bio-nexml 0.0.1
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- data/Gemfile +15 -0
- data/Gemfile.lock +24 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +47 -0
- data/Rakefile +55 -0
- data/TODO.txt +6 -0
- data/VERSION +1 -0
- data/bio-nexml.gemspec +126 -0
- data/extconf.rb +2 -0
- data/lib/bio-nexml.rb +0 -0
- data/lib/bio.rb +321 -0
- data/lib/bio/db/nexml.rb +109 -0
- data/lib/bio/db/nexml/mapper.rb +113 -0
- data/lib/bio/db/nexml/mapper/framework.rb +157 -0
- data/lib/bio/db/nexml/mapper/inflection.rb +99 -0
- data/lib/bio/db/nexml/mapper/repository.rb +59 -0
- data/lib/bio/db/nexml/matrix.rb +1046 -0
- data/lib/bio/db/nexml/parser.rb +622 -0
- data/lib/bio/db/nexml/schema/README.txt +21 -0
- data/lib/bio/db/nexml/schema/abstract.xsd +159 -0
- data/lib/bio/db/nexml/schema/characters/README.txt +1 -0
- data/lib/bio/db/nexml/schema/characters/abstractcharacters.xsd +361 -0
- data/lib/bio/db/nexml/schema/characters/characters.xsd +22 -0
- data/lib/bio/db/nexml/schema/characters/continuous.xsd +190 -0
- data/lib/bio/db/nexml/schema/characters/dna.xsd +282 -0
- data/lib/bio/db/nexml/schema/characters/protein.xsd +280 -0
- data/lib/bio/db/nexml/schema/characters/restriction.xsd +239 -0
- data/lib/bio/db/nexml/schema/characters/rna.xsd +283 -0
- data/lib/bio/db/nexml/schema/characters/standard.xsd +261 -0
- data/lib/bio/db/nexml/schema/external/sawsdl.xsd +21 -0
- data/lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd +177 -0
- data/lib/bio/db/nexml/schema/external/xlink.xsd +75 -0
- data/lib/bio/db/nexml/schema/external/xml.xsd +145 -0
- data/lib/bio/db/nexml/schema/meta/README.txt +2 -0
- data/lib/bio/db/nexml/schema/meta/annotations.xsd +100 -0
- data/lib/bio/db/nexml/schema/meta/meta.xsd +294 -0
- data/lib/bio/db/nexml/schema/nexml.xsd +104 -0
- data/lib/bio/db/nexml/schema/taxa/README.txt +2 -0
- data/lib/bio/db/nexml/schema/taxa/taxa.xsd +39 -0
- data/lib/bio/db/nexml/schema/trees/README.txt +2 -0
- data/lib/bio/db/nexml/schema/trees/abstracttrees.xsd +135 -0
- data/lib/bio/db/nexml/schema/trees/network.xsd +113 -0
- data/lib/bio/db/nexml/schema/trees/tree.xsd +149 -0
- data/lib/bio/db/nexml/schema/trees/trees.xsd +36 -0
- data/lib/bio/db/nexml/taxa.rb +147 -0
- data/lib/bio/db/nexml/trees.rb +663 -0
- data/lib/bio/db/nexml/writer.rb +265 -0
- data/test/data/nexml/test.xml +69 -0
- data/test/test_bio-nexml.rb +17 -0
- data/test/unit/bio/db/nexml/tc_factory.rb +119 -0
- data/test/unit/bio/db/nexml/tc_mapper.rb +78 -0
- data/test/unit/bio/db/nexml/tc_matrix.rb +551 -0
- data/test/unit/bio/db/nexml/tc_parser.rb +21 -0
- data/test/unit/bio/db/nexml/tc_taxa.rb +118 -0
- data/test/unit/bio/db/nexml/tc_trees.rb +370 -0
- data/test/unit/bio/db/nexml/tc_writer.rb +633 -0
- metadata +253 -0
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<?xml version="1.0" encoding="UTF-8"?>
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elementFormDefault="qualified">
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This module defines the components of networks, graphs
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where edges have an in-degree that may exceed 1. The
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types defined in this module are concrete implementations
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that inherit from the abstract types in the <a href="../abstract">
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abstract trees module
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</a>. <br /><br />
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Depending on the concrete subclass, edges in networks either
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A concrete network implementation, with floating point edge lengths.
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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targetNamespace="http://www.nexml.org/2009"
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xmlns="http://www.nexml.org/2009"
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elementFormDefault="qualified">
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<xs:annotation>
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<xs:documentation>
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This module defines the components of trees, graphs
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where edges have an in-degree that of 1. The
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types defined in this module are concrete implementations
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that inherit from the abstract types in the <a href="../abstract">
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abstract trees module</a>.<br /><br />
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Depending on the concrete subclass, edges in trees either
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have lengths formatted as integers or lengths formatted as
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floating point numbers.
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</xs:documentation>
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</xs:annotation>
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<xs:include schemaLocation="abstracttrees.xsd"/>
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<xs:complexType name="TreeNode" abstract="false">
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<xs:documentation>
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A concrete node implementation.
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</xs:annotation>
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A concrete edge implementation, no length type specified.
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-->
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A concrete edge implementation, with float length.
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A concrete root edge implementation, with float length.
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A concrete edge implementation, with int length.
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<xs:element minOccurs="1" maxOccurs="unbounded" name="node" type="TreeNode"/>
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<xs:element minOccurs="0" maxOccurs="1" name="rootedge" type="TreeFloatRootEdge"/>
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<xs:complexType name="IntTree" abstract="false">
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A concrete tree implementation, with integer edge lengths.
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<xs:element name="meta" type="Meta" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element minOccurs="1" maxOccurs="unbounded" name="node" type="TreeNode"/>
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<xs:element minOccurs="0" maxOccurs="1" name="rootedge" type="TreeIntRootEdge"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.nexml.org/2009"
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xmlns="http://www.nexml.org/2009" elementFormDefault="qualified">
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<xs:annotation>
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<xs:documentation>
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This module defines the complex type for a set of trees,
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analogous to the "trees" block in NEXUS files. The module
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includes the modules that define concrete instances of
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<a href="../tree">tree</a> objects and of <a href="../network">network</a>
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objects.
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</xs:documentation>
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</xs:annotation>
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<xs:include schemaLocation="tree.xsd"/>
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<xs:include schemaLocation="network.xsd"/>
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<xs:complexType name="Trees" abstract="false" mixed="true">
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<xs:annotation>
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<xs:documentation>
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A concrete container for tree objects.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent mixed="true">
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<xs:extension base="TaxaLinked">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:choice minOccurs="0" maxOccurs="unbounded">
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<xs:element name="network" type="AbstractNetwork" minOccurs="1"
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maxOccurs="unbounded"/>
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<xs:element name="tree" type="AbstractTree" minOccurs="1"
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maxOccurs="unbounded"/>
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</xs:choice>
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</xs:sequence>
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</xs:extension>
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</xs:complexContent>
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</xs:complexType>
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</xs:schema>
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@@ -0,0 +1,147 @@
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module Bio
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module NeXML
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# = DESCRIPTION
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# Otu represents a taxon; an implementation of the
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# <em>Taxon</em>[http://nexml.org/nexml/html/doc/schema-1/taxa/taxa/#Taxon] type.
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# An Otu must have an 'id' and may take an an optional 'label'.
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# taxon1 = Bio::NeXML::Otu.new( 'taxon1', :label => 'Label for taxon1' )
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# taxon1.id #=> 'taxon1'
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# taxon1.label #=> 'Label for taxon1'
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# taxon1.otus #=> otus object they belong to; see docs for Otus
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class Otu
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include Mapper
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@@writer = Bio::NeXML::Writer.new
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+
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# A file level unique identifier.
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attr_accessor :id
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+
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# A human readable description.
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attr_accessor :label
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+
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# An otu is contained in otus.
|
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belongs_to :otus
|
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+
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# An otu is referred to by several tree nodes.
|
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has_n :nodes
|
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+
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|
+
has_n :rows
|
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+
|
|
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|
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# Create a new otu.
|
|
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|
+
# otu = Bio::NeXML::Otu.id( 'o1' )
|
|
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|
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# otu = Bio::NeXML::Otu.id( 'o1', :label => 'A label' )
|
|
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|
+
def initialize( id, options = {}, &block )
|
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|
+
@id = id
|
|
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|
+
properties( options ) unless options.empty?
|
|
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|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
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|
+
end
|
|
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|
+
|
|
38
|
+
def to_xml
|
|
39
|
+
@@writer.create_node( "otu", @@writer.attributes( self, :id, :label ) )
|
|
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|
+
end
|
|
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+
|
|
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|
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end #end class Otu
|
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+
|
|
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|
+
# = DESCRIPTION
|
|
45
|
+
# Otus is a container for Otu objects; an implementation of the
|
|
46
|
+
# <em>Taxa</em>[http://nexml.org/nexml/html/doc/schema-1/taxa/taxa/#Taxa] type.
|
|
47
|
+
# An Otus must have an 'id' and may take an optional 'label'. Adding two or more Otu objects
|
|
48
|
+
# with the same 'id' to an Otus is not allowed. Doing so will overwrite the previous Otu object
|
|
49
|
+
# with the same the same 'id'.
|
|
50
|
+
# taxa1 = Bio::NeXML::Otus.new( 'taxa1', :label => 'Label for taxa1' )
|
|
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|
+
# taxa1.id #=> 'taxa1'
|
|
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|
+
# taxa1.label #=> 'Label for taxa1'
|
|
53
|
+
#
|
|
54
|
+
# taxon1 = Bio::NeXML::Otu.new( 'taxon1' )
|
|
55
|
+
# taxon2 = Bio::NeXML::Otu.new( 'taxon2' )
|
|
56
|
+
#
|
|
57
|
+
# taxa1 << taxon1 << taxon2
|
|
58
|
+
# taxa1.count #=> 2
|
|
59
|
+
# taxa1.each { |otu| puts otu.id }
|
|
60
|
+
# taxon2.otus #=> taxa1
|
|
61
|
+
# taxa1.include?( taxon1 ) #=> true
|
|
62
|
+
# taxa1.delete( taxon2 ) #=> taxon2
|
|
63
|
+
class Otus
|
|
64
|
+
include Enumerable
|
|
65
|
+
include Mapper
|
|
66
|
+
@@writer = Bio::NeXML::Writer.new
|
|
67
|
+
|
|
68
|
+
# A file level unique identifier.
|
|
69
|
+
attr_accessor :id
|
|
70
|
+
|
|
71
|
+
# A human readable description.
|
|
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|
+
attr_accessor :label
|
|
73
|
+
|
|
74
|
+
belongs_to :nexml
|
|
75
|
+
|
|
76
|
+
has_n :otus
|
|
77
|
+
has_n :trees, :singularize => false
|
|
78
|
+
has_n :characters, :singularize => false
|
|
79
|
+
|
|
80
|
+
def initialize( id, options = {}, &block )
|
|
81
|
+
@id = id
|
|
82
|
+
properties( options ) unless options.empty?
|
|
83
|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
|
84
|
+
end
|
|
85
|
+
|
|
86
|
+
# Returns an array of otu contained in <tt>self</tt>.
|
|
87
|
+
def otus; end if false # dummy for rdoc
|
|
88
|
+
# Taken an array of otu and adds it to <tt>self</tt>.
|
|
89
|
+
def otus=; end if false # dummy for rdoc
|
|
90
|
+
|
|
91
|
+
# Takes an otu object and appends it to <tt>self</tt>.
|
|
92
|
+
def <<( otu )
|
|
93
|
+
add_otu( otu )
|
|
94
|
+
self
|
|
95
|
+
end
|
|
96
|
+
|
|
97
|
+
# Creates and returns an otu after appending it to self
|
|
98
|
+
def create_otu( options = {} )
|
|
99
|
+
otu = Otu.new( Bio::NeXML.generate_id( Otu ), options )
|
|
100
|
+
self << otu
|
|
101
|
+
otu
|
|
102
|
+
end
|
|
103
|
+
|
|
104
|
+
# Takes an otu or its id and deletes it. Returns the object deleted or <tt>nil</tt>.
|
|
105
|
+
def delete( otu )
|
|
106
|
+
delete_otu( otu )
|
|
107
|
+
end
|
|
108
|
+
|
|
109
|
+
# Takes an otu or its id and returns <tt>true</tt> if it is contained in <tt>self</tt>.
|
|
110
|
+
def include?( object )
|
|
111
|
+
has_otu?( object )
|
|
112
|
+
end
|
|
113
|
+
|
|
114
|
+
# Returns the otu object with the given id; <tt>nil</tt> if an otu with the given id is not
|
|
115
|
+
# contained in <tt>self</tt>.
|
|
116
|
+
def []( id )
|
|
117
|
+
get_otu_by_id( id )
|
|
118
|
+
end
|
|
119
|
+
|
|
120
|
+
# Iterate over each otu in <tt>self</tt> passing it to the block given. If no block is provided,
|
|
121
|
+
# it returns an Enumerator.
|
|
122
|
+
def each( &block )
|
|
123
|
+
@otus.each( &block )
|
|
124
|
+
end
|
|
125
|
+
|
|
126
|
+
# Iterate over each otu in <tt>self</tt> passing the otu and its id to the block given. If no
|
|
127
|
+
# block is provided, it returns an Enumerator.
|
|
128
|
+
def each_with_id( &block )
|
|
129
|
+
@otus.each_with_id( &block )
|
|
130
|
+
end
|
|
131
|
+
|
|
132
|
+
# Return the number of otu in <tt>self</tt>.
|
|
133
|
+
def length
|
|
134
|
+
number_of_otus
|
|
135
|
+
end
|
|
136
|
+
|
|
137
|
+
def to_xml
|
|
138
|
+
node = @@writer.create_node( "otus", @@writer.attributes( self, :id, :label ) )
|
|
139
|
+
self.each do |otu|
|
|
140
|
+
node << otu.to_xml
|
|
141
|
+
end
|
|
142
|
+
node
|
|
143
|
+
end
|
|
144
|
+
|
|
145
|
+
end #end class Otus
|
|
146
|
+
end
|
|
147
|
+
end
|
|
@@ -0,0 +1,663 @@
|
|
|
1
|
+
require 'bio/tree'
|
|
2
|
+
|
|
3
|
+
module Bio
|
|
4
|
+
module NeXML
|
|
5
|
+
|
|
6
|
+
# Node represents a node of a Tree or a Network. A node must have a unique id. It may optionally
|
|
7
|
+
# have a human readable 'label' and may link to an 'otu'.
|
|
8
|
+
class Node < Bio::Tree::Node
|
|
9
|
+
include Mapper
|
|
10
|
+
@@writer = Bio::NeXML::Writer.new
|
|
11
|
+
|
|
12
|
+
def to_xml
|
|
13
|
+
@@writer.create_node( "node", @@writer.attributes( self, :id, :otu, :root, :label ) )
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
# A file level unique identifier.
|
|
17
|
+
attr_accessor :id
|
|
18
|
+
|
|
19
|
+
# Stores a boolean value to indicate a root node.
|
|
20
|
+
attr_accessor :root
|
|
21
|
+
|
|
22
|
+
# A human readable description.
|
|
23
|
+
attr_accessor :label
|
|
24
|
+
|
|
25
|
+
# A node may optionally refer to an Otu.
|
|
26
|
+
belongs_to :otu
|
|
27
|
+
|
|
28
|
+
# A node is deemed part of a Tree.
|
|
29
|
+
belongs_to :tree
|
|
30
|
+
|
|
31
|
+
# Create a new otu. Passing an 'id' is a must. While 'label' and 'otu' may be passed
|
|
32
|
+
# as an optional hash.
|
|
33
|
+
# node = Bio::NeXML::Node.new( 'node1' )
|
|
34
|
+
# node = Bio::NeXML::Node.new( 'node1', :label => 'A node' )
|
|
35
|
+
# node = Bio::NeXML::Node.new( 'node1', :label => 'A node', :otu => otu )
|
|
36
|
+
def initialize( id, options = {} )
|
|
37
|
+
super( id )
|
|
38
|
+
@id = id
|
|
39
|
+
properties( options ) unless options.empty?
|
|
40
|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
|
41
|
+
end
|
|
42
|
+
|
|
43
|
+
# Return the otu to which the node links to.
|
|
44
|
+
def otu; end if false # dummy for rdoc
|
|
45
|
+
|
|
46
|
+
# Link the node to the given otu.
|
|
47
|
+
def otu=( otu ); end if false # dummy for rdoc
|
|
48
|
+
|
|
49
|
+
# Returns true if the node is a root node; false otherwise.
|
|
50
|
+
def root?
|
|
51
|
+
root
|
|
52
|
+
end
|
|
53
|
+
end #end class Node
|
|
54
|
+
|
|
55
|
+
# Edge connect two nodes of a tree or a network. An edge should have a unique id. It should have
|
|
56
|
+
# a 'source' and a 'target' node and optionally a 'length' may be assigned to it.
|
|
57
|
+
class Edge < Bio::Tree::Edge
|
|
58
|
+
include Mapper
|
|
59
|
+
@@writer = Bio::NeXML::Writer.new
|
|
60
|
+
|
|
61
|
+
def to_xml
|
|
62
|
+
@@writer.create_node( "edge", @@writer.attributes( self, :id, :source, :target, :length, :label ) )
|
|
63
|
+
end
|
|
64
|
+
|
|
65
|
+
# A file level unique identifier.
|
|
66
|
+
attr_accessor :id
|
|
67
|
+
|
|
68
|
+
# Source of the edge.
|
|
69
|
+
attr_accessor :source
|
|
70
|
+
|
|
71
|
+
# Target of the edge.
|
|
72
|
+
attr_accessor :target
|
|
73
|
+
|
|
74
|
+
# A human readable description.
|
|
75
|
+
attr_accessor :label
|
|
76
|
+
|
|
77
|
+
# A node is deemed part of a Tree.
|
|
78
|
+
belongs_to :tree
|
|
79
|
+
|
|
80
|
+
# Create a new edge.
|
|
81
|
+
# edge = Bio::NeXML::Edge.new( 'edge1' )
|
|
82
|
+
# edge = Bio::NeXML::Edge.new( 'edge1', :source => node1, :target => node2 )
|
|
83
|
+
# edge = Bio::NeXML::Edge.new( 'edge1', :source => node1, :target => node2, :length => 1 )
|
|
84
|
+
def initialize( id, options = {} )
|
|
85
|
+
super( length )
|
|
86
|
+
@id = id
|
|
87
|
+
properties( options ) unless options.empty?
|
|
88
|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
|
89
|
+
end
|
|
90
|
+
|
|
91
|
+
# Return the length of an edge.
|
|
92
|
+
def length
|
|
93
|
+
distance
|
|
94
|
+
end
|
|
95
|
+
|
|
96
|
+
# Set the length of an edge.
|
|
97
|
+
def length=( length )
|
|
98
|
+
self.distance = length
|
|
99
|
+
end
|
|
100
|
+
end #end class Edge
|
|
101
|
+
|
|
102
|
+
# A rootedge is an edge without a source. It is used in context of coalescent trees. RootEdge
|
|
103
|
+
# inherits from Edge so the same functionality is available in rootedge too.
|
|
104
|
+
class RootEdge < Edge
|
|
105
|
+
@@writer = Bio::NeXML::Writer.new
|
|
106
|
+
def to_xml
|
|
107
|
+
@@writer.create_node( "rootedge", @@writer.attributes( self, :id, :target, :length, :label ) )
|
|
108
|
+
end
|
|
109
|
+
|
|
110
|
+
private :source=
|
|
111
|
+
|
|
112
|
+
def initialize( id, options = {} )
|
|
113
|
+
super
|
|
114
|
+
end
|
|
115
|
+
end
|
|
116
|
+
|
|
117
|
+
class FloatRootEdge < RootEdge
|
|
118
|
+
def initialize( id, options = {} )
|
|
119
|
+
super
|
|
120
|
+
end
|
|
121
|
+
def length
|
|
122
|
+
distance.to_f
|
|
123
|
+
end
|
|
124
|
+
end
|
|
125
|
+
|
|
126
|
+
class IntRootEdge < RootEdge
|
|
127
|
+
def initialize( id, options = {} )
|
|
128
|
+
super
|
|
129
|
+
end
|
|
130
|
+
def length
|
|
131
|
+
distance.to_i
|
|
132
|
+
end
|
|
133
|
+
end
|
|
134
|
+
|
|
135
|
+
# A float edge is an edge whose length is defined using a floating point
|
|
136
|
+
# number.
|
|
137
|
+
class FloatEdge < Edge
|
|
138
|
+
def initialize( id, options = {} )
|
|
139
|
+
super
|
|
140
|
+
end
|
|
141
|
+
def length
|
|
142
|
+
distance.to_f
|
|
143
|
+
end
|
|
144
|
+
end
|
|
145
|
+
|
|
146
|
+
# An int edge is an edge whose length is defined using an integer
|
|
147
|
+
class IntEdge < Edge
|
|
148
|
+
def initialize( id, options = {} )
|
|
149
|
+
super
|
|
150
|
+
end
|
|
151
|
+
def length
|
|
152
|
+
distance.to_i
|
|
153
|
+
end
|
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154
|
+
end
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155
|
+
|
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156
|
+
# An NeXML tree. A tree must have a unique 'id'. It may optionally take a 'label' and a 'rootedge'.
|
|
157
|
+
# This class inherits from Bio::Tree; naturally its functionality is leveraged here.
|
|
158
|
+
class Tree < Bio::Tree
|
|
159
|
+
include Mapper
|
|
160
|
+
@@writer = Bio::NeXML::Writer.new
|
|
161
|
+
|
|
162
|
+
def to_xml
|
|
163
|
+
node = @@writer.create_node( "tree", @@writer.attributes( self, :id, :'xsi:type', :label ) )
|
|
164
|
+
|
|
165
|
+
self.each_node do |n|
|
|
166
|
+
node << n.to_xml
|
|
167
|
+
end
|
|
168
|
+
|
|
169
|
+
rootedge = self.rootedge
|
|
170
|
+
node << rootedge.to_xml if rootedge
|
|
171
|
+
|
|
172
|
+
self.each_edge do |edge|
|
|
173
|
+
node << edge.to_xml
|
|
174
|
+
end
|
|
175
|
+
|
|
176
|
+
node
|
|
177
|
+
end
|
|
178
|
+
|
|
179
|
+
def create_node( options = {} )
|
|
180
|
+
node = Node.new( Bio::NeXML.generate_id( Node ), options )
|
|
181
|
+
self << node
|
|
182
|
+
node
|
|
183
|
+
end
|
|
184
|
+
|
|
185
|
+
def create_edge( options = {} )
|
|
186
|
+
raise "This is supposed to be an abstract method"
|
|
187
|
+
end
|
|
188
|
+
|
|
189
|
+
def create_rootedge( options = {} )
|
|
190
|
+
raise "This is supposed to be an abstract method"
|
|
191
|
+
end
|
|
192
|
+
|
|
193
|
+
# A file level unique identifier.
|
|
194
|
+
attr_accessor :id
|
|
195
|
+
|
|
196
|
+
# A human readable description.
|
|
197
|
+
attr_accessor :label
|
|
198
|
+
|
|
199
|
+
# A rootedge to indicate a time span leading up to the root.
|
|
200
|
+
attr_accessor :rootedge
|
|
201
|
+
|
|
202
|
+
# A tree is contained in Trees.
|
|
203
|
+
belongs_to :trees
|
|
204
|
+
|
|
205
|
+
# A tree will contain n number of nodes.
|
|
206
|
+
has_n :nodes
|
|
207
|
+
|
|
208
|
+
# A tree will contain n number of edges joining the nodes.
|
|
209
|
+
has_n :edges
|
|
210
|
+
|
|
211
|
+
# Create a new tree.
|
|
212
|
+
# tree = Bio::NeXML::Tree.new( 'tree1' )
|
|
213
|
+
# tree = Bio::NeXML::Tree.new( 'tree1', :label => 'A tree' )
|
|
214
|
+
#
|
|
215
|
+
# nodes = %w|node1 node2 node3|.map{ |n| Bio::NeXML::Node.new( n ) }
|
|
216
|
+
# edge1 = Bio::NeXML::Edge.new( 'edge1', :source => nodes[0], :target => nodes[1] )
|
|
217
|
+
# edge2 = Bio::NeXML::Edge.new( 'edge2', :source => nodes[0], :target => nodes[2] )
|
|
218
|
+
#
|
|
219
|
+
# tree = Bio::NeXML::Tree.new( 'tree1', :nodes => nodes )
|
|
220
|
+
# tree = Bio::NeXML::Tree.new do |t|
|
|
221
|
+
# t.label = 'A tree'
|
|
222
|
+
# t.nodes = nodes
|
|
223
|
+
# t.edges = [ edge1, edge2 ]
|
|
224
|
+
# # or, t << edge1 << edge2
|
|
225
|
+
# # or, t.add_edge( edge1 ); t.add_edge( edge2 )
|
|
226
|
+
#
|
|
227
|
+
# root = Bio::NeXML::Node.new( 'root1', :root => true )
|
|
228
|
+
# rootedge = Bio::NeXML::RootEdge.new( 're1', :target => root )
|
|
229
|
+
#
|
|
230
|
+
# t << root # or, t.add_otu( root )
|
|
231
|
+
# t.rootedge = rootedge
|
|
232
|
+
# end
|
|
233
|
+
def initialize( id = nil, options = {}, &block )
|
|
234
|
+
super()
|
|
235
|
+
@id = id
|
|
236
|
+
properties( options ) unless options.empty?
|
|
237
|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
|
238
|
+
end
|
|
239
|
+
|
|
240
|
+
# Returns an array of root nodes.
|
|
241
|
+
def roots
|
|
242
|
+
nodes.select{ |n| n.root? }
|
|
243
|
+
end
|
|
244
|
+
|
|
245
|
+
# Append a node or an edge to the tree. The method delegates the actuall addition to
|
|
246
|
+
# <tt>add_node</tt>, <tt>add_edge</tt> methods.
|
|
247
|
+
def <<( object )
|
|
248
|
+
case object
|
|
249
|
+
when Node
|
|
250
|
+
add_node( object )
|
|
251
|
+
when Edge
|
|
252
|
+
add_edge( object )
|
|
253
|
+
end
|
|
254
|
+
self
|
|
255
|
+
end
|
|
256
|
+
|
|
257
|
+
# :stopdoc:
|
|
258
|
+
alias __add_node__ add_node
|
|
259
|
+
# :startdoc:
|
|
260
|
+
# Add a node to the tree.
|
|
261
|
+
def add_node( node )
|
|
262
|
+
super( node )
|
|
263
|
+
__add_node__( node )
|
|
264
|
+
end
|
|
265
|
+
|
|
266
|
+
# :stopdoc:
|
|
267
|
+
alias __add_edge__ add_edge
|
|
268
|
+
# :startdoc:
|
|
269
|
+
# Add an edge to the tree.
|
|
270
|
+
def add_edge( edge )
|
|
271
|
+
super( edge.source, edge.target, edge )
|
|
272
|
+
__add_edge__( edge )
|
|
273
|
+
end
|
|
274
|
+
|
|
275
|
+
def add_rootedge( edge )
|
|
276
|
+
@rootedge = edge
|
|
277
|
+
end
|
|
278
|
+
|
|
279
|
+
# :stopdoc:
|
|
280
|
+
alias __delete_node__ delete_node
|
|
281
|
+
# :startdoc:
|
|
282
|
+
|
|
283
|
+
# Remove a node from the tree. Returns the deleted node. It automatically removes all edges
|
|
284
|
+
# connected to that node. Raises IndexError if the node is not found in the tree.
|
|
285
|
+
def remove_node( node )
|
|
286
|
+
return unless include?( node )
|
|
287
|
+
super( node )
|
|
288
|
+
__delete_node__( node )
|
|
289
|
+
end
|
|
290
|
+
alias delete_node remove_node
|
|
291
|
+
|
|
292
|
+
# :stopdoc:
|
|
293
|
+
alias __delete_edge__ delete_edge
|
|
294
|
+
# :startdoc:
|
|
295
|
+
|
|
296
|
+
# Remove an edge from the tree. Returns the edge deleted. If more than one edge exists between
|
|
297
|
+
# the source and the target, both of them will be removed. Raises IndexError if the edge is
|
|
298
|
+
# not found in the tree.
|
|
299
|
+
def remove_edge( edge )
|
|
300
|
+
return unless include?( edge )
|
|
301
|
+
super( edge.source, edge.target )
|
|
302
|
+
__delete_edge__( edge )
|
|
303
|
+
end
|
|
304
|
+
alias delete_edge remove_edge
|
|
305
|
+
|
|
306
|
+
# Fetch a node by the given id.
|
|
307
|
+
def get_node_by_id( id ); end if false # dummy for rdoc
|
|
308
|
+
|
|
309
|
+
# get_node_by_name is actually defined in Bio::Tree. I have aliased it to get_node_by_id
|
|
310
|
+
# as hash lookup is faster than searching through an enumerable.
|
|
311
|
+
alias get_node_by_name get_node_by_id
|
|
312
|
+
|
|
313
|
+
# Fetch an edge by the given id.
|
|
314
|
+
def get_edge_by_id( id ); end if false # dummy for rdoc
|
|
315
|
+
|
|
316
|
+
# Fetch a node, or an edge by its id.
|
|
317
|
+
def []( id )
|
|
318
|
+
get_node_by_id( id ) ||
|
|
319
|
+
get_edge_by_id( id )
|
|
320
|
+
end
|
|
321
|
+
|
|
322
|
+
# Returns true if the given node is a part of <tt>self</tt>.
|
|
323
|
+
def has_node?( node ); end if false # dummy for rdoc
|
|
324
|
+
|
|
325
|
+
# Returns true if the given edge is a part of <tt>self</tt>.
|
|
326
|
+
def has_edge?( edge ); end if false # dummy for rdoc
|
|
327
|
+
|
|
328
|
+
# Returns true if the given node or the edge object is a part of this tree; false otherwise.
|
|
329
|
+
def include?( object )
|
|
330
|
+
has_node?( object ) ||
|
|
331
|
+
has_edge?( object )
|
|
332
|
+
end
|
|
333
|
+
alias has? include?
|
|
334
|
+
|
|
335
|
+
# Iterate over each node. Return an Enumerator if no block is given.
|
|
336
|
+
def each_node( &block ); end if false # dummy for rdoc
|
|
337
|
+
|
|
338
|
+
# Iterate over each node passing id and the node itself to the given block.
|
|
339
|
+
# Returns an Enumerator if no block is given.
|
|
340
|
+
def each_node_with_id; end if false # dummy for rdoc
|
|
341
|
+
|
|
342
|
+
# Iterate over each edge. Return an Enumerator if no block is given.
|
|
343
|
+
def each_edge; end if false # :yield: edge
|
|
344
|
+
|
|
345
|
+
# Iterate over each node passing id and the node itself to the given block.
|
|
346
|
+
# Returns an Enumerator if no block is given.
|
|
347
|
+
def each_edge_with_id; end if false # dummy for rdoc
|
|
348
|
+
|
|
349
|
+
# Return the number of nodes in the tree.
|
|
350
|
+
def number_of_nodes; end if false #dummy for rdoc
|
|
351
|
+
|
|
352
|
+
# Return the number of edges in the tree.
|
|
353
|
+
def number_of_edges; end if false #dummy for rdoc
|
|
354
|
+
|
|
355
|
+
# :stopdoc:
|
|
356
|
+
# Following methods have been redifined from Bio::Tree to take advantage of multiple root
|
|
357
|
+
# nodes in NeXML. Since for each root a differrent solution is possible, the result returned
|
|
358
|
+
# is a ( root, solution) hash. The solution for each root is the same as that returned by its
|
|
359
|
+
# super method.
|
|
360
|
+
# :startdoc:
|
|
361
|
+
|
|
362
|
+
# Returns the parent of the given node corresponding to each root.
|
|
363
|
+
def parent( node, *roots )
|
|
364
|
+
if roots.empty?
|
|
365
|
+
raise IndexError, 'can not get parent for unrooted tree' if self.roots.empty?
|
|
366
|
+
roots = self.roots
|
|
367
|
+
end
|
|
368
|
+
parents = {}
|
|
369
|
+
roots.each do |r|
|
|
370
|
+
parents[ r ] = super( node, r )
|
|
371
|
+
end
|
|
372
|
+
parents
|
|
373
|
+
end
|
|
374
|
+
|
|
375
|
+
def children( node, *root )
|
|
376
|
+
if root.empty?
|
|
377
|
+
raise IndexError, 'can not get parent for unrooted tree' if self.root.empty?
|
|
378
|
+
root = self.root
|
|
379
|
+
end
|
|
380
|
+
childrens = {}
|
|
381
|
+
root.each do |r|
|
|
382
|
+
c = adjacent_nodes(node)
|
|
383
|
+
c.delete(parent(node, r)[ r ])
|
|
384
|
+
childrens[ r ] = c
|
|
385
|
+
end
|
|
386
|
+
|
|
387
|
+
childrens
|
|
388
|
+
end
|
|
389
|
+
|
|
390
|
+
def descendents( node, *root )
|
|
391
|
+
if root.empty?
|
|
392
|
+
raise IndexError, 'can not get parent for unrooted tree' if self.root.empty?
|
|
393
|
+
root = self.root
|
|
394
|
+
end
|
|
395
|
+
descendent = {}
|
|
396
|
+
root.each do |r|
|
|
397
|
+
descendent[ r ] = super( node, r )
|
|
398
|
+
end
|
|
399
|
+
descendent
|
|
400
|
+
end
|
|
401
|
+
|
|
402
|
+
def lowest_common_ancestor( node1, node2, *root )
|
|
403
|
+
if root.empty?
|
|
404
|
+
raise IndexError, 'can not get parent for unrooted tree' if self.root.empty?
|
|
405
|
+
root = self.root
|
|
406
|
+
end
|
|
407
|
+
lca = {}
|
|
408
|
+
root.each do |r|
|
|
409
|
+
lca[ r ] = super( node1, node2, r )
|
|
410
|
+
end
|
|
411
|
+
lca
|
|
412
|
+
end
|
|
413
|
+
|
|
414
|
+
def ancestors( node, *root )
|
|
415
|
+
if root.empty?
|
|
416
|
+
raise IndexError, 'can not get parent for unrooted tree' if self.root.empty?
|
|
417
|
+
root = self.root
|
|
418
|
+
end
|
|
419
|
+
ancestor = {}
|
|
420
|
+
root.each do |r|
|
|
421
|
+
ancestor[ r ] = super( node, r )
|
|
422
|
+
end
|
|
423
|
+
ancestor
|
|
424
|
+
end
|
|
425
|
+
end #end class Tree
|
|
426
|
+
|
|
427
|
+
class IntTree < Tree
|
|
428
|
+
def initialize( id = nil, options = {}, &block )
|
|
429
|
+
super
|
|
430
|
+
end
|
|
431
|
+
|
|
432
|
+
def add_edge( edge )
|
|
433
|
+
edge.length = edge.length.to_i
|
|
434
|
+
super
|
|
435
|
+
end
|
|
436
|
+
|
|
437
|
+
def create_edge( options = {} )
|
|
438
|
+
edge = IntEdge.new( Bio::NeXML.generate_id( IntEdge ), options )
|
|
439
|
+
self << edge
|
|
440
|
+
edge
|
|
441
|
+
end
|
|
442
|
+
|
|
443
|
+
def create_rootedge( options = {} )
|
|
444
|
+
rootedge = IntRootEdge.new( Bio::NeXML.generate_id( IntRootEdge ), options )
|
|
445
|
+
self << rootedge
|
|
446
|
+
rootedge
|
|
447
|
+
end
|
|
448
|
+
|
|
449
|
+
end
|
|
450
|
+
|
|
451
|
+
class FloatTree < Tree
|
|
452
|
+
def initialize( id = nil, options = {}, &block )
|
|
453
|
+
super
|
|
454
|
+
end
|
|
455
|
+
|
|
456
|
+
def add_edge( edge )
|
|
457
|
+
edge.length = edge.length.to_f
|
|
458
|
+
super
|
|
459
|
+
end
|
|
460
|
+
|
|
461
|
+
def create_edge( options = {} )
|
|
462
|
+
edge = FloatEdge.new( Bio::NeXML.generate_id( FloatEdge ), options )
|
|
463
|
+
self << edge
|
|
464
|
+
edge
|
|
465
|
+
end
|
|
466
|
+
|
|
467
|
+
def create_rootedge( options = {} )
|
|
468
|
+
rootedge = FloatRootEdge.new( Bio::NeXML.generate_id( FloatRootEdge ), options )
|
|
469
|
+
self << rootedge
|
|
470
|
+
rootedge
|
|
471
|
+
end
|
|
472
|
+
|
|
473
|
+
end
|
|
474
|
+
|
|
475
|
+
class Network < Tree
|
|
476
|
+
@@writer = Bio::NeXML::Writer.new
|
|
477
|
+
belongs_to :trees
|
|
478
|
+
def initialize( id, options = {}, &block )
|
|
479
|
+
super
|
|
480
|
+
end
|
|
481
|
+
|
|
482
|
+
def to_xml
|
|
483
|
+
node = @@writer.create_node( "network", @@writer.attributes( self, :id, :'xsi:type', :label ) )
|
|
484
|
+
|
|
485
|
+
self.each_node do |n|
|
|
486
|
+
node << n.to_xml
|
|
487
|
+
end
|
|
488
|
+
|
|
489
|
+
self.each_edge do |edge|
|
|
490
|
+
node << edge.to_xml
|
|
491
|
+
end
|
|
492
|
+
|
|
493
|
+
node
|
|
494
|
+
end
|
|
495
|
+
end
|
|
496
|
+
|
|
497
|
+
class IntNetwork < Network
|
|
498
|
+
def initialize( id, options = {}, &block )
|
|
499
|
+
super
|
|
500
|
+
end
|
|
501
|
+
|
|
502
|
+
def add_edge( edge )
|
|
503
|
+
edge.length = edge.length.to_i
|
|
504
|
+
super
|
|
505
|
+
end
|
|
506
|
+
|
|
507
|
+
def create_edge( options = {} )
|
|
508
|
+
edge = IntEdge.new( Bio::NeXML.generate_id( IntEdge ), options )
|
|
509
|
+
self << edge
|
|
510
|
+
edge
|
|
511
|
+
end
|
|
512
|
+
|
|
513
|
+
end
|
|
514
|
+
|
|
515
|
+
class FloatNetwork < Network
|
|
516
|
+
def initialize( id, options = {}, &block )
|
|
517
|
+
super
|
|
518
|
+
end
|
|
519
|
+
|
|
520
|
+
def add_edge( edge )
|
|
521
|
+
edge.length = edge.length.to_f
|
|
522
|
+
super
|
|
523
|
+
end
|
|
524
|
+
|
|
525
|
+
def create_edge( options = {} )
|
|
526
|
+
edge = FloatEdge.new( Bio::NeXML.generate_id( FloatEdge ), options )
|
|
527
|
+
self << edge
|
|
528
|
+
edge
|
|
529
|
+
end
|
|
530
|
+
|
|
531
|
+
end
|
|
532
|
+
|
|
533
|
+
class Trees
|
|
534
|
+
include Mapper
|
|
535
|
+
@@writer = Bio::NeXML::Writer.new
|
|
536
|
+
|
|
537
|
+
def to_xml
|
|
538
|
+
node = @@writer.create_node( "trees", @@writer.attributes( self, :id, :label, :otus ) )
|
|
539
|
+
|
|
540
|
+
self.each_tree do |tree|
|
|
541
|
+
node << tree.to_xml
|
|
542
|
+
end
|
|
543
|
+
|
|
544
|
+
self.each_network do |network|
|
|
545
|
+
node << network.to_xml
|
|
546
|
+
end
|
|
547
|
+
|
|
548
|
+
node
|
|
549
|
+
end
|
|
550
|
+
|
|
551
|
+
def create_tree( int = false, options = {} )
|
|
552
|
+
type = int ? Bio::NeXML::IntTree : Bio::NeXML::FloatTree
|
|
553
|
+
tree = type.new( Bio::NeXML.generate_id( type ), options )
|
|
554
|
+
self << tree
|
|
555
|
+
tree
|
|
556
|
+
end
|
|
557
|
+
|
|
558
|
+
def create_network( int = false, options = {} )
|
|
559
|
+
type = int ? Bio::NeXML::IntNetwork : Bio::NeXML::FloatNetwork
|
|
560
|
+
network = type.new( Bio::NeXML.generate_id( type ), options )
|
|
561
|
+
self << network
|
|
562
|
+
network
|
|
563
|
+
end
|
|
564
|
+
|
|
565
|
+
attr_accessor :id
|
|
566
|
+
attr_accessor :label
|
|
567
|
+
|
|
568
|
+
# A trees refers links to an otu.
|
|
569
|
+
belongs_to :otus
|
|
570
|
+
|
|
571
|
+
# Trees is a container for trees and networks.
|
|
572
|
+
has_n :trees
|
|
573
|
+
has_n :networks
|
|
574
|
+
|
|
575
|
+
belongs_to :nexml
|
|
576
|
+
|
|
577
|
+
# Create a trees object.
|
|
578
|
+
def initialize( id = nil, options = {}, &block )
|
|
579
|
+
@id = id
|
|
580
|
+
properties( options ) unless options.empty?
|
|
581
|
+
block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
|
|
582
|
+
end
|
|
583
|
+
|
|
584
|
+
# Add a tree to self.
|
|
585
|
+
def add_tree; end if false # dummy for rdoc
|
|
586
|
+
|
|
587
|
+
# Add a networ to self.
|
|
588
|
+
def add_network; end if false # dummy for rdoc
|
|
589
|
+
|
|
590
|
+
# Add a tree or a network to self.
|
|
591
|
+
def <<( object )
|
|
592
|
+
case object
|
|
593
|
+
when Network
|
|
594
|
+
add_network( object )
|
|
595
|
+
when Tree
|
|
596
|
+
add_tree( object )
|
|
597
|
+
end
|
|
598
|
+
self
|
|
599
|
+
end
|
|
600
|
+
|
|
601
|
+
# Delete a tree from self.
|
|
602
|
+
def delete_tree; end if false # dummy for rdoc
|
|
603
|
+
|
|
604
|
+
# Delete a network from self.
|
|
605
|
+
def delete_network; end if false # dummy for rdoc
|
|
606
|
+
|
|
607
|
+
# Fetch a tree by id.
|
|
608
|
+
def get_tree_by_id; end if false # dummy for rdoc
|
|
609
|
+
|
|
610
|
+
# Fetch a network by id.
|
|
611
|
+
def get_network_by_id; end if false # dummy for rdoc
|
|
612
|
+
|
|
613
|
+
# Fetch a tree or a network by id.
|
|
614
|
+
def []( id )
|
|
615
|
+
get_tree_by_id( id ) ||
|
|
616
|
+
get_network_by_id( id )
|
|
617
|
+
end
|
|
618
|
+
|
|
619
|
+
# Returns true if tree is containes in self.
|
|
620
|
+
def has_tree?( tree ); end if false # dummy for rdoc
|
|
621
|
+
|
|
622
|
+
# Returns true if the given network is containes in self; false otherwise.
|
|
623
|
+
def has_network?( tree ); end if false # dummy for rdoc
|
|
624
|
+
|
|
625
|
+
def include?( object )
|
|
626
|
+
has_tree?( object ) ||
|
|
627
|
+
has_network?( object )
|
|
628
|
+
end
|
|
629
|
+
alias has? include?
|
|
630
|
+
|
|
631
|
+
# Returns the number of trees contained in self.
|
|
632
|
+
def number_of_trees; end if false # dummy for rdoc
|
|
633
|
+
|
|
634
|
+
# Returns the number of networks contained in self.
|
|
635
|
+
def number_of_networks; end if false # dummy for rdoc
|
|
636
|
+
|
|
637
|
+
# Returns total number of trees and networks.
|
|
638
|
+
def count
|
|
639
|
+
number_of_trees + number_of_networks
|
|
640
|
+
end
|
|
641
|
+
alias length count
|
|
642
|
+
|
|
643
|
+
# Iterate over each tree. Returns an Enumerator if no block is given.
|
|
644
|
+
def each_tree( &block ); end if false # dummy for rdoc
|
|
645
|
+
|
|
646
|
+
# Iterate over each tree passing the id and the tree itself to the block.
|
|
647
|
+
# Returns an Enumerator if no block is given.
|
|
648
|
+
def each_tree_with_id( &block ); end if false # dummy for rdoc
|
|
649
|
+
|
|
650
|
+
# Iterate over each network. Returns an Enumerator if no block is given.
|
|
651
|
+
def each_network( &block ); end if false # dummy for rdoc
|
|
652
|
+
|
|
653
|
+
# Iterate over each network passing the id and the tree itself to the block.
|
|
654
|
+
# Returns an Enumerator if no block is given.
|
|
655
|
+
def each_network_with_id( &block ); end if false # dummy for rdoc
|
|
656
|
+
|
|
657
|
+
# Iterate over each element. Returns an Enumerator if no block is given.
|
|
658
|
+
def each( &block )
|
|
659
|
+
@trees.merge( @networks ).each( &block )
|
|
660
|
+
end
|
|
661
|
+
end #end class Trees
|
|
662
|
+
end #end module NeXML
|
|
663
|
+
end #end module Bio
|