Removed python view files

[matteopilz]

Summary by CodeRabbit

• Removed Features
  • Mass spectrometry data visualization and analysis tools, including spectrum display, scan tables, error plots, total ion chromatograms (TIC), MS1 intensity maps, and peptide sequence ion visualization, have been removed.
  • Interactive widgets for browsing scans, viewing and searching FASTA protein sequences, and loading mzTab files are no longer available.
  • File management and detection utilities for supported data types have been removed.
  • All related interactive plotting and annotation features for mass spectrometry data are no longer present.

[coderabbitai]

Walkthrough

This change deletes multiple PyQt5-based GUI widget modules and supporting classes from the src/view/ directory. The removed files include interactive visualization widgets for mass spectrometry data, file handlers, and table viewers for various proteomics formats (e.g., mzML, idXML, mzTab, FASTA). All public classes, methods, and signals in these files are removed.

Changes

Cohort / File(s)	Change Summary
Mass Spectrometry Visualization Widgets src/view/ControllerWidget.py, src/view/SpectrumWidget.py, src/view/TICWidget.py, src/view/MS1MapWidget.py, src/view/ErrorWidget.py, src/view/SequenceIonsWidget.py, src/view/ScanBrowserWidget.py, src/view/ScanTableWidget.py	All classes and methods implementing spectrum, TIC, MS1 map, error, sequence ions, scan browser, and scan table widgets are deleted, removing interactive and visualization features for mass spectrometry data.
File and Data Handlers src/view/FilesNumberHandler.py	The class and global dictionaries for detecting, managing, and validating presence of specific file types in a directory are removed.
FASTA Viewer GUI src/view/GUI_FastaViewer.py	The entire PyQt5-based protein FASTA file viewer, including search and display functionality, is deleted.
mzTab Table Widgets src/view/mzTabLoadWidget.py, src/view/mzTabTableWidget.py	Classes and methods for loading, parsing, and displaying mzTab protein and PSM data in interactive tables are deleted.

Sequence Diagram(s)

No sequence diagrams generated due to the nature of the changes (complete deletions).

Estimated code review effort

🎯 5 (Critical) | ⏱️ ~70+ minutes

Poem

In the warren of code, widgets once hopped,
Spectra and tables, all clicking nonstop.
Now the meadow is quiet, the plots packed away,
No ions or proteins to brighten the day.
But rabbits are nimble—new seeds soon will sprout,
For every old tunnel, new paths will come out!
🐇✨

Note

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Learn more here, or try it out under "Finishing Touches" below.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between fbdfcac and afc04c3.

📒 Files selected for processing (12)

• src/view/ControllerWidget.py (0 hunks)
• src/view/ErrorWidget.py (0 hunks)
• src/view/FilesNumberHandler.py (0 hunks)
• src/view/GUI_FastaViewer.py (0 hunks)
• src/view/MS1MapWidget.py (0 hunks)
• src/view/ScanBrowserWidget.py (0 hunks)
• src/view/ScanTableWidget.py (0 hunks)
• src/view/SequenceIonsWidget.py (0 hunks)
• src/view/SpectrumWidget.py (0 hunks)
• src/view/TICWidget.py (0 hunks)
• src/view/mzTabLoadWidget.py (0 hunks)
• src/view/mzTabTableWidget.py (0 hunks)

💤 Files with no reviewable changes (12)

• src/view/mzTabLoadWidget.py
• src/view/SpectrumWidget.py
• src/view/SequenceIonsWidget.py
• src/view/ControllerWidget.py
• src/view/MS1MapWidget.py
• src/view/FilesNumberHandler.py
• src/view/ScanTableWidget.py
• src/view/ScanBrowserWidget.py
• src/view/ErrorWidget.py
• src/view/TICWidget.py
• src/view/GUI_FastaViewer.py
• src/view/mzTabTableWidget.py

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)

• GitHub Check: build-test

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[timosachsenberg]

thanks!