bio-nexml 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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<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 subclasses of the dictionaries
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defined in the <a href="../annotations">annotations</a>
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module. The subclasses are used to attach metadata about
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revision control status of a file (the RCS* types),
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<a href="http://dublincore.org/">dublin core</a> metadata
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and common web formats (XHTML, RSS).
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</xs:documentation>
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<xs:include schemaLocation="annotations.xsd"/>
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<!-- a simple key/value pair, where key
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<!-- same thing for svn $Rev: $ -->
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<!-- same thing for svn $Header: $ -->
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<!-- this is just syntax sugar to indicate that
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Dublin Core metadata -->
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namespace="http://purl.org/dc/elements/1.1/ http://purl.org/dc/terms/ http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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processContents="lax"
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<!-- this is a wrapper around RSS -->
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<xs:simpleType name="RSSKey">
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namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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processContents="lax"
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<!--xs:complexType name="RSS">
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<xs:element name="key" type="RSSKey" minOccurs="1" maxOccurs="1"/>
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</xs:complexType-->
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema xmlns="http://www.nexml.org/2009" xmlns:xs="http://www.w3.org/2001/XMLSchema"
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targetNamespace="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 constitutes in effect the 'main' class of the nexml schema.
|
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It defines the complex type for the root <<a href="#Nexml">nex:nexml</a>>
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element and a simple type for the schema <a href="#Nexml1_0">"version" attribute</a>
|
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|
+
of the root element. In addition, this module includes the main schema modules for
|
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<a href="../taxa/taxa">OTUs</a>, <a href="../characters/characters">characters</a>,
|
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+
<a href="../trees/trees">trees</a> and <a href="../meta/meta">metadata</a>. The data
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type definitions in these included schema modules are then used to define element
|
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instances in the child substructures of the <nex:nexml> root element.
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$Id: $
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</xs:documentation>
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</xs:annotation>
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<xs:include schemaLocation="taxa/taxa.xsd"/>
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<xs:include schemaLocation="characters/characters.xsd"/>
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<xs:include schemaLocation="trees/trees.xsd"/>
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<xs:include schemaLocation="meta/annotations.xsd"/>
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<!-- xs:include schemaLocation="meta/meta.xsd"/-->
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<!--<xs:include schemaLocation="models/models.xsd"/>-->
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<xs:simpleType name="Nexml1_0">
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<xs:annotation>
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<xs:documentation>
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This simple type is the fixed version value, which in this
|
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+
iteration must be constrained to 0.9 (and will be incremented
|
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in future versions).
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</xs:documentation>
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</xs:annotation>
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<xs:restriction base="xs:decimal">
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<xs:pattern value="0\.9"/>
|
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</xs:restriction>
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</xs:simpleType>
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+
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+
<xs:complexType name="Nexml" mixed="true">
|
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40
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+
<xs:annotation>
|
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41
|
+
<xs:documentation>
|
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42
|
+
The root element for nexml.
|
|
43
|
+
</xs:documentation>
|
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44
|
+
</xs:annotation>
|
|
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|
+
<xs:complexContent mixed="true">
|
|
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|
+
<xs:extension base="Annotated">
|
|
47
|
+
<xs:sequence maxOccurs="unbounded" minOccurs="0">
|
|
48
|
+
<xs:element maxOccurs="unbounded" minOccurs="1" name="otus" type="Taxa"/>
|
|
49
|
+
<xs:sequence maxOccurs="unbounded" minOccurs="0">
|
|
50
|
+
<xs:choice>
|
|
51
|
+
<xs:element maxOccurs="unbounded" minOccurs="0" name="characters" type="AbstractBlock"/>
|
|
52
|
+
<xs:element maxOccurs="unbounded" minOccurs="0" name="trees" type="Trees">
|
|
53
|
+
<xs:key name="tree">
|
|
54
|
+
<xs:selector xpath="./tree"/>
|
|
55
|
+
<xs:field xpath="@id"/>
|
|
56
|
+
</xs:key>
|
|
57
|
+
</xs:element>
|
|
58
|
+
</xs:choice>
|
|
59
|
+
</xs:sequence>
|
|
60
|
+
</xs:sequence>
|
|
61
|
+
<xs:attribute name="version" type="Nexml1_0" use="required"/>
|
|
62
|
+
<xs:attribute name="generator" type="xs:string" use="optional"/>
|
|
63
|
+
</xs:extension>
|
|
64
|
+
</xs:complexContent>
|
|
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|
+
</xs:complexType>
|
|
66
|
+
|
|
67
|
+
<!-- the root of the document -->
|
|
68
|
+
<xs:element name="nexml" type="Nexml">
|
|
69
|
+
|
|
70
|
+
<!-- keys for child-of-root biodata containers: taxa, characters trees -->
|
|
71
|
+
<xs:key name="taxa">
|
|
72
|
+
<xs:selector xpath="./taxa"/>
|
|
73
|
+
<xs:field xpath="@id"/>
|
|
74
|
+
</xs:key>
|
|
75
|
+
<xs:key name="characters">
|
|
76
|
+
<xs:selector xpath="./characters"/>
|
|
77
|
+
<xs:field xpath="@id"/>
|
|
78
|
+
</xs:key>
|
|
79
|
+
<xs:key name="trees">
|
|
80
|
+
<xs:selector xpath="./trees"/>
|
|
81
|
+
<xs:field xpath="@id"/>
|
|
82
|
+
</xs:key>
|
|
83
|
+
|
|
84
|
+
<xs:key name="taxon">
|
|
85
|
+
<xs:selector xpath="./taxa/taxon"/>
|
|
86
|
+
<xs:field xpath="@id"/>
|
|
87
|
+
</xs:key>
|
|
88
|
+
|
|
89
|
+
<!-- links to taxon objects: from row to taxon, from node to taxon -->
|
|
90
|
+
<xs:keyref name="rowTaxonRef" refer="taxon">
|
|
91
|
+
<xs:selector xpath="./characters/matrix/row"/>
|
|
92
|
+
<xs:field xpath="@taxon"/>
|
|
93
|
+
</xs:keyref>
|
|
94
|
+
<xs:keyref name="listNodeTaxonRef" refer="taxon">
|
|
95
|
+
<xs:selector xpath="./trees/tree/terminal"/>
|
|
96
|
+
<xs:field xpath="@taxon"/>
|
|
97
|
+
</xs:keyref>
|
|
98
|
+
<xs:keyref name="nestedNodeTaxonRef" refer="taxon">
|
|
99
|
+
<xs:selector xpath="./trees/tree/root/internal/*/terminal"/>
|
|
100
|
+
<xs:field xpath="@taxon"/>
|
|
101
|
+
</xs:keyref>
|
|
102
|
+
|
|
103
|
+
</xs:element>
|
|
104
|
+
</xs:schema>
|
|
@@ -0,0 +1,39 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
+
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.nexml.org/2009"
|
|
3
|
+
xmlns:sawsdl="http://www.w3.org/ns/sawsdl" xmlns="http://www.nexml.org/2009"
|
|
4
|
+
elementFormDefault="qualified">
|
|
5
|
+
<xs:annotation>
|
|
6
|
+
<xs:documentation>
|
|
7
|
+
This module defines complex types for <a href="#Taxon">OTU</a>
|
|
8
|
+
objects and their <a href="#Taxa">container objects</a>. These
|
|
9
|
+
types are analogous to the "taxa" block in NEXUS files. They
|
|
10
|
+
are used in the nexml schema, and in instance documents, to
|
|
11
|
+
normalize the cardinality between nodes in trees and rows in
|
|
12
|
+
matrices.
|
|
13
|
+
</xs:documentation>
|
|
14
|
+
</xs:annotation>
|
|
15
|
+
<xs:include schemaLocation="../abstract.xsd"/>
|
|
16
|
+
<!--
|
|
17
|
+
The following type definitions build up a taxa block
|
|
18
|
+
-->
|
|
19
|
+
|
|
20
|
+
<!-- Otu data type -->
|
|
21
|
+
<xs:complexType name="Taxon"
|
|
22
|
+
sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#TU">
|
|
23
|
+
<xs:complexContent>
|
|
24
|
+
<xs:extension base="IDTagged"/>
|
|
25
|
+
</xs:complexContent>
|
|
26
|
+
</xs:complexType>
|
|
27
|
+
|
|
28
|
+
<!-- Otus data type -->
|
|
29
|
+
<xs:complexType name="Taxa">
|
|
30
|
+
<xs:complexContent mixed="true">
|
|
31
|
+
<xs:extension base="IDTagged">
|
|
32
|
+
<xs:sequence>
|
|
33
|
+
<xs:element name="otu" type="Taxon" minOccurs="0" maxOccurs="unbounded"/>
|
|
34
|
+
</xs:sequence>
|
|
35
|
+
</xs:extension>
|
|
36
|
+
</xs:complexContent>
|
|
37
|
+
</xs:complexType>
|
|
38
|
+
|
|
39
|
+
</xs:schema>
|
|
@@ -0,0 +1,135 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
+
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
|
|
3
|
+
targetNamespace="http://www.nexml.org/2009" xmlns="http://www.nexml.org/2009"
|
|
4
|
+
elementFormDefault="qualified">
|
|
5
|
+
<xs:annotation>
|
|
6
|
+
<xs:documentation>
|
|
7
|
+
This module defines abstract superclasses for tree components.
|
|
8
|
+
Nexml defines trees as a sequence of nodes, zero or one root edge
|
|
9
|
+
and a sequence of edges. There are different concrete instances
|
|
10
|
+
of edges, namely those with lengths formatted as integers, and
|
|
11
|
+
lengths formatted as floating point numbers.
|
|
12
|
+
<br/><br/>
|
|
13
|
+
In addition, there are different types of trees: those where nodes
|
|
14
|
+
have an in-degree of 1 - true trees - and those with in-degree that
|
|
15
|
+
can exceed 1 - networks.
|
|
16
|
+
</xs:documentation>
|
|
17
|
+
</xs:annotation>
|
|
18
|
+
|
|
19
|
+
<xs:include schemaLocation="../abstract.xsd"/>
|
|
20
|
+
|
|
21
|
+
<xs:complexType name="AbstractNode" abstract="true"
|
|
22
|
+
sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#Node">
|
|
23
|
+
<xs:annotation>
|
|
24
|
+
<xs:documentation>
|
|
25
|
+
The AbstractNode superclass is what concrete nodes inherit
|
|
26
|
+
from by restriction. It represents a node element much like
|
|
27
|
+
that of GraphML, i.e. an element that is connected into a
|
|
28
|
+
tree by edge elements.
|
|
29
|
+
</xs:documentation>
|
|
30
|
+
</xs:annotation>
|
|
31
|
+
<xs:complexContent>
|
|
32
|
+
<xs:extension base="OptionalTaxonLinked">
|
|
33
|
+
<xs:attribute name="root" type="xs:boolean" default="false" use="optional"/>
|
|
34
|
+
</xs:extension>
|
|
35
|
+
</xs:complexContent>
|
|
36
|
+
</xs:complexType>
|
|
37
|
+
|
|
38
|
+
<xs:complexType name="AbstractEdge" abstract="true"
|
|
39
|
+
sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#Edge">
|
|
40
|
+
<xs:annotation>
|
|
41
|
+
<xs:documentation>
|
|
42
|
+
The AbstractEdge superclass is what concrete edges inherit
|
|
43
|
+
from by restriction. It represents an edge element much like
|
|
44
|
+
that of GraphML, i.e. an element that connects node elements.
|
|
45
|
+
</xs:documentation>
|
|
46
|
+
<xs:appinfo>Edge</xs:appinfo>
|
|
47
|
+
</xs:annotation>
|
|
48
|
+
<xs:complexContent>
|
|
49
|
+
<xs:extension base="IDTagged">
|
|
50
|
+
<xs:attribute name="source" type="xs:IDREF" use="required"/>
|
|
51
|
+
<xs:attribute name="target" type="xs:IDREF" use="required"/>
|
|
52
|
+
<xs:attribute name="length" type="xs:anySimpleType" use="optional"/>
|
|
53
|
+
</xs:extension>
|
|
54
|
+
</xs:complexContent>
|
|
55
|
+
</xs:complexType>
|
|
56
|
+
|
|
57
|
+
<xs:complexType name="AbstractRootEdge" abstract="true">
|
|
58
|
+
<xs:annotation>
|
|
59
|
+
<xs:documentation>
|
|
60
|
+
The AbstractRootEdge complex type is a superclass for the
|
|
61
|
+
edge that leads into a root, i.e. an edge with only a target
|
|
62
|
+
attribute, but no source attribute. This type of edge is
|
|
63
|
+
used for coalescent trees, where the initial lineage has
|
|
64
|
+
a certain length before things start splitting up.
|
|
65
|
+
</xs:documentation>
|
|
66
|
+
</xs:annotation>
|
|
67
|
+
<xs:complexContent>
|
|
68
|
+
<xs:extension base="IDTagged">
|
|
69
|
+
<xs:attribute name="target" type="xs:IDREF" use="required"/>
|
|
70
|
+
<xs:attribute name="length" type="xs:anySimpleType" use="optional"/>
|
|
71
|
+
</xs:extension>
|
|
72
|
+
</xs:complexContent>
|
|
73
|
+
</xs:complexType>
|
|
74
|
+
|
|
75
|
+
<xs:complexType name="AbstractTree" abstract="true"
|
|
76
|
+
sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#Tree">
|
|
77
|
+
<xs:annotation>
|
|
78
|
+
<xs:documentation>
|
|
79
|
+
The AbstractTree superclass is what a concrete tree inherits
|
|
80
|
+
from.
|
|
81
|
+
</xs:documentation>
|
|
82
|
+
</xs:annotation>
|
|
83
|
+
<xs:complexContent mixed="true">
|
|
84
|
+
<xs:extension base="IDTagged">
|
|
85
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
86
|
+
<xs:element name="node" type="AbstractNode" minOccurs="1" maxOccurs="unbounded"/>
|
|
87
|
+
<xs:element name="rootedge" type="AbstractRootEdge" minOccurs="0" maxOccurs="1"/>
|
|
88
|
+
<xs:element name="edge" type="AbstractEdge" minOccurs="1" maxOccurs="unbounded"
|
|
89
|
+
/>
|
|
90
|
+
</xs:sequence>
|
|
91
|
+
</xs:extension>
|
|
92
|
+
</xs:complexContent>
|
|
93
|
+
</xs:complexType>
|
|
94
|
+
|
|
95
|
+
<xs:complexType name="AbstractNetwork" abstract="true"
|
|
96
|
+
sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#Network">
|
|
97
|
+
<xs:annotation>
|
|
98
|
+
<xs:documentation>
|
|
99
|
+
The AbstractNetwork superclass is what a concrete network inherits
|
|
100
|
+
from.
|
|
101
|
+
</xs:documentation>
|
|
102
|
+
</xs:annotation>
|
|
103
|
+
<xs:complexContent mixed="true">
|
|
104
|
+
<xs:extension base="IDTagged">
|
|
105
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
106
|
+
<xs:element name="node" type="AbstractNode" minOccurs="1" maxOccurs="unbounded"/>
|
|
107
|
+
<xs:element name="edge" type="AbstractEdge" minOccurs="1" maxOccurs="unbounded"
|
|
108
|
+
/>
|
|
109
|
+
</xs:sequence>
|
|
110
|
+
</xs:extension>
|
|
111
|
+
</xs:complexContent>
|
|
112
|
+
</xs:complexType>
|
|
113
|
+
|
|
114
|
+
<xs:complexType name="AbstractTrees" abstract="true">
|
|
115
|
+
<xs:annotation>
|
|
116
|
+
<xs:documentation>
|
|
117
|
+
The AbstractTrees superclass is what concrete trees inherit
|
|
118
|
+
from.
|
|
119
|
+
</xs:documentation>
|
|
120
|
+
</xs:annotation>
|
|
121
|
+
<xs:complexContent mixed="true">
|
|
122
|
+
<xs:extension base="IDTagged">
|
|
123
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
124
|
+
<xs:choice minOccurs="0" maxOccurs="unbounded">
|
|
125
|
+
<xs:element name="network" type="AbstractNetwork" minOccurs="1"
|
|
126
|
+
maxOccurs="unbounded"/>
|
|
127
|
+
<xs:element name="tree" type="AbstractTree" minOccurs="1"
|
|
128
|
+
maxOccurs="unbounded"/>
|
|
129
|
+
</xs:choice>
|
|
130
|
+
</xs:sequence>
|
|
131
|
+
</xs:extension>
|
|
132
|
+
</xs:complexContent>
|
|
133
|
+
</xs:complexType>
|
|
134
|
+
|
|
135
|
+
</xs:schema>
|