Class: Rafflesia::FoldSearchRequest

Inherits:
Types::BaseModel
  • Object
show all
Defined in:
lib/rafflesia/proteins/fold_search_request.rb

Constant Summary collapse

HASH_ATTRS = 
{
  concurrency: :concurrency,
  database: :database,
  dry_run: :dry_run,
  exact_rerank: :exact_rerank,
  exact_rerank_backend: :exact_rerank_backend,
  exact_rerank_rank_key: :exact_rerank_rank_key,
  foldseek_alignment_type: :foldseek_alignment_type,
  foldseek_binary_path: :foldseek_binary_path,
  foldseek_exhaustive_search: :foldseek_exhaustive_search,
  foldseek_gpu: :foldseek_gpu,
  foldseek_kmer_size: :foldseek_kmer_size,
  foldseek_lddt_threshold: :foldseek_lddt_threshold,
  foldseek_prefilter_mode: :foldseek_prefilter_mode,
  foldseek_result_order: :foldseek_result_order,
  foldseek_sensitivity: :foldseek_sensitivity,
  foldseek_sort_by_structure_bits: :foldseek_sort_by_structure_bits,
  foldseek_threads: :foldseek_threads,
  foldseek_tmscore_threshold: :foldseek_tmscore_threshold,
  force_full_scan: :force_full_scan,
  index_ref: :index_ref,
  limit: :limit,
  manifest_object_id: :manifest_object_id,
  manifest_path: :manifest_path,
  max_candidates: :max_candidates,
  max_exact_shards: :max_exact_shards,
  max_materialized_bytes: :max_materialized_bytes,
  max_object_bytes: :max_object_bytes,
  max_object_reads: :max_object_reads,
  nprobe: :nprobe,
  object_store_root: :object_store_root,
  output_format: :output_format,
  output_relation: :output_relation,
  partition_by: :partition_by,
  preview_limit: :preview_limit,
  profile: :profile,
  query_id: :query_id,
  query_mode: :query_mode,
  query_structure_file_name: :query_structure_file_name,
  query_structure_object_id: :query_structure_object_id,
  query_structure_path: :query_structure_path,
  relation: :relation,
  release: :release,
  require_routing: :require_routing,
  require_zero_materialization: :require_zero_materialization,
  rerank_limit: :rerank_limit,
  shards: :shards,
  sort_by: :sort_by,
  target_dir: :target_dir,
  target_structure_objects: :target_structure_objects,
  target_structure_paths: :target_structure_paths,
  tmalign_binary_path: :tmalign_binary_path,
  verify_index: :verify_index
}.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(json) ⇒ FoldSearchRequest

Returns a new instance of FoldSearchRequest.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 117

def initialize(json)
  super()
  hash = self.class.normalize(json)
  @concurrency = hash[:concurrency]
  @database = hash[:database]
  @dry_run = hash[:dry_run]
  @exact_rerank = hash[:exact_rerank]
  @exact_rerank_backend = hash[:exact_rerank_backend]
  @exact_rerank_rank_key = hash[:exact_rerank_rank_key]
  @foldseek_alignment_type = hash[:foldseek_alignment_type]
  @foldseek_binary_path = hash[:foldseek_binary_path]
  @foldseek_exhaustive_search = hash[:foldseek_exhaustive_search]
  @foldseek_gpu = hash[:foldseek_gpu]
  @foldseek_kmer_size = hash[:foldseek_kmer_size]
  @foldseek_lddt_threshold = hash[:foldseek_lddt_threshold]
  @foldseek_prefilter_mode = hash[:foldseek_prefilter_mode]
  @foldseek_result_order = hash[:foldseek_result_order]
  @foldseek_sensitivity = hash[:foldseek_sensitivity]
  @foldseek_sort_by_structure_bits = hash[:foldseek_sort_by_structure_bits]
  @foldseek_threads = hash[:foldseek_threads]
  @foldseek_tmscore_threshold = hash[:foldseek_tmscore_threshold]
  @force_full_scan = hash[:force_full_scan]
  @index_ref = hash[:index_ref]
  @limit = hash[:limit]
  @manifest_object_id = hash[:manifest_object_id]
  @manifest_path = hash[:manifest_path]
  @max_candidates = hash[:max_candidates]
  @max_exact_shards = hash[:max_exact_shards]
  @max_materialized_bytes = hash[:max_materialized_bytes]
  @max_object_bytes = hash[:max_object_bytes]
  @max_object_reads = hash[:max_object_reads]
  @nprobe = hash[:nprobe]
  @object_store_root = hash[:object_store_root]
  @output_format = hash[:output_format]
  @output_relation = hash[:output_relation]
  @partition_by = (hash[:partition_by] || [])
  @preview_limit = hash[:preview_limit]
  @profile = hash[:profile]
  @query_id = hash[:query_id]
  @query_mode = hash[:query_mode]
  @query_structure_file_name = hash[:query_structure_file_name]
  @query_structure_object_id = hash[:query_structure_object_id]
  @query_structure_path = hash[:query_structure_path]
  @relation = hash[:relation]
  @release = hash[:release]
  @require_routing = hash[:require_routing]
  @require_zero_materialization = hash[:require_zero_materialization]
  @rerank_limit = hash[:rerank_limit]
  @shards = (hash[:shards] || [])
  @sort_by = (hash[:sort_by] || [])
  @target_dir = hash[:target_dir]
  @target_structure_objects = hash[:target_structure_objects] || {}
  @target_structure_paths = hash[:target_structure_paths] || {}
  @tmalign_binary_path = hash[:tmalign_binary_path]
  @verify_index = hash[:verify_index]
end

Instance Attribute Details

#concurrency ⇒ Object

Returns the value of attribute concurrency.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def concurrency
  @concurrency
end

#database ⇒ Object

Returns the value of attribute database.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def database
  @database
end

#dry_run ⇒ Object

Returns the value of attribute dry_run.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def dry_run
  @dry_run
end

#exact_rerank ⇒ Object

Returns the value of attribute exact_rerank.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def exact_rerank
  @exact_rerank
end

#exact_rerank_backend ⇒ Object

Returns the value of attribute exact_rerank_backend.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def exact_rerank_backend
  @exact_rerank_backend
end

#exact_rerank_rank_key ⇒ Object

Returns the value of attribute exact_rerank_rank_key.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def exact_rerank_rank_key
  @exact_rerank_rank_key
end

#foldseek_alignment_type ⇒ Object

Returns the value of attribute foldseek_alignment_type.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_alignment_type
  @foldseek_alignment_type
end

#foldseek_binary_path ⇒ Object

Returns the value of attribute foldseek_binary_path.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_binary_path
  @foldseek_binary_path
end

#foldseek_exhaustive_search ⇒ Object

Returns the value of attribute foldseek_exhaustive_search.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_exhaustive_search
  @foldseek_exhaustive_search
end

#foldseek_gpu ⇒ Object

Returns the value of attribute foldseek_gpu.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_gpu
  @foldseek_gpu
end

#foldseek_kmer_size ⇒ Object

Returns the value of attribute foldseek_kmer_size.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_kmer_size
  @foldseek_kmer_size
end

#foldseek_lddt_threshold ⇒ Object

Returns the value of attribute foldseek_lddt_threshold.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_lddt_threshold
  @foldseek_lddt_threshold
end

#foldseek_prefilter_mode ⇒ Object

Returns the value of attribute foldseek_prefilter_mode.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_prefilter_mode
  @foldseek_prefilter_mode
end

#foldseek_result_order ⇒ Object

Returns the value of attribute foldseek_result_order.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_result_order
  @foldseek_result_order
end

#foldseek_sensitivity ⇒ Object

Returns the value of attribute foldseek_sensitivity.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_sensitivity
  @foldseek_sensitivity
end

#foldseek_sort_by_structure_bits ⇒ Object

Returns the value of attribute foldseek_sort_by_structure_bits.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_sort_by_structure_bits
  @foldseek_sort_by_structure_bits
end

#foldseek_threads ⇒ Object

Returns the value of attribute foldseek_threads.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_threads
  @foldseek_threads
end

#foldseek_tmscore_threshold ⇒ Object

Returns the value of attribute foldseek_tmscore_threshold.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def foldseek_tmscore_threshold
  @foldseek_tmscore_threshold
end

#force_full_scan ⇒ Object

Returns the value of attribute force_full_scan.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def force_full_scan
  @force_full_scan
end

#index_ref ⇒ Object

Returns the value of attribute index_ref.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def index_ref
  @index_ref
end

#limit ⇒ Object

Returns the value of attribute limit.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def limit
  @limit
end

#manifest_object_id ⇒ Object

Returns the value of attribute manifest_object_id.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def manifest_object_id
  @manifest_object_id
end

#manifest_path ⇒ Object

Returns the value of attribute manifest_path.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def manifest_path
  @manifest_path
end

#max_candidates ⇒ Object

Returns the value of attribute max_candidates.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def max_candidates
  @max_candidates
end

#max_exact_shards ⇒ Object

Returns the value of attribute max_exact_shards.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def max_exact_shards
  @max_exact_shards
end

#max_materialized_bytes ⇒ Object

Returns the value of attribute max_materialized_bytes.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def max_materialized_bytes
  @max_materialized_bytes
end

#max_object_bytes ⇒ Object

Returns the value of attribute max_object_bytes.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def max_object_bytes
  @max_object_bytes
end

#max_object_reads ⇒ Object

Returns the value of attribute max_object_reads.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def max_object_reads
  @max_object_reads
end

#nprobe ⇒ Object

Returns the value of attribute nprobe.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def nprobe
  @nprobe
end

#object_store_root ⇒ Object

Returns the value of attribute object_store_root.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def object_store_root
  @object_store_root
end

#output_format ⇒ Object

Returns the value of attribute output_format.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def output_format
  @output_format
end

#output_relation ⇒ Object

Returns the value of attribute output_relation.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def output_relation
  @output_relation
end

#partition_by ⇒ Object

Returns the value of attribute partition_by.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def partition_by
  @partition_by
end

#preview_limit ⇒ Object

Returns the value of attribute preview_limit.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def preview_limit
  @preview_limit
end

#profile ⇒ Object

Returns the value of attribute profile.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def profile
  @profile
end

#query_id ⇒ Object

Returns the value of attribute query_id.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def query_id
  @query_id
end

#query_mode ⇒ Object

Returns the value of attribute query_mode.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def query_mode
  @query_mode
end

#query_structure_file_name ⇒ Object

Returns the value of attribute query_structure_file_name.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def query_structure_file_name
  @query_structure_file_name
end

#query_structure_object_id ⇒ Object

Returns the value of attribute query_structure_object_id.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def query_structure_object_id
  @query_structure_object_id
end

#query_structure_path ⇒ Object

Returns the value of attribute query_structure_path.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def query_structure_path
  @query_structure_path
end

#relation ⇒ Object

Returns the value of attribute relation.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def relation
  @relation
end

#release ⇒ Object

Returns the value of attribute release.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def release
  @release
end

#require_routing ⇒ Object

Returns the value of attribute require_routing.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def require_routing
  @require_routing
end

#require_zero_materialization ⇒ Object

Returns the value of attribute require_zero_materialization.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def require_zero_materialization
  @require_zero_materialization
end

#rerank_limit ⇒ Object

Returns the value of attribute rerank_limit.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def rerank_limit
  @rerank_limit
end

#shards ⇒ Object

Returns the value of attribute shards.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def shards
  @shards
end

#sort_by ⇒ Object

Returns the value of attribute sort_by.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def sort_by
  @sort_by
end

#target_dir ⇒ Object

Returns the value of attribute target_dir.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def target_dir
  @target_dir
end

#target_structure_objects ⇒ Object

Returns the value of attribute target_structure_objects.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def target_structure_objects
  @target_structure_objects
end

#target_structure_paths ⇒ Object

Returns the value of attribute target_structure_paths.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def target_structure_paths
  @target_structure_paths
end

#tmalign_binary_path ⇒ Object

Returns the value of attribute tmalign_binary_path.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def tmalign_binary_path
  @tmalign_binary_path
end

#verify_index ⇒ Object

Returns the value of attribute verify_index.



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# File 'lib/rafflesia/proteins/fold_search_request.rb', line 63

def verify_index
  @verify_index
end