Struct mzdata::io::mzml::MzMLReaderType

pub struct MzMLReaderType<R: Read, C: CentroidPeakAdapting = CentroidPeak, D: DeconvolutedPeakAdapting = DeconvolutedPeak> {
    pub state: MzMLParserState,
    pub spectrum_index: OffsetIndex,
    pub chromatogram_index: Box<OffsetIndex>,
    pub reference_param_groups: HashMap<String, Vec<Param>>,
    pub detail_level: DetailLevel,
    pub run: MassSpectrometryRun,
    /* private fields */
}

An mzML parser that supports iteration and random access. The parser produces Spectrum instances, which may be converted to RawSpectrum or CentroidSpectrum as is appropriate to the data.

When the readable stream the parser is wrapped around supports io::Seek, additional random access operations are available.

Fields

state: MzMLParserState

The state the parser was in last.

spectrum_index: OffsetIndex

A spectrum ID to byte offset for fast random access

chromatogram_index: Box<OffsetIndex>

reference_param_groups: HashMap<String, Vec<Param>>

A cache of repeated paramters

detail_level: DetailLevel

run: MassSpectrometryRun

Implementations

impl<'a, 'b: 'a, 'inner, 'outer: 'inner + 'event, 'event: 'inner, R: Read, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> MzMLReaderType<R, C, D>

pub fn new(file: R) -> MzMLReaderType<R, C, D>

Create a new MzMLReaderType instance, wrapping the io::Read handle provided with an io::BufReader and parses the metadata section of the file.

pub fn with_buffer_capacity_and_detail_level( file: R, capacity: usize, detail_level: DetailLevel ) -> MzMLReaderType<R, C, D>

pub fn read_into( &mut self, spectrum: &mut MultiLayerSpectrum<C, D> ) -> Result<usize, MzMLParserError>

Populate a new Spectrum in-place on the next available spectrum data. This allocates memory to build the spectrum’s attributes but then moves it into spectrum rather than copying it.

pub fn read_next(&mut self) -> Option<MultiLayerSpectrum<C, D>>

Read the next spectrum directly. Used to implement iteration.

impl<R: SeekRead, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> MzMLReaderType<R, C, D>

When the underlying stream supports random access, this type can read the index at the end of an indexedmzML document and use the offset map to jump to immediately jump to a specific spectrum

pub fn check_stream(&mut self, next_tag: &str) -> Result<bool, MzMLParserError>

pub fn get_chromatogram_by_id(&mut self, id: &str) -> Option<Chromatogram>

pub fn get_chromatogram_by_index( &mut self, index: usize ) -> Option<Chromatogram>

pub fn iter_chromatograms(&mut self) -> ChromatogramIter<'_, R, C, D>

impl<R: SeekRead, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> MzMLReaderType<R, C, D>

pub fn new_indexed(file: R) -> MzMLReaderType<R, C, D>

Construct a new MzMLReaderType and build an offset index using Self::build_index

pub fn with_buffer_capacity_and_detail_level_indexed( file: R, capacity: usize, detail_level: DetailLevel ) -> MzMLReaderType<R, C, D>

pub fn seek(&mut self, pos: SeekFrom) -> Result<u64>

pub fn stream_position(&mut self) -> Result<u64, Error>

pub fn read_index_from_end(&mut self) -> Result<u64, MzMLIndexingError>

Read the offset index at the end of an <indexedmzML> document, though this index may be malformed in some older files.

pub fn build_index(&mut self) -> u64

Builds an offset index to each <spectrum> XML element by doing a fast pre-scan of the XML file.

Trait Implementations

impl<R: Read, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> Iterator for MzMLReaderType<R, C, D>

MzMLReaderType instances are Iterators over Spectrum

type Item = MultiLayerSpectrum<C, D>

The type of the elements being iterated over.

fn next(&mut self) -> Option<Self::Item>

Advances the iterator and returns the next value.

fn next_chunk<const N: usize>( &mut self ) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>

where Self: Sized,

🔬This is a nightly-only experimental API. (iter_next_chunk)

Advances the iterator and returns an array containing the next N values.

fn size_hint(&self) -> (usize, Option<usize>)

Returns the bounds on the remaining length of the iterator.

fn count(self) -> usize

where Self: Sized,

Consumes the iterator, counting the number of iterations and returning it.

fn last(self) -> Option<Self::Item>

where Self: Sized,

Consumes the iterator, returning the last element.

fn advance_by(&mut self, n: usize) -> Result<(), NonZero<usize>>

🔬This is a nightly-only experimental API. (iter_advance_by)

Advances the iterator by n elements.

fn nth(&mut self, n: usize) -> Option<Self::Item>

Returns the nth element of the iterator.

fn step_by(self, step: usize) -> StepBy<Self>

where Self: Sized,

Creates an iterator starting at the same point, but stepping by the given amount at each iteration.

fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator<Item = Self::Item>,

Takes two iterators and creates a new iterator over both in sequence.

fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator,

‘Zips up’ two iterators into a single iterator of pairs.

fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>

where Self: Sized, G: FnMut() -> Self::Item,

🔬This is a nightly-only experimental API. (iter_intersperse)

Creates a new iterator which places an item generated by separator between adjacent items of the original iterator.

fn map<B, F>(self, f: F) -> Map<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> B,

Takes a closure and creates an iterator which calls that closure on each element.

fn for_each<F>(self, f: F)

where Self: Sized, F: FnMut(Self::Item),

Calls a closure on each element of an iterator.

fn filter<P>(self, predicate: P) -> Filter<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator which uses a closure to determine if an element should be yielded.

fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both filters and maps.

fn enumerate(self) -> Enumerate<Self>

where Self: Sized,

Creates an iterator which gives the current iteration count as well as the next value.

fn peekable(self) -> Peekable<Self>

where Self: Sized,

Creates an iterator which can use the peek and peek_mut methods to look at the next element of the iterator without consuming it. See their documentation for more information.

fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that skips elements based on a predicate.

fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that yields elements based on a predicate.

fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>

where Self: Sized, P: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both yields elements based on a predicate and maps.

fn skip(self, n: usize) -> Skip<Self>

where Self: Sized,

Creates an iterator that skips the first n elements.

fn take(self, n: usize) -> Take<Self>

where Self: Sized,

Creates an iterator that yields the first n elements, or fewer if the underlying iterator ends sooner.

fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>

where Self: Sized, F: FnMut(&mut St, Self::Item) -> Option<B>,

An iterator adapter which, like fold, holds internal state, but unlike fold, produces a new iterator.

fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>

where Self: Sized, U: IntoIterator, F: FnMut(Self::Item) -> U,

Creates an iterator that works like map, but flattens nested structure.

fn map_windows<F, R, const N: usize>(self, f: F) -> MapWindows<Self, F, N>

where Self: Sized, F: FnMut(&[Self::Item; N]) -> R,

🔬This is a nightly-only experimental API. (iter_map_windows)

Calls the given function f for each contiguous window of size N over self and returns an iterator over the outputs of f. Like slice::windows(), the windows during mapping overlap as well.

fn fuse(self) -> Fuse<Self>

where Self: Sized,

Creates an iterator which ends after the first None.

fn inspect<F>(self, f: F) -> Inspect<Self, F>

where Self: Sized, F: FnMut(&Self::Item),

Does something with each element of an iterator, passing the value on.

fn by_ref(&mut self) -> &mut Self

where Self: Sized,

Borrows an iterator, rather than consuming it.

fn collect<B>(self) -> B

where B: FromIterator<Self::Item>, Self: Sized,

Transforms an iterator into a collection.

fn collect_into<E>(self, collection: &mut E) -> &mut E

where E: Extend<Self::Item>, Self: Sized,

🔬This is a nightly-only experimental API. (iter_collect_into)

Collects all the items from an iterator into a collection.

fn partition<B, F>(self, f: F) -> (B, B)

where Self: Sized, B: Default + Extend<Self::Item>, F: FnMut(&Self::Item) -> bool,

Consumes an iterator, creating two collections from it.

fn is_partitioned<P>(self, predicate: P) -> bool

where Self: Sized, P: FnMut(Self::Item) -> bool,

🔬This is a nightly-only experimental API. (iter_is_partitioned)

Checks if the elements of this iterator are partitioned according to the given predicate, such that all those that return true precede all those that return false.

fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R

where Self: Sized, F: FnMut(B, Self::Item) -> R, R: Try<Output = B>,

An iterator method that applies a function as long as it returns successfully, producing a single, final value.

fn try_for_each<F, R>(&mut self, f: F) -> R

where Self: Sized, F: FnMut(Self::Item) -> R, R: Try<Output = ()>,

An iterator method that applies a fallible function to each item in the iterator, stopping at the first error and returning that error.

fn fold<B, F>(self, init: B, f: F) -> B

where Self: Sized, F: FnMut(B, Self::Item) -> B,

Folds every element into an accumulator by applying an operation, returning the final result.

fn reduce<F>(self, f: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(Self::Item, Self::Item) -> Self::Item,

Reduces the elements to a single one, by repeatedly applying a reducing operation.

fn try_reduce<F, R>( &mut self, f: F ) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType

where Self: Sized, F: FnMut(Self::Item, Self::Item) -> R, R: Try<Output = Self::Item>, <R as Try>::Residual: Residual<Option<Self::Item>>,

🔬This is a nightly-only experimental API. (iterator_try_reduce)

Reduces the elements to a single one by repeatedly applying a reducing operation. If the closure returns a failure, the failure is propagated back to the caller immediately.

fn all<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if every element of the iterator matches a predicate.

fn any<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if any element of the iterator matches a predicate.

fn find<P>(&mut self, predicate: P) -> Option<Self::Item>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Searches for an element of an iterator that satisfies a predicate.

fn find_map<B, F>(&mut self, f: F) -> Option<B>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Applies function to the elements of iterator and returns the first non-none result.

fn try_find<F, R>( &mut self, f: F ) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType

where Self: Sized, F: FnMut(&Self::Item) -> R, R: Try<Output = bool>, <R as Try>::Residual: Residual<Option<Self::Item>>,

🔬This is a nightly-only experimental API. (try_find)

Applies function to the elements of iterator and returns the first true result or the first error.

fn position<P>(&mut self, predicate: P) -> Option<usize>

where Self: Sized, P: FnMut(Self::Item) -> bool,

Searches for an element in an iterator, returning its index.

fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the maximum value from the specified function.

fn max_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the maximum value with respect to the specified comparison function.

fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the minimum value from the specified function.

fn min_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the minimum value with respect to the specified comparison function.

fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)

where FromA: Default + Extend<A>, FromB: Default + Extend<B>, Self: Sized + Iterator<Item = (A, B)>,

Converts an iterator of pairs into a pair of containers.

fn copied<'a, T>(self) -> Copied<Self>

where T: 'a + Copy, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which copies all of its elements.

fn cloned<'a, T>(self) -> Cloned<Self>

where T: 'a + Clone, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which clones all of its elements.

fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>

where Self: Sized,

🔬This is a nightly-only experimental API. (iter_array_chunks)

Returns an iterator over N elements of the iterator at a time.

fn sum<S>(self) -> S

where Self: Sized, S: Sum<Self::Item>,

Sums the elements of an iterator.

fn product<P>(self) -> P

where Self: Sized, P: Product<Self::Item>,

Iterates over the entire iterator, multiplying all the elements

fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,

🔬This is a nightly-only experimental API. (iter_order_by)

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn partial_cmp<I>(self, other: I) -> Option<Ordering>

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Lexicographically compares the PartialOrd elements of this Iterator with those of another. The comparison works like short-circuit evaluation, returning a result without comparing the remaining elements. As soon as an order can be determined, the evaluation stops and a result is returned.

fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,

🔬This is a nightly-only experimental API. (iter_order_by)

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn eq<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are equal to those of another.

fn eq_by<I, F>(self, other: I, eq: F) -> bool

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,

🔬This is a nightly-only experimental API. (iter_order_by)

Determines if the elements of this Iterator are equal to those of another with respect to the specified equality function.

fn ne<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are not equal to those of another.

fn lt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less than those of another.

fn le<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less or equal to those of another.

fn gt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than those of another.

fn ge<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than or equal to those of another.

fn is_sorted_by<F>(self, compare: F) -> bool

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> bool,

🔬This is a nightly-only experimental API. (is_sorted)

Checks if the elements of this iterator are sorted using the given comparator function.

fn is_sorted_by_key<F, K>(self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> K, K: PartialOrd,

🔬This is a nightly-only experimental API. (is_sorted)

Checks if the elements of this iterator are sorted using the given key extraction function.

impl<R: Read, C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> MSDataFileMetadata for MzMLReaderType<R, C, D>

fn data_processings(&self) -> &Vec<DataProcessing>

The series of DataProcessing workflows applied to spectra in this data file.

fn instrument_configurations(&self) -> &HashMap<u32, InstrumentConfiguration>

A mapping over different InstrumentConfiguration modes that spectra were acquired under.

fn file_description(&self) -> &FileDescription

A description of the contents and the sources for this mass spectrometry data file.

fn softwares(&self) -> &Vec<Software>

The series of Software applied to the data file to apply different DataProcessing methods.

fn data_processings_mut(&mut self) -> &mut Vec<DataProcessing>

Mutably access the DataProcessing list for this data file

fn instrument_configurations_mut( &mut self ) -> &mut HashMap<u32, InstrumentConfiguration>

Mutably access the InstrumentConfiguration mapping for this data file

fn file_description_mut(&mut self) -> &mut FileDescription

Mutably access the FileDescription description of the contents and the sources for this mass spectrometry data file.

fn softwares_mut(&mut self) -> &mut Vec<Software>

Mutably access the list of Software of this data file.

fn spectrum_count_hint(&self) -> Option<u64>

A hint about how many spectra are in this data file

fn run_description(&self) -> Option<&MassSpectrometryRun>

Access the MassSpectrometryRun metadata record if it is available

fn run_description_mut(&mut self) -> Option<&mut MassSpectrometryRun>

Mutably access the MassSpectrometryRun metadata record if it is available

fn copy_metadata_from(&mut self, source: &impl MSDataFileMetadata)

Copy the metadata from another MSDataFileMetadata implementation into this one.

fn source_file_name(&self) -> Option<&str>

Get the name of the primary source file, if available

impl<C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> MZFileReader<C, D> for MzMLReaderType<File, C, D>

fn open_file(source: File) -> Result<Self>

Given a regular file, construct a new instance without indexing.

fn construct_index_from_stream(&mut self) -> u64

An on-trait method of constructing an index. Assumed to be a trivial wrapper.

fn read_index(&mut self, reader: Box<dyn Read>) -> Result<&Self, Error>

Re-construct an offset index from this readable object, assuming it is a JSON stream over the serialized index.

fn write_index(&self, writer: Box<dyn Write>) -> Result<&Self, Error>

fn open_path<P>(path: P) -> Result<Self>

where P: Into<PathBuf> + Clone,

The preferred method of opening a file from a path-like object. This method will open the file at the provided path, test whether there is an accompanied index file next to it on the file system, and if not, build one and save it or otherwise read in the index.

impl<R: SeekRead, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> RandomAccessSpectrumIterator<C, D> for MzMLReaderType<R, C, D>

The iterator can also be updated to move to a different location in the stream efficiently.

fn start_from_id(&mut self, id: &str) -> Result<&mut Self, SpectrumAccessError>

Start iterating from the spectrum whose native ID matches id

fn start_from_index( &mut self, index: usize ) -> Result<&mut Self, SpectrumAccessError>

Start iterating from the spectrum whose index is index

fn start_from_time( &mut self, time: f64 ) -> Result<&mut Self, SpectrumAccessError>

Start iterating from the spectrum starting closest to time

impl<R: SeekRead, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> SpectrumSource<C, D> for MzMLReaderType<R, C, D>

They can also be used to fetch specific spectra by ID, index, or start time when the underlying file stream supports io::Seek.

fn get_spectrum_by_id(&mut self, id: &str) -> Option<MultiLayerSpectrum<C, D>>

Retrieve a spectrum by it’s native ID

fn get_spectrum_by_index( &mut self, index: usize ) -> Option<MultiLayerSpectrum<C, D>>

Retrieve a spectrum by it’s integer index

fn reset(&mut self)

Return the data stream to the beginning

fn get_index(&self) -> &OffsetIndex

Access the spectrum offset index to enumerate all spectra by ID

fn set_index(&mut self, index: OffsetIndex)

Set the spectrum offset index. This method shouldn’t be needed if not writing a new adapter

fn get_spectrum_by_time(&mut self, time: f64) -> Option<S>

Retrieve a spectrum by its scan start time Considerably more complex than seeking by ID or index, this involves a binary search over the spectrum index and assumes that spectra are stored in chronological order.

fn len(&self) -> usize

Retrieve the number of spectra in source file

fn is_empty(&self) -> bool

fn _offset_of_id(&self, id: &str) -> Option<u64>

Helper method to support seeking to an ID

fn _offset_of_index(&self, index: usize) -> Option<u64>

Helper method to support seeking to an index

fn _offset_of_time(&mut self, time: f64) -> Option<u64>

Helper method to support seeking to a specific time. Considerably more complex than seeking by ID or index.

fn iter(&mut self) -> SpectrumIterator<'_, C, D, S, Self>

where Self: Sized,

Open a new iterator over this stream.

fn groups( &mut self ) -> SpectrumGroupingIterator<SpectrumIterator<'_, C, D, S, Self>, C, D, S>

where Self: Sized,

Create a new SpectrumIterator over self and use that state to drive a SpectrumGroupIterator

fn into_groups(self) -> SpectrumGroupingIterator<Self, C, D, S>

where Self: Sized,

Consume self to create a SpectrumGroupIterator. This is ideal for non-rewindable streams like io::stdin which don’t implement io::Seek