fix off by one error in crosslink position calculation

[NeleRiediger]

Description

fixes #453
Already explained in the Issue description.

Changes

• I fixed the off-by-one error.
• Then I fixed the tests that used 0 as a value for 1-based positions (those tests worked before because of the bug).
• I also updated a docstring stating that the CL position within peptides was 0-based, while this is clearly not the case as stated elsewhere.
• Lastly I also added a test making sure the amino acid of the CL position within peptides on the peptide sequence is the same as the amino acid of the absolute CL position on the whole protein sequence. So this would hopefully be caught in the future. (I had to move the function in question one layer up for this)

Testing

I described in the issue description how to reproduce the bug and you can check whether everything is correct now the same way.

PR checklist

Development

• If necessary, I have updated the documentation (README, docstrings, etc.)
• If necessary, I have created / updated tests.

Mergeability

• main-branch has been merged into local branch to resolve conflicts
• The tests and linter have passed AFTER local merge
• The backend code has been formatted with black
• The frontend code has been formatted with pnpm format and checked with pnpm lint

Code review

• I have self-reviewed my code.
• At least one other developer reviewed and approved the changes

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
backend/main
views_helper.py					290-293
backend/protzilla/data_analysis
crosslinking_validation.py
backend/protzilla/importing
crosslinking_import.py
Project Total

This report was generated by python-coverage-comment-action

[AnnaPolensky]

Looks good and I was able to validate the positions.

Small suggestion: Maybe we could include in the column names that the positions are 1-based.

[3dot141592]

I reproduced the issue you described in #453, and everything appears to be correct. Code looks perfect :).

[NeleRiediger]

Looks good and I was able to validate the positions.

Small suggestion: Maybe we could include in the column names that the positions are 1-based.

I adjusted the column names for "crosslinker_position1/2" to "1-based_crosslinker_position1/2" and "CL_position_within_peptide1/2" to "1_based_CL_position_within_peptide1/2". Maybe just sanity check if I messed anything up :)

[AnnaPolensky]

Looks good :)