Class: BioTable::Table

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/bio-table/table.rb

Overview

In memory table representation - note that the default parser/emitter does not use this class as it expects all data to be in memory.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(header = nil) ⇒ Table

Returns a new instance of Table.



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# File 'lib/bio-table/table.rb', line 12

def initialize header=nil
  @header = header if header
  @logger = Bio::Log::LoggerPlus['bio-table']
  @rows = []
  @rownames = []
end

Instance Attribute Details

#filename ⇒ Object (readonly)

Returns the value of attribute filename.



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# File 'lib/bio-table/table.rb', line 9

def filename
  @filename
end

#header ⇒ Object (readonly)

Returns the value of attribute header.



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# File 'lib/bio-table/table.rb', line 10

def header
  @header
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/bio-table/table.rb', line 9

def name
  @name
end

#rownames ⇒ Object (readonly)

Returns the value of attribute rownames.



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# File 'lib/bio-table/table.rb', line 10

def rownames
  @rownames
end

#rows ⇒ Object (readonly)

Returns the value of attribute rows.



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# File 'lib/bio-table/table.rb', line 10

def rows
  @rows
end

Instance Method Details

#[](row) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 87

def [] row
  if row
    TableRow.new(@rownames[row],@rows[row])
  else
    nil
  end
end

#each ⇒ Object 



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# File 'lib/bio-table/table.rb', line 125

def each 
  @rows.each_with_index do | row,i |
    yield TableRow.new(@rownames[i], row)
  end
end

#find_fields(rowname) ⇒ Object

Find a record by rowname and return the fields. Empty fields are nils.



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# File 'lib/bio-table/table.rb', line 96

def find_fields rowname
  row = row_by_name(rowname)
  fields = (row ? row.fields : [])
  # fill fields with nil to match header length
  # say header=5 fields=2 fill=2 (skip rowname)
  fields.fill(nil,fields.size,header.size-1-fields.size)
end

#push(rownames, fields = nil) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 77

def push rownames,fields = nil
  if fields == nil and rownames.kind_of?(TableRow)
    @rownames << rownames.rowname
    @rows << rownames.fields
  else
    @rownames << rownames
    @rows << fields
  end
end

#read_file(filename, options = {}) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 48

def read_file filename, options = {}
  lines = []
  if not options[:in_format] and filename =~ /\.csv$/
    @logger.debug "Autodetected CSV file"
    options[:in_format] = :csv
  end
  @logger.debug(options)
  # Read the file lines into an Array, not lazy FIXME 
  File.open(filename).each_line do | line |
    lines.push line
  end
  read_lines(lines, options)
end

#read_lines(lines, options = {}) ⇒ Object

Read lines (list/array of string) and add them to the table, setting row names and row fields. The first row is assumed to be the header and ignored if the header has been set (the case with merge/concat tables).



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# File 'lib/bio-table/table.rb', line 28

def read_lines lines, options = {}
  table_apply = TableApply.new(options)

  header = table_apply.parse_header(lines[0], options)
  Validator::valid_header?(header, @header)  # compare against older header when merging
  column_index,header = table_apply.column_index(header) # we may rewrite the header
  @header = header if not @header

  # parse the rest
  prev_line = @header[1..-1]
  (lines[1..-1]).each_with_index do | line, line_num |
    rowname, data_fields = table_apply.parse_row(line_num, line, column_index, prev_line, options)
    if data_fields
      @rownames << rowname if not options[:with_rownames] # otherwise doubles rownames
      @rows << data_fields if data_fields
    end
    prev_line = data_fields
  end
end

#row_by_columns(zip, idx = nil) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 108

def row_by_columns zip,idx=nil
  index = zip.first[0]
  value = zip.first[1]
  if idx 
    row = idx[zip.transpose[1]]
    return row if row.match_all_fields?(zip)
  else
    each do | row | 
      fields = row.all_fields
      if fields[index] == value
        return row if row.match_all_fields?(zip)
      end
    end
  end
  nil
end

#row_by_name(name) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 104

def row_by_name name
  self[rownames.index(name)]
end

#set_name(fn) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 19

def set_name fn
  @filename = fn
  @name = File.basename(fn,File.extname(fn))
end

#write(options = {}) ⇒ Object 



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# File 'lib/bio-table/table.rb', line 62

def write options = {}
  format = options[:format]
  format = :tab if not format
  evaluate = nil
  if format == :eval
    evaluate = options[:evaluate]
  end
  formatter = FormatFactory::create(format,evaluate)
  formatter.write(@header) if options[:write_header]
  each do | tablerow,num |
    # p tablerow
    formatter.write(tablerow.all_fields) if tablerow.all_valid?
  end
end