Class Bio::Nexus::NexusMatrix
In: lib/bio/db/nexus.rb
Parent: Object

DESCRIPTION

Bio::Nexus::NexusMatrix represents a characters or distance matrix, where the names are stored in column zero.

USAGE

  require 'bio/db/nexus'

  # Create a new parser:
  nexus = Bio::Nexus.new( nexus_data_as_string )
  # Get distances block(s):
  distances_block = nexus.get_distances_blocks[ 0 ]
  # Get matrix as Bio::Nexus::NexusMatrix object:
  matrix = distances_blocks.get_matrix
  # Get value (column 0 are names):
  val = matrix.get_value( 1, 5 )
  # Return first row as String (all columns except column 0),
  # values are separated by "_":
  row_str_0 = matrix.get_row_string( 0, "_" )
  # Return all rows named "ciona" as String (all columns except column 0),
  # values are separated by "+":
  ciona_rows = matrix.get_row_strings_by_name( "ciona", "+" )

Methods

get_max_col   get_max_row   get_name   get_row_string   get_row_strings_by_name   get_value   is_empty?   new   set_value   to_nexus_row_array   to_s   to_str  

Classes and Modules

Class Bio::Nexus::NexusMatrix::NexusMatrixError

Public Class methods

new()

Creates new NexusMatrix.

[Source]

      # File lib/bio/db/nexus.rb, line 1585
1585:       def initialize()
1586:         @rows = Hash.new
1587:         @max_row = -1
1588:         @max_col = -1
1589:       end

Public Instance methods

get_max_col()

Returns the maximal columns number.

Returns:Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1641
1641:       def get_max_col 
1642:         return @max_col
1643:       end
get_max_row()

Returns the maximal row number.

Returns:Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1648
1648:       def get_max_row 
1649:         return @max_row
1650:       end
get_name( row )

Convenience method which return the value of column 0 and row ‘row’ which is usually the name.

Arguments:

  • (required) row: Integer
Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1667
1667:       def get_name( row )
1668:         get_value( row, 0 ).to_s
1669:       end
get_row_string( row, spacer = "" )

Returns the values of columns 1 to maximal column length in row ‘row’ concatenated as string. Individual values can be separated by ‘spacer’.

Arguments:

  • (required) row: Integer
  • (optional) spacer: String
Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1680
1680:       def get_row_string( row, spacer = "" )
1681:         row_str = String.new
1682:         if is_empty?
1683:           return row_str
1684:         end
1685:         for col in 1 .. get_max_col
1686:           row_str << get_value( row, col ) << spacer
1687:         end
1688:         row_str
1689:       end
get_row_strings_by_name( name, spacer = "" )

Returns all rows as Array of Strings separated by ‘spacer’ for which column 0 is ‘name’.

Arguments:

Returns:Array

[Source]

      # File lib/bio/db/nexus.rb, line 1698
1698:       def get_row_strings_by_name( name, spacer = "" )
1699:         row_strs = Array.new
1700:         if is_empty?
1701:           return row_strs
1702:         end
1703:         for row in 0 .. get_max_row
1704:           if ( get_value( row, 0 ) == name )
1705:             row_strs.push( get_row_string( row, spacer ) )  
1706:           end
1707:         end
1708:         row_strs
1709:       end
get_value( row, col )

Returns the value at row ‘row’ and column ‘col’.

Arguments:

  • (required) row: Integer
  • (required) col: Integer
Returns:Object

[Source]

      # File lib/bio/db/nexus.rb, line 1623
1623:       def get_value( row, col )
1624:         if ( ( row > get_max_row() ) || ( row < 0 ) ) 
1625:           raise( NexusMatrixError, "value for row (" + row.to_s +
1626:             ") is out of range [max row: " + get_max_row().to_s + "]" )
1627:         elsif ( ( col > get_max_col() ) || ( row < 0 ) )
1628:           raise( NexusMatrixError, "value for column (" + col.to_s +
1629:            ") is out of range [max column: " + get_max_col().to_s + "]" )
1630:         end
1631:         r = @rows[ row ]
1632:         if ( ( r == nil ) || ( r.length < 1 ) ) 
1633:           return nil
1634:         end
1635:         r[ col ]
1636:       end
is_empty?()

Returns true of matrix is empty.

Returns:true or false

[Source]

      # File lib/bio/db/nexus.rb, line 1656
1656:       def is_empty?
1657:         return get_max_col < 0 || get_max_row < 0
1658:       end
set_value( row, col, value )

Sets the value at row ‘row’ and column ‘col’ to ‘value’.

Arguments:

  • (required) row: Integer
  • (required) col: Integer
  • (required) value: Object

[Source]

      # File lib/bio/db/nexus.rb, line 1597
1597:       def set_value( row, col, value ) 
1598:         if ( ( row < 0 ) || ( col < 0 ) )
1599:             raise( NexusTableError, "attempt to use negative values for row or column" )
1600:         end
1601:         if ( row > get_max_row() ) 
1602:           set_max_row( row )
1603:         end
1604:         if ( col > get_max_col() ) 
1605:           set_max_col( col )
1606:         end
1607:         row_map = nil
1608:         if ( @rows.has_key?( row ) ) 
1609:           row_map = @rows[ row ]
1610:         else 
1611:           row_map = Hash.new
1612:           @rows[ row ] = row_map
1613:         end
1614:         row_map[ col ] = value
1615:       end
to_nexus_row_array( spacer = "", append_delimiter = true )

Helper method to produce nexus formatted data.

Arguments:

  • (optional) spacer: String
  • (optional) append_delimiter: true or false
Returns:Array

[Source]

      # File lib/bio/db/nexus.rb, line 1733
1733:       def to_nexus_row_array( spacer = "", append_delimiter = true )
1734:         ary = Array.new
1735:         if is_empty?
1736:           return ary
1737:         end
1738:         max_length = 10
1739:         for row in 0 .. get_max_row
1740:           l = get_value( row, 0 ).length
1741:           if ( l > max_length )
1742:             max_length = l
1743:           end
1744:         end  
1745:         for row in 0 .. get_max_row
1746:           row_str = String.new
1747:           ary.push( row_str )
1748:           name = get_value( row, 0 )
1749:           name = name.ljust( max_length + 1 )
1750:           row_str << name << " " << get_row_string( row, spacer )
1751:           if ( spacer != nil && spacer.length > 0 )
1752:             row_str.chomp!( spacer )
1753:           end
1754:           if ( append_delimiter && row == get_max_row )
1755:             row_str << DELIMITER 
1756:           end
1757:         end
1758:         ary
1759:       end
to_s()

Returns matrix as String, returns "empty" if empty.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1714
1714:       def to_s
1715:         if is_empty?
1716:           return "empty"  
1717:         end
1718:         str = String.new
1719:         row_array = to_nexus_row_array( spacer = " ", false )
1720:         row_array.each do | row |
1721:           str << row << END_OF_LINE
1722:         end
1723:         str
1724:       end
to_str()

Alias for to_s

[Validate]