(tdf_path) => {
#[cfg(feature = "sdk")]
return Some(MzConverter::Sdk(
return Some(Self::Sdk(
timsrust_sdk::WrappedTof2MzConverterSDK::new(
tdf_path.tdf().as_ref(),
)?,
));
#[cfg(feature = "patched")]
return Some(MzConverter::Bps(
return Some(Self::Bps(
timsrust_patched::Tof2MzConverter::from_tdf(
tdf_path.tdf().as_ref(),
)?,
));
Some(MzConverter::Tdf(timsrust_tdf::Tof2MzConverter::new(
Some(Self::Tdf(timsrust_tdf::Tof2MzConverter::new(
tdf_path.tdf().as_ref(),
)))
},
TimsTofFileType::MiniTdf(_) => Some(MzConverter::MiniTdf),
TimsTofFileType::MiniTdf(_) => Some(Self::MiniTdf),
TimsTofFileType::Parquet(_) => {
Some(MzConverter::Bit(timsrust_core::BitConverter()))
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tsf(_) => Some(MzConverter::TSF(
TimsTofFileType::Tsf(_) => Some(Self::TSF(
timsrust_tsf::Tof2MzConverter::new(timstof.as_ref()),
)),
}
Expand Down Expand Up @@ -95,29 +99,33 @@ impl ImConverter {
let timstof = TimsTofPath::new(path.as_ref()).ok()?;
#[allow(unreachable_code)]
match timstof.file_type() {
#[cfg(feature = "patched")]
TimsTofFileType::Patched(_) => {
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tdf(tdf_path) => {
#[cfg(feature = "sdk")]
return Some(ImConverter::Sdk(
return Some(Self::Sdk(
timsrust_sdk::WrappedScan2ImConverterSDK::new(
tdf_path.tdf().as_ref(),
)?,
));
#[cfg(feature = "patched")]
return Some(ImConverter::Bps(
return Some(Self::Bps(
timsrust_patched::Scan2ImConverter::from_tdf(
tdf_path.tdf().as_ref(),
)?,
));
Some(ImConverter::Tdf(timsrust_tdf::Scan2ImConverter::new(
Some(Self::Tdf(timsrust_tdf::Scan2ImConverter::new(
tdf_path.tdf().as_ref(),
)))
},
TimsTofFileType::MiniTdf(_) => Some(ImConverter::MiniTdf),
TimsTofFileType::MiniTdf(_) => Some(Self::MiniTdf),
TimsTofFileType::Parquet(_) => {
Some(ImConverter::Bit(timsrust_core::BitConverter()))
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tsf(_) => {
Some(ImConverter::Bit(timsrust_core::BitConverter()))
Some(Self::Bit(timsrust_core::BitConverter()))
},
}
}
Expand Down Expand Up @@ -162,15 +170,19 @@ impl RtConverter {
pub fn new(path: impl AsRef<str>) -> Option<Self> {
let timstof = TimsTofPath::new(path.as_ref()).ok()?;
match timstof.file_type() {
TimsTofFileType::Tdf(tdf_path) => Some(RtConverter::Tdf(
#[cfg(feature = "patched")]
TimsTofFileType::Patched(_) => {
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tdf(tdf_path) => Some(Self::Tdf(
timsrust_tdf::Frame2RtConverter::new(tdf_path.tdf().as_ref()),
)),
TimsTofFileType::MiniTdf(_) => Some(RtConverter::MiniTdf),
TimsTofFileType::MiniTdf(_) => Some(Self::MiniTdf),
TimsTofFileType::Parquet(_) => {
Some(RtConverter::Bit(timsrust_core::BitConverter()))
Some(Self::Bit(timsrust_core::BitConverter()))
},
TimsTofFileType::Tsf(_) => {
Some(RtConverter::Bit(timsrust_core::BitConverter()))
Some(Self::Bit(timsrust_core::BitConverter()))
},
}
}
Expand Down
7 changes: 7 additions & 0 deletions crates/timsrust/src/precursor_reader.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,10 @@ impl PrecursorReaderBuilder {
Some(path) => path,
};
let precursor_reader = match path.file_type() {
#[cfg(feature = "patched")]
TimsTofFileType::Patched(_) => {
return Err(PrecursorReaderError::PatchedNotSupported);
},
TimsTofFileType::MiniTdf(mini_path) => {
Inner::MiniTDF(mini_path.precursor_reader()?)
},
Expand Down Expand Up @@ -142,4 +146,7 @@ pub enum PrecursorReaderError {
TimsTofPathError(#[from] TimsTofPathError),
#[error("TSF datasets do not provide precursor information")]
TsfNotSupported,
#[cfg(feature = "patched")]
#[error("Patched datasets are not supported")]
PatchedNotSupported,
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}
35 changes: 35 additions & 0 deletions crates/timsrust/src/spectrum_reader.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,8 @@ enum Inner {
timsrust_parquet_spectra::spectrum_reader::ParquetSpectrumReader,
),
Tsf(TSFSpectrumReader),
#[cfg(feature = "patched")]
Patched(timsrust_patched::PatchedSpectrumReader),
}

impl Inner {
Expand All @@ -47,6 +49,10 @@ impl Inner {
Inner::MiniTdf(reader) => Ok(reader.get(index)?),
Inner::ParquetSpectra(reader) => Ok(reader.get(index)?),
Inner::Tsf(reader) => Ok(reader.get(index)?),
#[cfg(feature = "patched")]
Inner::Patched(_) => {
Err(SpectrumReaderError::PatchedRandomAccessNotSupported)
},
}
}

Expand All @@ -57,6 +63,8 @@ impl Inner {
Inner::Centroider(reader) => reader.len(),
Inner::ParquetSpectra(reader) => reader.len(),
Inner::Tsf(reader) => reader.len(),
#[cfg(feature = "patched")]
Inner::Patched(reader) => reader.len(),
}
}

Expand All @@ -75,6 +83,8 @@ impl Inner {
Inner::MiniTdf(reader) => A::MiniTdf(reader),
Inner::ParquetSpectra(reader) => A::ParquetSpectra(reader),
Inner::Tsf(reader) => A::Tsf(reader),
#[cfg(feature = "patched")]
Inner::Patched(reader) => A::Patched(reader),
}
}
}
Expand All @@ -94,6 +104,8 @@ enum A<'a> {
&'a timsrust_parquet_spectra::spectrum_reader::ParquetSpectrumReader,
),
Tsf(&'a TSFSpectrumReader),
#[cfg(feature = "patched")]
Patched(&'a timsrust_patched::PatchedSpectrumReader),
}

impl<'a> ParallelIterator for A<'a> {
Expand Down Expand Up @@ -130,6 +142,12 @@ impl<'a> ParallelIterator for A<'a> {
|s| s.ok(),
)
.drive_unindexed(consumer),
#[cfg(feature = "patched")]
Self::Patched(reader) => rayon::iter::ParallelIterator::filter_map(
reader.par_iter(),
|s| s.ok(),
)
.drive_unindexed(consumer),
}
}
}
Expand Down Expand Up @@ -251,6 +269,9 @@ pub enum SpectrumReaderError {
NoPath,
#[error("Centroider is not supported")]
CentroiderNotSupported,
#[cfg(feature = "patched")]
#[error("Random access is not supported for patched datasets")]
PatchedRandomAccessNotSupported,
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}

#[derive(Debug, Default, Clone)]
Expand Down Expand Up @@ -285,6 +306,20 @@ impl SpectrumReaderBuilder {
Some(path) => path,
};
let spectrum_reader = match path.file_type() {
#[cfg(feature = "patched")]
TimsTofFileType::Patched(_) => {
if let Ok(reader) = timsrust_patched::PatchedSpectrumReader::from_file(path.as_ref()) {
let spectrum_reader = Inner::Patched(reader);
let mz_converter =
Arc::new(MzConverter::Bit(timsrust_core::BitConverter()));
return Ok(SpectrumReader {
spectrum_reader,
mz_converter,
});
} else {
return Err(SpectrumReaderError::PatchedRandomAccessNotSupported);
}
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},
TimsTofFileType::Tdf(tdf_path) => {
if Metadata::new(tdf_path.as_ref()).unwrap().acquisition_type()
== AcquisitionType::DIAPASEF
Expand Down
11 changes: 11 additions & 0 deletions crates/timsrust/src/timstof.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ pub(crate) enum TimsTofFileType {
Tdf(TDFPath),
Parquet(ParquetSpectrumPath),
Tsf(TSFPath),
#[cfg(feature = "patched")]
Patched(timsrust_patched::PatchedTimsTofPath),
}

#[derive(Debug, Clone, PartialEq, Eq, Hash)]
Expand All @@ -34,6 +36,15 @@ impl TimsTofPath {
pub fn new(path: impl AsRef<str>) -> Result<Self, TimsTofPathError> {
let uri = Uri::from(path.as_ref()).local_representation();
for path in [uri.as_ref(), path.as_ref()] {
#[cfg(feature = "patched")]
if let Ok(patched_path) =
timsrust_patched::PatchedTimsTofPath::new(path)
{
return Ok(Self {
uri: uri.clone(),
file_type: TimsTofFileType::Patched(patched_path),
});
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}
if let Ok(tdf) = TDFPath::new(path) {
return Ok(Self {
uri: tdf.uri().clone(),
Expand Down
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