Enum MZReaderType

#[non_exhaustive]
pub enum MZReaderType<R, C = CentroidPeak, D = DeconvolutedPeak>
where
    R: Read + Seek,
    C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap,
    D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,
{
    Unknown(Box<dyn SpectrumSourceWithMetadata<C, D, Item = MultiLayerSpectrum<C, D>> + Send + Sync>, PhantomData<R>),
}

An explicit file format dispatching ADT that provides the complete SpectrumSource, RandomAccessSpectrumIterator, MZFileReader and MSDataFileMetadata APIs. The preferred means of creating an instance is through the MZReaderType::open_path function.

This type internally wraps a concrete type and each operation has to perform a very fast test to decide which implementation to invoke. This overhead should be trivial for the vast majority of operations, as compared to the I/O being performed otherwise.

Please refer to each concrete implementation type for details about those types. Keep in mind that formats that require specific features to be enabled to be available won’t even be visible if their required features aren’t set since their variants would have an unknown size at compile time.

Variants (Non-exhaustive)

Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.

Unknown(Box<dyn SpectrumSourceWithMetadata<C, D, Item = MultiLayerSpectrum<C, D>> + Send + Sync>, PhantomData<R>)

Implementations

impl<R, C, D> MZReaderType<R, C, D>

where R: Read + Seek, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,

pub fn builder() -> MZReaderBuilder<C, D>

Create a MZReaderBuilder which can be used to configure the created reader, setting DetailLevel and buffer capacity The builder can create a reader from any type that the direct creation functions support.

pub fn as_format(&self) -> MassSpectrometryFormat

Get the file format for this reader

pub fn detail_level(&self) -> &DetailLevel

Get the DetailLevel the reader currently uses

pub fn set_detail_level(&mut self, detail_level: DetailLevel)

Set the DetailLevel for the reader, changing the amount of work done immediately on loading a spectrum.

Note

Not all readers support all detail levels, and the behavior when requesting one of those levels will depend upon the underlying reader.

pub fn open_read_seek(stream: R) -> Result<MZReaderType<R, C, D>, Error>

Create a reader from a type that supports io::Read and io::Seek.

Note

Not all formats can be read from an io type, these will fail to open and an error will be returned

pub fn open_gzipped_read_seek( stream: R, ) -> Result<MZReaderType<RestartableGzDecoder<BufReader<R>>, C, D>, Error>

Create a reader from a type that supports io::Read and io::Seek that is gzip-compressed.

Note

This method will return an error if the stream is not gzip-compressed.

Not all formats can be read from an io type, these will fail to open and an error will be returned

impl<R, C, D> MZReaderType<PreBufferedStream<R>, C, D>

where R: Read, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,

pub fn open_read( stream: R, ) -> Result<StreamingSpectrumIterator<C, D, MultiLayerSpectrum<C, D>, MZReaderType<PreBufferedStream<R>, C, D>>, Error>

Create a reader from a type that supports io::Read.

This will internally wrap the file in a PreBufferedStream for metadata reading, but does not construct an index for full random access. Attempting to use the reader to access spectra may move the reader forwards, but it can never go backwards.

Note

Not all formats can be read from an io type, these will fail to open and an error will be returned

pub fn open_gzipped_read( stream: R, ) -> Result<StreamingSpectrumIterator<C, D, MultiLayerSpectrum<C, D>, MZReaderType<PreBufferedStream<GzDecoder<PreBufferedStream<R>>>, C, D>>, Error>

Create a reader from a type that supports io::Read is gzip-compressed.

This will internally wrap the file in a PreBufferedStream for metadata reading, but does not construct an index for full random access. Attempting to use the reader to access spectra may move the reader forwards, but it can never go backwards.

Note

This method will return an error if the stream is not gzip-compressed.

Not all formats can be read from an io type, these will fail to open and an error will be returned

pub fn open_read_with_buffer_size( stream: R, buffer_size: usize, ) -> Result<StreamingSpectrumIterator<C, D, MultiLayerSpectrum<C, D>, MZReaderType<PreBufferedStream<R>, C, D>>, Error>

See MZReaderType::open_read.

This function lets the caller specify the prebuffering size for files with large headers that exceed the default buffer size.

Trait Implementations

impl<R, C, D> ChromatogramSource for MZReaderType<R, C, D>

where R: Read + Seek, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,

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

Get a Chromatogram by its identifier, if it exists.

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

Get a Chromatogram by its index, if it exists.

fn iter_chromatograms(&mut self) -> ChromatogramIterator<'_, Self>

where Self: Sized,

Iterate over Chromatograms with a ChromatogramIterator

impl<R, C, D> Debug for MZReaderType<R, C, D>

where R: Read + Seek, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl<C, D, R> IntoIonMobilityFrameSource<C, D> for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

type IonMobilityFrameSource<CF: FeatureLike<MZ, IonMobility>, DF: FeatureLike<Mass, IonMobility> + KnownCharge> = IMMZReaderType<R, CF, DF, C, D>

The IonMobilityFrameSource-implementing type for this SpectrumSource.

fn try_into_frame_source<CF, DF>( self, ) -> Result<<MZReaderType<R, C, D> as IntoIonMobilityFrameSource<C, D>>::IonMobilityFrameSource<CF, DF>, IntoIonMobilityFrameSourceError>

where CF: FeatureLike<MZ, IonMobility>, DF: FeatureLike<Mass, IonMobility> + KnownCharge,

Attempt to convert the SpectrumSource into an IonMobilityFrameSource, returning IntoIonMobilityFrameSourceError if it is not possible

fn into_frame_source<CF, DF>(self) -> Self::IonMobilityFrameSource<CF, DF>

where CF: FeatureLike<MZ, IonMobility>, DF: FeatureLike<Mass, IonMobility> + KnownCharge,

Call IntoIonMobilityFrameSource::try_into_frame_source, panicking if an error is returned.

fn has_ion_mobility(&mut self) -> Option<HasIonMobility>

Reads a sparse 1% of the entries from the SpectrumSource, testing for the presence of ion mobility data.

impl<C, D, R> Iterator for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

type Item = MultiLayerSpectrum<C, D>

The type of the elements being iterated over.

fn next(&mut self) -> Option<<MZReaderType<R, C, D> as Iterator>::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(self, separator: Self::Item) -> Intersperse<Self>

where Self: Sized, Self::Item: Clone,

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

Creates a new iterator which places a copy of separator between adjacent items of the original iterator.

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 flatten(self) -> Flatten<Self>

where Self: Sized, Self::Item: IntoIterator,

Creates an iterator that 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,

Creates a “by reference” adapter for this instance of Iterator.

fn collect<B>(self) -> B

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

Transforms an iterator into a collection.

fn try_collect<B>( &mut self, ) -> <<Self::Item as Try>::Residual as Residual<B>>::TryType

where Self: Sized, Self::Item: Try, <Self::Item as Try>::Residual: Residual<B>, B: FromIterator<<Self::Item as Try>::Output>,

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

Fallibly transforms an iterator into a collection, short circuiting if a failure is encountered.

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 partition_in_place<'a, T, P>(self, predicate: P) -> usize

where T: 'a, Self: Sized + DoubleEndedIterator<Item = &'a mut T>, P: FnMut(&T) -> bool,

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

Reorders the elements of this iterator in-place according to the given predicate, such that all those that return true precede all those that return false. Returns the number of true elements found.

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<R>( &mut self, f: impl FnMut(Self::Item, Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType

where Self: Sized, 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<R>( &mut self, f: impl FnMut(&Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType

where Self: Sized, 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 rposition<P>(&mut self, predicate: P) -> Option<usize>

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

Searches for an element in an iterator from the right, returning its index.

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

where Self: Sized, Self::Item: Ord,

Returns the maximum element of an iterator.

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

where Self: Sized, Self::Item: Ord,

Returns the minimum element of an iterator.

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 rev(self) -> Rev<Self>

where Self: Sized + DoubleEndedIterator,

Reverses an iterator’s direction.

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 cycle(self) -> Cycle<Self>

where Self: Sized + Clone,

Repeats an iterator endlessly.

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<I>(self, other: I) -> Ordering

where I: IntoIterator<Item = Self::Item>, Self::Item: Ord, Self: Sized,

Lexicographically compares the elements of this Iterator with those of another.

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(self) -> bool

where Self: Sized, Self::Item: PartialOrd,

Checks if the elements of this iterator are sorted.

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

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

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,

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

impl<C, D, R> MSDataFileMetadata for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

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 samples(&self) -> &Vec<Sample>

A list of sample descriptions that were measured in this data file if available.

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 samples_mut(&mut self) -> &mut Vec<Sample>

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

Get the name of the primary source file, if available

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

Access the MassSpectrometryRun metadata record if it is available

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

A hint about how many spectra are in this data file

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

where Self: Sized,

Copy the metadata from another MSDataFileMetadata implementation into this one.

fn set_spectrum_count_hint(&mut self, _value: Option<u64>)

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

Mutably access the MassSpectrometryRun metadata record if it is available

impl<C, D> MZFileReader<C, D> for MZReaderType<File, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap,

fn construct_index_from_stream(&mut self) -> u64

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

fn open_path<P>(path: P) -> Result<MZReaderType<File, C, D>, Error>

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.

fn open_file(source: File) -> Result<MZReaderType<File, C, D>, Error>

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

impl<C, D, R> RandomAccessSpectrumIterator<C, D> for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

fn start_from_id( &mut self, id: &str, ) -> Result<&mut MZReaderType<R, C, D>, SpectrumAccessError>

Start iterating from the spectrum whose native ID matches id

fn start_from_index( &mut self, index: usize, ) -> Result<&mut MZReaderType<R, C, D>, SpectrumAccessError>

Start iterating from the spectrum whose index is index

fn start_from_time( &mut self, time: f64, ) -> Result<&mut MZReaderType<R, C, D>, SpectrumAccessError>

Start iterating from the spectrum starting closest to time

impl<C, D, R> SpectrumSource<C, D> for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

fn reset(&mut self)

Rewind the current position of the source to the beginning

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 get_spectrum_by_time( &mut self, time: f64, ) -> Option<MultiLayerSpectrum<C, D>>

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 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 detail_level(&self) -> &DetailLevel

Get the DetailLevel the reader currently uses

fn set_detail_level(&mut self, detail_level: DetailLevel)

Set the DetailLevel for the reader, changing the amount of work done immediately on loading a spectrum.

fn len(&self) -> usize

Retrieve the number of spectra in source file, usually by getting the length of the index. If the index isn’t initialized, this will be 0.

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 get_group_by_index(&mut self, index: usize) -> Option<SpectrumGroup<C, D, S>>

where Self: Sized,

Get the nth SpectrumGroup from this source

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 SpectrumGroupingIterator

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

where Self: Sized,

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