wiki:Extensions/SpectrumFileInspector

Spectrum File Inspector

Extension to inspect spectra in a selected spectrum file.

Download: SpectrumFileInspectorExtension-0.4-2.9.0.ext.jar, More...

Author: Olle Månsson, Department of Theoretical Physics, Lund University, Sweden

License: GNU General Public License version 2.

Documentation

The extension allows inspection of spectra in a selected spectrum file. It shows a list of spectrum Id values in the file. Clicking on a spectrum Id value will display the corresponding spectrum.

General specification:

  • If more than one file are selected, the first one is used.
  • If the file is not a supported type of spectrum file (including non-spectrum files), a message reporting this is shown.
  • A table of spectrum id values for the spectra in the file is shown. For a spectrum file without explicit spectrum id values, the order number of the spectra in the file is used.
  • Clicking on a spectrum id value shows a plot of the corresponding spectrum next to the table. Initially the first spectrum in the table is plotted.
  • The extension uses existing classes to get a reader for the spectrum file and plot the spectra, in order to take advantage of later enhancements of these classes, e.g. by supporting more types of spectrum files and showing more detailed spectrum plots.

Version 0.2:

  • For MGF (Mascot Generic Format) files, if an optional spectrum title exists, the spectrum order number is appended by " - " and the spectrum title (also available for version 0.1 if used with Proteios SE 2.5).
  • Spectrum properties are displayed in a box below the spectrum plot.

Version 0.3:

  • Spectrum file instrument and contact properties are displayed in a box below the spectrum properties. Spectrum file properties are currently only supported for mzData and mzML spectrum files.

Version 0.4:

  • Spectrum file inspector extension updated to forward action to class InspectActiveSpectrumFile, that is part of the standard Proteios SE code since version 2.7.0. Features of spectrum file inspector extension therefore now depends on the Proteios SE version number. For Proteios SE 2.7.0 and 2.8.0, the functionality of Spectrum file inspector extension version 0.4 should equal that of version 0.3.

Active development of Spectrum File Inspector as external extension terminated as of Proteios SE 2.14.0:

  • Starting with Proteios SE 2.14.0, Spectrum File Inspector is a core extension included in the standard Proteios SE installation (see Proteios SE Ticket #727 "Spectrum File Inspector Extension should be made a Core Extension"), and it is therefore not needed, nor recommended, to install the external extension separately on systems of Proteios SE version 2.14.0 or later. On Proteios SE version 2.13.0 or earlier, it will still be needed to install the extension separately in order to use its functionality, and it will therefore continue to be available for download.

Older Downloads

SpectrumFileInspectorExtension-0.1-2.3.ext.jar

SpectrumFileInspectorExtension-0.2-2.5.0.ext.jar

SpectrumFileInspectorExtension-0.3-2.7.0.ext.jar (Use SpectrumFileInspectorExtension-0.4-2.9.0.ext.jar instead)

Source Checkout

The extension source code can be checked out from the subversion repository using the following command:

svn co https://dev.thep.lu.se/proteios_extensions/svn/se/lu/thep/SpectrumFileInspector/trunk

Development Ticket

Ticket #1 (Extension to inspect spectra in a selected spectrum file)

Ticket #3 (Spectrum File Inspector Extension should display Spectrum Properties)

Ticket #4 (Spectrum File Inspector Extension should display Spectrum File Info)

Ticket #5 (Spectrum File Inspector Extension should forward action to InspectActiveSpectrumFile)

Last modified 18 months ago Last modified on Jun 9, 2021, 7:31:59 PM