class Bio::Nexus::NexusMatrix
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", "+" )
Public Class Methods
Source
# File lib/bio/db/nexus.rb 1586 def initialize() 1587 @rows = Hash.new 1588 @max_row = -1 1589 @max_col = -1 1590 end
Creates new NexusMatrix.
Public Instance Methods
Source
# File lib/bio/db/nexus.rb 1642 def get_max_col 1643 return @max_col 1644 end
Returns the maximal columns number.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1649 def get_max_row 1650 return @max_row 1651 end
Returns the maximal row number.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1668 def get_name( row ) 1669 get_value( row, 0 ).to_s 1670 end
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 1681 def get_row_string( row, spacer = "" ) 1682 row_str = String.new 1683 if is_empty? 1684 return row_str 1685 end 1686 for col in 1 .. get_max_col 1687 row_str << get_value( row, col ) << spacer 1688 end 1689 row_str 1690 end
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 1699 def get_row_strings_by_name( name, spacer = "" ) 1700 row_strs = Array.new 1701 if is_empty? 1702 return row_strs 1703 end 1704 for row in 0 .. get_max_row 1705 if ( get_value( row, 0 ) == name ) 1706 row_strs.push( get_row_string( row, spacer ) ) 1707 end 1708 end 1709 row_strs 1710 end
Returns all rows as Array of Strings separated by ‘spacer’ for which column 0 is ‘name’.
Arguments:
-
(required) name: String
-
(optional) spacer: String
- Returns
-
Array
Source
# File lib/bio/db/nexus.rb 1624 def get_value( row, col ) 1625 if ( ( row > get_max_row() ) || ( row < 0 ) ) 1626 raise( NexusMatrixError, "value for row (" + row.to_s + 1627 ") is out of range [max row: " + get_max_row().to_s + "]" ) 1628 elsif ( ( col > get_max_col() ) || ( row < 0 ) ) 1629 raise( NexusMatrixError, "value for column (" + col.to_s + 1630 ") is out of range [max column: " + get_max_col().to_s + "]" ) 1631 end 1632 r = @rows[ row ] 1633 if ( ( r == nil ) || ( r.length < 1 ) ) 1634 return nil 1635 end 1636 r[ col ] 1637 end
Returns the value at row ‘row’ and column ‘col’.
Arguments:
-
(required) row: Integer
-
(required) col: Integer
- Returns
Source
# File lib/bio/db/nexus.rb 1657 def is_empty? 1658 return get_max_col < 0 || get_max_row < 0 1659 end
Returns true of matrix is empty.
- Returns
-
true or false
Source
# File lib/bio/db/nexus.rb 1598 def set_value( row, col, value ) 1599 if ( ( row < 0 ) || ( col < 0 ) ) 1600 raise( NexusTableError, "attempt to use negative values for row or column" ) 1601 end 1602 if ( row > get_max_row() ) 1603 set_max_row( row ) 1604 end 1605 if ( col > get_max_col() ) 1606 set_max_col( col ) 1607 end 1608 row_map = nil 1609 if ( @rows.has_key?( row ) ) 1610 row_map = @rows[ row ] 1611 else 1612 row_map = Hash.new 1613 @rows[ row ] = row_map 1614 end 1615 row_map[ col ] = value 1616 end
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 1734 def to_nexus_row_array( spacer = "", append_delimiter = true ) 1735 ary = Array.new 1736 if is_empty? 1737 return ary 1738 end 1739 max_length = 10 1740 for row in 0 .. get_max_row 1741 l = get_value( row, 0 ).length 1742 if ( l > max_length ) 1743 max_length = l 1744 end 1745 end 1746 for row in 0 .. get_max_row 1747 row_str = String.new 1748 ary.push( row_str ) 1749 name = get_value( row, 0 ) 1750 name = name.ljust( max_length + 1 ) 1751 row_str << name << " " << get_row_string( row, spacer ) 1752 if ( spacer != nil && spacer.length > 0 ) 1753 row_str.chomp!( spacer ) 1754 end 1755 if ( append_delimiter && row == get_max_row ) 1756 row_str << DELIMITER 1757 end 1758 end 1759 ary 1760 end
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 1715 def to_s 1716 if is_empty? 1717 return "empty" 1718 end 1719 str = String.new 1720 row_array = to_nexus_row_array( " ", false ) 1721 row_array.each do | row | 1722 str << row << END_OF_LINE 1723 end 1724 str 1725 end
Returns matrix as String, returns “empty” if empty.
- Returns
-
String