API

src/io.rs

@@ -11,7 +11,9 @@ pub mod infer_format;
 pub(crate) mod compression;
 
 pub use crate::io::mgf::{MGFReader, MGFError, MGFWriter};
-pub use crate::io::mzml::{MzMLReader, MzMLParserError};
+pub use crate::io::mzml::{MzMLReader, MzMLParserError, MzMLWriter};
+#[cfg(feature = "async")]
+pub use crate::io::mzml::AsyncMzMLReaderType;
 #[cfg(feature = "mzmlb")]
 pub use crate::io::mzmlb::{MzMLbReader, MzMLbError};
 pub use crate::io::offset_index::OffsetIndex;

src/io/infer_format.rs

@@ -21,6 +21,9 @@ use crate::io::compression::{is_gzipped, is_gzipped_extension};
 #[cfg(feature = "mzmlb")]
 use super::traits::MZFileReader;
 
+
+/// Mass spectrometry file formats that [`mzdata`]
+/// supports
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
 pub enum MassSpectrometryFormat {
     MGF,
@@ -31,6 +34,8 @@ pub enum MassSpectrometryFormat {
 }
 
 
+/// Given a path, infer the file format and whether or not the file at that path is
+/// GZIP compressed
 pub(crate) fn infer_from_path<P: Into<path::PathBuf>,>(path: P) -> (MassSpectrometryFormat, bool) {
     let path: path::PathBuf = path.into();
     let (is_gzipped, path) = is_gzipped_extension(path);
@@ -53,6 +58,8 @@ pub(crate) fn infer_from_path<P: Into<path::PathBuf>,>(path: P) -> (MassSpectrom
 }
 
 
+/// Given a stream of bytes, infer the file format and whether or not the
+/// stream is GZIP compressed. This assumes the stream is seekable.
 pub(crate) fn infer_from_stream<R: Read + Seek>(stream: &mut R) -> io::Result<(MassSpectrometryFormat, bool)> {
     let mut buf = Vec::with_capacity(100);
     let current_pos = stream.seek(io::SeekFrom::Current(0))?;
@@ -76,6 +83,9 @@ pub(crate) fn infer_from_stream<R: Read + Seek>(stream: &mut R) -> io::Result<(M
 }
 
 
+/// Given a path, infer the file format and whether or not the file at that path is
+/// GZIP compressed, using both the file name and by trying to open and read the file
+/// header
 pub(crate) fn infer_format<P: Into<path::PathBuf>>(path: P) -> io::Result<(MassSpectrometryFormat, bool)> {
     let path: path::PathBuf = path.into();
 
@@ -94,6 +104,8 @@ pub(crate) fn infer_format<P: Into<path::PathBuf>>(path: P) -> io::Result<(MassS
 }
 
 
+/// Given a local file system path, infer the file format, and attempt to open it
+/// for reading.
 pub fn open_file<P: Into<path::PathBuf>>(path: P) -> io::Result<Box<dyn ScanSource>>{
     let path = path.into();
     let (format, is_gzipped) = infer_format(path.clone())?;

src/io/mzml/writer.rs

@@ -417,8 +417,7 @@ where
         if self.state < MzMLWriterState::DocumentOpen {
             self.start_document()?;
         } else {
-            panic!(
-                "Cannot start writing the header of mzML, currently in state {:?} which happens after.", self.state)
+            return self.transition_err(MzMLWriterState::Header)
         }
         self.write_cv_list()?;
         self.write_file_description()?;

src/io/prelude.rs

@@ -1,9 +1,9 @@
 pub use super::traits::{
-    MZFileReader, RandomAccessSpectrumIterator, ScanAccessError, SpectrumIterator, ScanSource, ScanWriter,
-    SeekRead, SpectrumGroup, SpectrumGrouping, SpectrumGroupingIterator,
+    MZFileReader, RandomAccessSpectrumIterator, ScanAccessError, ScanSource, ScanWriter, SeekRead,
+    SpectrumGroup, SpectrumGrouping, SpectrumGroupingIterator, SpectrumIterator,
 };
 pub use crate::meta::MSDataFileMetadata;
 pub use crate::params::{ParamDescribed, ParamLike};
-pub use crate::spectrum::{PrecursorSelection, SpectrumBehavior, IonProperties};
+pub use crate::spectrum::{IonProperties, PrecursorSelection, SpectrumBehavior};
 pub use std::convert::TryInto;
 pub use std::io::prelude::*;

src/io/traits.rs

@@ -17,6 +17,8 @@ pub trait SeekRead: io::Read + io::Seek {}
 impl<T: io::Read + io::Seek> SeekRead for T {}
 
 /// A base trait defining the behaviors of a source of spectra.
+///
+/// A [`ScanSource`]
 pub trait ScanSource<
     C: CentroidLike + Default = CentroidPeak,
     D: DeconvolutedCentroidLike + Default = DeconvolutedPeak,
@@ -293,12 +295,10 @@ pub trait MZFileReader<
                             Ok(_) => {}
                             Err(_err) => {
                                 reader.construct_index_from_stream();
-                                // _save_index(&index_path, &reader)?;
                             }
                         }
                     } else {
                         reader.construct_index_from_stream();
-                        // _save_index(&index_path, &reader)?;
                     }
                 }
                 Ok(reader)

src/io/utils.rs

@@ -96,8 +96,9 @@ where
     }
 }
 
+/// A writable stream that keeps a running MD5 checksum of all bytes
 #[derive(Clone)]
-pub struct MD5HashingStream<T: io::Write> {
+pub(crate) struct MD5HashingStream<T: io::Write> {
     pub stream: T,
     pub context: MD5Context,
 }