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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<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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xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
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xmlns:xml="http://www.w3.org/XML/1998/namespace"
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elementFormDefault="qualified">
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<xs:include schemaLocation="abstractcharacters.xsd"/>
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<!--
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<xs:import namespace="http://www.w3.org/XML/1998/namespace"
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schemaLocation="http://www.w3.org/2001/xml.xsd"/>-->
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<xs:annotation>
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<xs:documentation>
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This module defines concrete subclasses for the
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<a href="../abstract">abstract</a> character matrix components
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that all character matrices must implement. The subclasses
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defined here apply to RNA character data. In a verbose notation,
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this data is represented as the "state" attribute of the <cell>
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element, whose value-space is limited to the IUPAC single character
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nucleotide symbols (except T). In a compact notation, the same data
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is represented as a sequence of tokens (whitespace is allowed but has no meaning).
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</xs:documentation>
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</xs:annotation>
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<xs:simpleType name="RNAToken">
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<xs:annotation>
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<xs:documentation>
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The RNAToken simple type is a restriction of AbstractSymbol that defines
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a token of a IUPAC single character nucleotide token.
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</xs:documentation>
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</xs:annotation>
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<xs:restriction base="AbstractSymbol">
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<xs:pattern value="[\-\?ABCDGHKMNRSUVWXY]"/>
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<xs:length value="1"/>
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</xs:restriction>
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</xs:simpleType>
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<!--
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The following types would be used if we explicitly defined ambiguity mappings,
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allowed states, etc. But we don't, because we use the IUPAC symbols anyway.
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-->
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<xs:complexType name="RNAMapping">
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<xs:annotation>
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<xs:documentation>
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An IUPAC ambiguity mapping.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractMapping" />
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAState">
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<xs:annotation>
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<xs:documentation>
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This is a concrete implementation of the state element, which requires
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a symbol element, in this case restricted to RNAToken, i.e. a single IUPAC nucleotide
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symbol, and optional mapping elements to refer to other states.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractState">
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<xs:sequence minOccurs="1" maxOccurs="1"/>
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<xs:attribute name="symbol" type="RNAToken" use="required"></xs:attribute>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAUncertainStateSet">
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<xs:annotation>
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<xs:documentation>
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The AbstractState type is the superclass for a state definition.
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The element encloses a required AbstractSymbol element that in restricted concrete
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subclasses must be of a sensible type such as a single IUPAC character. It may
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enclose zero or more AbstractMapping elements to resolve ambiguities.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractUncertainStateSet">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="member" type="RNAMapping" minOccurs="0" maxOccurs="unbounded"/>
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</xs:sequence>
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<xs:attribute name="symbol" type="RNAToken" use="required"></xs:attribute>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAPolymorphicStateSet">
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<xs:annotation>
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<xs:documentation>
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The AbstractState type is the superclass for a state definition.
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The element encloses a required AbstractSymbol element that in restricted concrete
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subclasses must be of a sensible type such as a single IUPAC character. It may
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enclose zero or more AbstractMapping elements to resolve ambiguities.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractPolymorphicStateSet">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="member" type="RNAMapping" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="uncertain_state_set" type="RNAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
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</xs:sequence>
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<xs:attribute name="symbol" type="RNAToken" use="required"></xs:attribute>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAStates">
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<xs:annotation>
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<xs:documentation>
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A container for a set of states.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractStates">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="state" type="RNAState" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="polymorphic_state_set" type="RNAPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="uncertain_state_set" type="RNAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#RNAResidueCharacter">
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<xs:annotation>
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<xs:documentation>
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A concrete implementation of the AbstractChar element. In this implementation
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there is no reference to explicitly defined states, as we use the IUPAC standard.
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There may be a CodonPosition ("codon") attribute, and there must be an identifier
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("id") that is of type xs:nonNegativeInteger to define the column number.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractChar">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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</xs:sequence>
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<xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
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<xs:attribute name="states" type="xs:IDREF" use="required"/>
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<xs:attribute name="codon" type="CodonPosition" use="optional"/>
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<xs:attribute name="id" type="xs:ID" use="required"/>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAFormat" abstract="false">
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<xs:annotation>
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<xs:documentation> The RNAFormat class is the container of RNA column definitions.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractFormat">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="states" type="RNAStates" minOccurs="1" maxOccurs="unbounded"/>
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<xs:element name="char" type="RNAChar" minOccurs="1" maxOccurs="unbounded"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#RNAResidueStateDatum">
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<xs:annotation>
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<xs:documentation> This is a single cell in a matrix containing a nucleotide
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observation. </xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractObs">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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</xs:sequence>
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<xs:attribute name="char" use="required" type="xs:IDREF"/>
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<xs:attribute name="state" use="required" type="xs:IDREF"/>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:simpleType name="RNASeq">
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<xs:annotation>
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<xs:documentation> This is a simple type that specifies a sequence of RNA characters,
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following IUPAC single character symbols for nucleotides (and ambiguities).
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</xs:documentation>
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</xs:annotation>
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<xs:restriction base="AbstractSeq">
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<xs:pattern value="[\-\?ABCDGHKMNRSUVWXY\s]*"/>
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</xs:restriction>
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</xs:simpleType>
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<xs:complexType name="RNAMatrixSeqRow" abstract="false">
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<xs:annotation>
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<xs:documentation> This is a row in a matrix of RNA data containing raw sequence data. </xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractSeqRow">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="seq" minOccurs="1" maxOccurs="1" type="RNASeq"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexType>
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<xs:complexType name="RNAMatrixObsRow" abstract="false">
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<xs:annotation>
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<xs:documentation> This is a row in a matrix of RNA data containing granular observations. </xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractObsRow">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="cell" minOccurs="1" maxOccurs="unbounded" type="RNAObs"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexType>
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<xs:complexType name="RNASeqMatrix" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A matrix of rows with seq strings of type RNA.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractSeqMatrix">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="RNAMatrixSeqRow"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RNAObsMatrix" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A matrix of rows with single character observations.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractObsMatrix">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="RNAMatrixObsRow"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="RnaSeqs" abstract="false">
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<xs:annotation>
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<xs:documentation>
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This module defines concrete subclasses for the
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that all character matrices must implement. The subclasses
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defined here apply to "standard" categorical character data, such as
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counts of morpholical features. In a verbose notation, this data
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element. In a compact notation, the same data is represented as
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elements to refer to other states. </xs:documentation>
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The AbstractState type is the superclass for a state definition.
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The element encloses a required AbstractSymbol element that in restricted concrete
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subclasses must be of a sensible type such as a single IUPAC character. It may
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The AbstractState type is the superclass for a state definition.
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A container for a set of states.
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<xs:element name="state" type="StandardState" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="polymorphic_state_set" type="StandardPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/>
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<xs:complexType name="StandardChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardCharacter">
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a states attribute to refer to a set of defined states </xs:documentation>
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<xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
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<xs:attribute name="states" type="xs:IDREF" use="required"/>
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<xs:attribute name="codon" type="CodonPosition" use="prohibited"/>
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<xs:complexType name="StandardFormat" abstract="false">
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<xs:documentation> The StandardFormat class is the container of standard column definitions.
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<xs:element name="states" type="StandardStates" minOccurs="1" maxOccurs="unbounded"/>
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<xs:complexType name="StandardObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardStateDatum">
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<xs:documentation> This is a single cell in a matrix containing a standard
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observation. </xs:documentation>
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<xs:attribute name="char" use="required" type="xs:IDREF"/>
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<xs:simpleType name="StandardSeq">
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<xs:documentation> This is a simple type that specifies a sequence of standard characters.
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<xs:restriction base="AbstractTokenList">
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<xs:pattern value="[0-9\-\?]+(\s[0-9\-\?]+)*"></xs:pattern>
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</xs:simpleType>
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<xs:complexType name="StandardMatrixSeqRow" abstract="false">
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<xs:documentation> This is a row in a matrix of standard data as character sequences. </xs:documentation>
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="seq" minOccurs="1" maxOccurs="1" type="StandardSeq"/>
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</xs:complexType>
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<xs:complexType name="StandardMatrixObsRow" abstract="false">
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<xs:documentation> This is a row in a matrix of standard data as granular obervations. </xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractObsRow">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="cell" minOccurs="1" maxOccurs="unbounded" type="StandardObs"/>
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</xs:sequence>
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</xs:complexType>
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<xs:complexType name="StandardSeqMatrix" abstract="false">
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<xs:documentation>
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A matrix of rows with seq strings of type standard.
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</xs:documentation>
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</xs:annotation>
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<xs:restriction base="AbstractSeqMatrix">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="StandardMatrixSeqRow"/>
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</xs:sequence>
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</xs:complexType>
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<xs:complexType name="StandardObsMatrix" abstract="false">
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<xs:annotation>
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A matrix of rows with single character observations.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractObsMatrix">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="StandardMatrixObsRow"/>
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</xs:sequence>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="StandardSeqs" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A standard characters block consisting of sequences preceded by metadata.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractSeqs">
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<xs:sequence minOccurs="1" maxOccurs="1">
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<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
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<xs:element name="format" minOccurs="1" maxOccurs="1" type="StandardFormat"/>
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<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="StandardSeqMatrix"/>
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</xs:sequence>
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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<xs:complexType name="StandardCells" abstract="false">
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<xs:annotation>
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<xs:documentation>
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|
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A standard characters block consisting of granular cells preceded by metadata.
|
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractCells">
|
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|
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<xs:sequence minOccurs="1" maxOccurs="1">
|
|
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|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
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|
+
<xs:element name="format" minOccurs="1" maxOccurs="1" type="StandardFormat"/>
|
|
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|
+
<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="StandardObsMatrix"/>
|
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|
+
</xs:sequence>
|
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</xs:restriction>
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</xs:complexContent>
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</xs:complexType>
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</xs:schema>
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