Add PeptideShaker import UI support for InstaNovo result files

[BioGeek]

InstaNovo is a de novo peptide sequencing tool.

This PR updates the import UI for normalized CSV output from InstaNovo v1.2.2 in three modes:

• InstaNovo: de novo peptide sequencing with the transformer-based InstaNovo model.
• InstaNovo+: de novo peptide sequencing with the diffusion-based InstaNovo+ model.
• InstaNovo with refinement: InstaNovo predictions refined with InstaNovo+.

Changes

• Adds separate identification-file chooser filters for:
  • InstaNovo (.instanovo.csv, .instanovo.csv.gz)
  • InstaNovo+ (.instanovoplus.csv, .instanovoplus.csv.gz)
  • InstaNovo with refinement (.instanovo.refined.csv, .instanovo.refined.csv.gz)
• Keeps refined output visible as its own workflow instead of grouping it under both InstaNovo and InstaNovo+.

De Novo Projects Without A FASTA

PeptideShaker can now create and open de novo only projects that have no protein sequence database, so InstaNovo results can be imported directly:

• De novo only runs (no FASTA) produce a PSM level project with target/decoy FDR disabled.
• An empty sequence provider is used; peptides are kept without protein mapping (the "peptide not matching to the database" filter no longer drops them when there is no database).
• FastaSummary, gene mapping, protein inference, project export and the report Database field are skipped or guarded when the FASTA is null (previously this crashed with an NPE).
• The empty target/decoy map no longer throws while estimating probabilities.
• The New Project dialog allows creating a de novo project without a FASTA (after a confirmation); existing de novo projects open without prompting for a database.
• Note: de novo projects have no target/decoy FDR. I intend to submit a follow-up PR where Winnow is used for de novo FDR control.

Commits: Support de novo only projects without a protein database, Handle de novo only projects in the GUI.

Implementation Notes

• The actual CSV parsing support is introduced in the matching Compomics Utilities PR.
• This PR updates the PeptideShaker import UI and the import/open pipeline to match those supported file types.

Screenshot

Tests

Ran:

mvn -Dtest=eu.isas.peptideshaker.test.fileimport.InstaNovoIdentificationFileUtilsTest,eu.isas.peptideshaker.test.cmd.PeptideShakerInstaNovoCLITest test
mvn -DskipTests -Dmaven.javadoc.skip=true package

• PeptideShakerInstaNovoCLITest is an end-to-end CLI integration test: it runs the PeptideShaker command line on InstaNovo CSV output with no FASTA and verifies a PSM level project is created.

Merge Order

Recommended order:

1. Add InstaNovo and InstaNovo+ import support compomics-utilities#73
2. Add SearchGUI support for InstaNovo and InstaNovo+ searchgui#387
3. This PR
4. Add DeNovoGUI compatibility APIs to Utilities compomics-utilities#74
5. Add InstaNovo support to DeNovoGUI denovogui#53
6. Update SearchGUI recipe to 4.3.17 bioconda/bioconda-recipes#66604
7. Update PeptideShaker recipe to 3.0.13 bioconda/bioconda-recipes#66603
8. Expose InstaNovo workflows in online input form barsnes-group/peptide-shaker-online#30
9. Bump PeptideShaker wrappers for InstaNovo support galaxyproteomics/tools-galaxyp#828