Class: BioTable::TableApply
- Inherits:
-
Object
- Object
- BioTable::TableApply
- Defined in:
- lib/bio-table/table_apply.rb
Overview
Apply filters/rewrite etc. to a table, visiting a row at a time. For optimization this class contains some state
Instance Method Summary collapse
- #column_index(header) ⇒ Object
-
#initialize(options) ⇒ TableApply
constructor
A new instance of TableApply.
- #parse_header(line, options) ⇒ Object
- #parse_row(line_num, line, column_idx, last_fields, options) ⇒ Object
Constructor Details
#initialize(options) ⇒ TableApply
Returns a new instance of TableApply.
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# File 'lib/bio-table/table_apply.rb', line 7 def initialize @logger = Bio::Log::LoggerPlus['bio-table'] @num_filter = [:num_filter] @logger.debug "Filtering on #{@num_filter}" if @num_filter @rewrite = [:rewrite] @logger.debug "Rewrite #{@rewrite}" if @rewrite @use_columns = [:columns] @logger.debug "Filtering on columns #{@use_columns}" if @use_columns @column_filter = [:column_filter] @logger.debug "Filtering on column names #{@column_filter}" if @column_filter @include_rownames = [:with_rownames] @logger.debug "Include row names" if @include_rownames @first_column = (@include_rownames ? 0 : 1) end |
Instance Method Details
#column_index(header) ⇒ Object
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# File 'lib/bio-table/table_apply.rb', line 27 def column_index(header) column_idx = Filter::create_column_index(@use_columns,header) column_idx = Filter::filter_column_index(column_idx,header,@column_filter) new_header = Filter::apply_column_filter(header,column_idx) return column_idx, new_header end |
#parse_header(line, options) ⇒ Object
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# File 'lib/bio-table/table_apply.rb', line 23 def parse_header(line, ) LineParser::parse(line, [:in_format]) end |
#parse_row(line_num, line, column_idx, last_fields, options) ⇒ Object
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# File 'lib/bio-table/table_apply.rb', line 34 def parse_row(line_num, line, column_idx, last_fields, ) fields = LineParser::parse(line, [:in_format]) fields = Filter::apply_column_filter(fields,column_idx) return nil,nil if fields == [] rowname = fields[0] data_fields = fields[@first_column..-1] if data_fields.size > 0 return nil,nil if not Validator::valid_row?(line_num, data_fields, last_fields) return nil,nil if not Filter::numeric(@num_filter,data_fields) (rowname, data_fields) = Rewrite::rewrite(@rewrite,rowname,data_fields) end return rowname, data_fields end |