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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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: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 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: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: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: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: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:complexType name="RNASeqMatrix" abstract="false">
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A matrix of rows with seq strings of type RNA.
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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:complexType name="RNAObsMatrix" abstract="false">
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A matrix of rows with single character observations.
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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:complexType>
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<xs:complexType name="RnaSeqs" abstract="false">
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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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counts of morpholical features. In a verbose notation, this data
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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: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="codon" type="CodonPosition" use="prohibited"/>
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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:annotation>
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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 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: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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A matrix of rows with seq strings of type standard.
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</xs:annotation>
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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: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: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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|
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</xs:documentation>
|
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|
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</xs:annotation>
|
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|
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<xs:complexContent>
|
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|
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<xs:restriction base="AbstractCells">
|
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|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
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|
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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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