3.GUI: a pairwise spectrum view
This GUI enables the manual inspection of how spectra actually look alike and can be downloaded here.
1-Start the application: GUI can be started by running a command prompt in a folder that contains spectrum_similarity_pairwise_GUI-X.Y.Z.jar (X.Y.Z shows the current version number). On the command prompt, the following line needs to be executed:
java -jar spectrum_similarity_pairwise_GUI-0.1.jar
2-Introduce the files:
The required inputs
- Two folders containing spectra that are compared (specA and specB, and must be mgf files)
- A text file containing calculated scores
- Indices of spectrum titles from these two spectra folders in a given text file
3-Create: Click on the CREATE button to start visualizing pairwise spectra.
A pairwise spectra can be inspected either as bubble spectra (see above) or mirrored spectra (see below).
FILTERING: Each visualization can be also inspected by applying noise filtering. Clicking the NoiseFilter button applies an adaptive noise filtering from pride-asa-pipeline. The resulted remaining percentage can be automatically given.
Alternatively, the sliding bar allows the removal of low-intense peaks corresponding to the remaining percentage of peaks in a given spectrum.
Note that column colors and spectrum colors in visualization match.