Process sequence-related parameters — process_sequence

Standardizes sequence parameters (e.g., radius, gap) from flexible input formats into a vector named by sequence IDs. Supported formats:

Usage

process_sequence_param(
  param,
  seqs,
  param_name,
  default_value = NULL,
  allow_null = FALSE
)

Arguments

param: Input parameter (can be NULL, single value, vector, named vector, or list)
seqs: Character vector, list of sequence IDs
param_name: Character, name of the parameter (used in error messages)
default_value: Default value when param is NULL, default NULL
allow_null: Logical, whether to allow param to be NULL, default FALSE

Value

Named vector (names are seq_ids), standardized parameter values

Details

1. A single value, recycled to every sequence. 2. A named vector by sequence ID, e.g. `c("MT108731.1" = 3, "OR222515.1" = 1)`. 3. An unnamed vector with length equal to the number of sequences (matched by sequence order). 4. A list named by sequence ID. 5. A list named by sequence order ("1", "2", ...). 6. An unnamed list matched by sequence order (length 1 or equal to the number of sequences); a length-one list recycles.