Add --view flag to launch StrucTTY viewer after easy-search

[LunaJang]

Summary

• Add --view boolean flag to easy-search workflow (default: off)
• When enabled, automatically launches StrucTTY with query structure, result file, and target DB after search completion
• If StrucTTY is not found in PATH, prints a warning and exits normally — search results are always preserved

Changed files

• LocalParameters.h/cpp — register --view parameter
• EasyStructureSearch.cpp — pass VIEW_RESULTS and QUERY_INPUT to shell script
• easystructuresearch.sh — StrucTTY invocation logic (before REMOVE_TMP)

Test plan

• easy-search without --view: no behavior change
• easy-search --view 1 without StrucTTY in PATH: warning message, results preserved
• easy-search --view 1 with StrucTTY in PATH: viewer launches with correct arguments

🤖 Generated with Claude Code

[LunaJang]

@milot-mirdita
Hi, sorry to tag you directly...

This PR adds a --view flag to invoke StrucTTY for terminal visualization of Foldseek hits.
It builds cleanly locally, but CI is failing with -Werror promotions coming from existing submodule code (lib/mmseqs/src/commons/CSProfile.cpp, lib/foldcomp/src/database_writer.cpp, and a few others) — files my PR doesn't touch.
The last successful master build was in March, so... I suspect the CI toolchain may have picked up new warnings since then, but I'd really appreciate a second pair of eyes before I rule out my own changes....!

Happy to rebase/update submodules/adjust anything on my end if you can point me in the right direction. Thanks!!!!

[LunaJang]

Summary

• Add --view boolean flag to easy-search, search, easy-rbh, iterative-search,
  and profile workflows (default: off) to launch StrucTTY after the search
  completes
• Add --structty parameter for specifying the StrucTTY binary outside of
  PATH; passing it implicitly enables view mode
• Add standalone foldseek view command that launches StrucTTY directly against
  an existing .m8 file without re-running a search (foldseek view <i:queryFile> <i:resultM8> [<i:targetDB>] )
• Extract the StrucTTY invocation logic into a shared helper script
  structty_viewer.sh, embedded into the binary and emitted to tmpDir at runtime,
  so every workflow shares the same binary-resolution and command-assembly logic
• For search-style workflows that produce alignment DBs (not .m8), automatically
  run convertalis (29-col format) before invoking the viewer so StrucTTY can
  consume the output
• If StrucTTY is not found on PATH and --structty is unset, print a warning and
  exit normally — search results are always preserved; if --structty points to a
  missing or non-executable path, error out explicitly

Changed files

• src/commons/LocalParameters.h/cpp — register PARAM_VIEW_RESULTS and
  PARAM_STRUCTTY_PATH; add viewworkflow parameter set; promote --view to
  structuresearchworkflow in addition to easystructuresearchworkflow
• src/FoldseekBase.cpp + src/LocalCommandDeclarations.h — register the new view
  command
• src/workflow/StructTTYView.cpp (new) + src/workflow/CMakeLists.txt —
  implementation of the standalone foldseek view workflow
• src/workflow/EasyStructureSearch.cpp — pass VIEW_RESULTS, STRUCTTY_PATH,
  QUERY_INPUT to the shell script and emit structty_viewer.sh to tmpDir
• src/workflow/StructureSearch.cpp — same wiring for the search workflow plus
  convertalis parameter handling
• src/workflow/EasyStructureRbh.cpp — post-process StrucTTY invocation in C++
  since easyrbh.sh lives in the mmseqs library and cannot be modified
• data/structty_viewer.sh (new) + data/CMakeLists.txt — shared helper that
  resolves the StrucTTY binary (explicit path → PATH → warning) and assembles
  StrucTTY --foldseek --db
• data/easystructuresearch.sh — replace inline StrucTTY block with a call to
  structty_viewer.sh
• data/structuresearch.sh, data/structureiterativesearch.sh,
  data/structureprofile.sh — run convertalis to a temp .m8 then invoke
  structty_viewer.sh before REMOVE_TMP
• data/easystructurerbh.sh — viewer hook for the easy-rbh path

[LunaJang]

Summary

• Add StrucTTY viewer integration to launch an interactive terminal-based
  structure viewer directly from Foldseek search results.

• Add --view flag to easy-search, search, and easy-rbh to automatically launch
  StrucTTY after a search

• Add --structty flag to specify a custom StrucTTY binary path (also implicitly
  activates the viewer)

• Add foldseek structty subcommand to view existing result files independently

Usage:

• Launch viewer after search
  foldseek easy-search query.pdb target/ result.m8 tmp --view 1

• Specify custom StrucTTY binary path
  foldseek easy-search query.pdb target/ result.m8 tmp --structty
  /path/to/StrucTTY

• View existing results
  foldseek structty query.pdb result.m8 [targetDB]

Changed Files

• src/commons/LocalParameters.h/.cpp — Add --view and --structty parameters;
  register them to structuresearchworkflow, easystructuresearchworkflow, and
  structtyworkflow
• src/workflow/StructTTYView.cpp — New file; implements the structty subcommand
  that writes and executes structty_viewer.sh at runtime
• src/FoldseekBase.cpp — Register structty as a new COMMAND_EASY subcommand
• src/LocalCommandDeclarations.h — Declare structtyview function
• data/structty_viewer.sh — Shell script that handles StrucTTY invocation logic
• data/easystructuresearch.sh, data/easystructurerbh.sh,
  data/structuresearch.sh, data/structureiterativesearch.sh,
  data/structureprofile.sh — Add --view / --structty handling to trigger the
  viewer after search completion
• data/CMakeLists.txt, src/workflow/CMakeLists.txt — Add new files to the build
• README.md — Add "Visualize Results with StrucTTY" section and structty to the
  command list