UIMFLibrary 3.8.26

UIMF Library

This software package includes a library of C# functions to create, modify and extract data from UIMF files. UIMF files are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL).

NuGet

The UIMFLibrary is available on NuGet at:

• https://www.nuget.org/packages/UIMFLibrary/

Continuous Integration

The latest version of the application may be available on the AppVeyor CI server, but builds are deleted after 6 months.

How to use the UIMFLibrary in C#:

• Use the NuGet package manager to add a reference to the UIMFLibrary
  • Note that it depends on System.Data.SQLite

using UIMFLibrary;

• Declare the DataReader and DataWriter classes in your main code:
• Now the functions can be called as such:

UIMFReader DataReader = new UIMFReader(filePath);
DataReader.GetSpectrum(frameNumber, DataReader.FrameType.MS1, scanNumber, out var mzArray, out var intensityArray)
    ......

UIMFWriter DataWriter = new UIMFWriter(filePath);
DataWriter.CreateTables();

How to use the UIMFLibrary in C++:

• Copy UIMFLibrary.dll and System.Data.SQLite.DLL from either
  • UIMFLibrary\bin\x86
  • UIMFLibrary\bin\x64
• Open the Solution Explorer, add UIMFLibrary to your Project/References
• Add this using statement at the top of your code:

using namespace UIMFLibrary;

• In your .h file, declare the DataReader and DataWriter classes:

gcroot<UIMFReader*> ReadUIMF;
gcroot<UIMFWriter*> WriteUIMF;

• In you .cpp file, instantantiate the reader and the writer:

• Now the functions can be called as such:

ReadUIMF = new UIMFReader(filePath);
ReadUIMF->GetSpectrum(frameNumber, scanNumber, mzArray, intensityArray);
  ......

WriteUIMF = new UIMFWriter(filePath);
WriteUIMF->CreateTables();

Examples

To see examples of how to create, modify, and extract data out of the database, refer to the UIMFLibrary_Demo solution (see GitHub)

UIMF database structure:

Tables in a UIMF database file:

The UIMFWriter can optionally populate the legacy tables, but their use was phased out starting in 2015.

Global_Params

Frame_Param_Keys

Frame_Params

Frame_Scans table

Log_Entries table

Bin_Intensities table

Legacy Global_Parameters table

Legacy Frame_Parameters table

Contacts

Written by PNNL Staff for the Department of Energy (PNNL, Richland, WA)
Copyright 2009, Battelle Memorial Institute. All Rights Reserved.

Contributors include:
Kevin Crowell, Bill Danielson, Bryson Gibbons, Matthew Monroe, Spencer Prost, Yan Shi, Anuj Shah, Gordon Slysz

E-mail: matthew.monroe@pnnl.gov or proteomics@pnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/UIMF-Library

License

Licensed under the Educational Community License, Version 2.0 (the "License"); you may not use this program except in compliance with the License. You may obtain a copy of the License at

https://opensource.org/licenses/ECL-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.