Abgabe MzML

.gitignore

@@ -34,5 +34,4 @@ cmake-*-build
 _CPack_Packages
 _deps
 Modules
-src/openms_gui/OpenMS_GUI_autogen
-src/openms/OpenMS_autogen
+src/openms_gui/OpenMS_GUI_autogen

.vscode/settings.json

@@ -1,5 +1,5 @@
 {
     "githubPullRequests.ignoredPullRequestBranches": [
         "develop"
-    ]
+    ],
 }

src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLHandler.h

@@ -6,6 +6,7 @@
 // $Authors: Marc Sturm, Chris Bielow, Hannes Roest $
 // --------------------------------------------------------------------------
 
+
 #pragma once
 
 #include <OpenMS/CONCEPT/Helpers.h>
@@ -22,6 +23,14 @@
 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
 #include <OpenMS/FORMAT/ControlledVocabulary.h>
 #include <OpenMS/FORMAT/VALIDATORS/SemanticValidator.h>
+#include <vector>
+#include <string>
+#include <utility>
+#include <OpenMS/CONCEPT/Types.h>       // for Int64
+#include <memory>
+
+
+
 
 #include <map>
 
@@ -122,9 +131,34 @@ namespace OpenMS
       /// Docu in base class XMLHandler::characters
       void characters(const XMLCh* const chars, const XMLSize_t length) override;
 
-      /// Docu in base class XMLHandler::writeTo
+      /**  
+    This function serializes the mzML data structure to the provided `std::ostream`.  
+    If the filename (stored in `file_`) ends with `.gz`, the output will be **gzip-compressed**.
+
+    ### Compression Behavior  
+    - Uses **zlib** (via `boost::iostreams`) with **fastest compression level** by default.  
+    - If **pigz** (parallel implementation of gzip) is **installed and available**, it will be used for faster compression.  
+    - Falls back to **Boost**-based compression if `pigz` is not available.  
+    - **Requires seekable streams** (e.g., file streams).    
+      - Use `storeBuffer()` for non-seekable targets (e.g., network streams).  
+
+    ### Error Handling  
+    @exception Exception::ConversionError  
+      - If **compression fails** (e.g., `boost::iostreams::gzip_error`).  
+      - If the **stream is non-seekable** but compression was requested.  
+      - If **writing/flushing** fails (`std::ios_base::failure`).  
+
+    @note  
+    - Compression is **determined solely by `file_`'s extension**, not the stream's state.  
+
+    @see MzMLHandlerHelper::writeFooter_  
+    @see storeBuffer()  
+    @see writeHeader_, writeSpectrum_, writeChromatogram_  
+*/
+
       void writeTo(std::ostream& os) override;
 
+
       //@}
 
       /**@name PeakFileOptions setters/getters
@@ -185,6 +219,12 @@ namespace OpenMS
 
       typedef MzMLHandlerHelper::BinaryData BinaryData;
 
+      const bool compress;
+      struct MzMLHandlerInternalState; // forward declaration
+      std::unique_ptr<MzMLHandlerInternalState> internal_state_;
+
+
+
       /**@name Helper functions for storing data in memory
        * @anchor helper_read
        */
@@ -380,6 +420,7 @@ namespace OpenMS
       /// map pointer for writing
       const MapType* cexp_{ nullptr };
 
+
       /// Options that can be set for loading/storing
       PeakFileOptions options_;
 
@@ -492,4 +533,3 @@ namespace OpenMS
 
   } // namespace Internal
 } // namespace OpenMS
-

src/openms/include/OpenMS/FORMAT/HANDLERS/XMLHandler.h

@@ -363,8 +363,32 @@ namespace OpenMS
       /// Parsing method for closing tags
       void endElement(const XMLCh * const uri, const XMLCh * const localname, const XMLCh * const qname) override;
 
-      /// Writes the contents to a stream.
-      virtual void writeTo(std::ostream & /*os*/);
+      /**
+      @brief Writes the mzML contents to a given output stream.
+
+      This function serializes the mzML data structure to the provided `std::ostream`.  
+      If the filename (stored in `file_`) ends with `.gz`, the output will be **gzip-compressed**.
+
+      ### Compression Behavior  
+      - Uses **zlib** (via `boost::iostreams`) with **fastest compression level** by default.  
+      - **Requires seekable streams** (e.g., file streams).    
+        - Use `storeBuffer()` for non-seekable targets (e.g., network streams).  
+
+      ### Error Handling  
+      @exception Exception::ConversionError  
+        - If **compression fails** (e.g., `boost::iostreams::gzip_error`).  
+        - If the **stream is non-seekable** but compression was requested.  
+        - If **writing/flushing** fails (`std::ios_base::failure`).  
+
+      @note  
+      - Compression is **determined solely by `file_`'s extension**, not the stream's state.  
+
+
+      @see MzMLHandlerHelper::writeFooter_  
+      @see storeBuffer()  
+      @see writeHeader_, writeSpectrum_, writeChromatogram_  
+    */
+      virtual void writeTo(std::ostream& os);
 
       /// handler which support partial loading, implement this method
       virtual LOADDETAIL getLoadDetail() const;

src/openms/include/OpenMS/FORMAT/MzMLFile.h

@@ -81,13 +81,22 @@ namespace OpenMS
     void loadSize(const String & filename, Size& scount, Size& ccount);
 
     /**
-      @brief Stores a map in an MzML file.
-
-      @p map has to be an MSExperiment or have the same interface.
-
-      @exception Exception::UnableToCreateFile is thrown if the file could not be created
-    */
-    void store(const String& filename, const PeakMap& map) const;
+  @brief Stores a map in an MzML file with gzip compression.
+
+  The method writes the data in gzip-compressed format using Boost Iostreams.
+
+  @p map has to be an MSExperiment or have the same interface.
+
+  @note The output is automatically compressed using gzip (boost::iostreams::gzip_compressor).
+  All data is flushed and files are properly closed after writing.
+
+  @param filename The name of the output file (will be created or overwritten)
+  @param map The PeakMap data to be stored
+
+  @exception Exception::UnableToCreateFile is thrown if the file could not be created
+  @exception Exception::IOException may be thrown if writing or compression fails
+*/
+void store(const String& filename, const PeakMap& map) const;
 
     /**
       @brief Stores a map in an output string.