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 xmlns:xs="http://www.w3.org/2001/XMLSchema"
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targetNamespace="http://www.nexml.org/2009"
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xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
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xmlns="http://www.nexml.org/2009"
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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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<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 amino acid 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. 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="AAToken">
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<xs:annotation>
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<xs:documentation>
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The AAToken simple type is a restriction of AbstractSymbol
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that defines an IUPAC single character amino acid symbol.
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</xs:documentation>
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<xs:appinfo>AminoAcid</xs:appinfo>
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</xs:annotation>
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<xs:restriction base="AbstractSymbol">
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<xs:pattern value="[\*\-\?ABCDEFGHIKLMNPQRSTUVWXYZ]"/>
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<xs:length value="1"/>
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</xs:restriction>
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</xs:simpleType>
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<xs:complexType name="AAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueCharacter">
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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 must be an identifier ("id") that is of type xs:nonNegativeInteger to
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define the column number.
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</xs:documentation>
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<xs:appinfo>Amino_Acid_Character</xs:appinfo>
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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="prohibited"/>
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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="AAFormat" abstract="false">
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<xs:annotation>
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<xs:documentation> The AAFormat class is the container of amino acid 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="AAStates" minOccurs="1" maxOccurs="unbounded"/>
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<xs:element name="char" type="AAChar" 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="AAStates">
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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="AAState" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="polymorphic_state_set" type="AAPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="uncertain_state_set" type="AAUncertainStateSet" 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="AAPolymorphicStateSet">
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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="AAMapping" minOccurs="0" maxOccurs="unbounded"/>
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<xs:element name="uncertain_state_set" type="AAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
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</xs:sequence>
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<xs:attribute name="symbol" type="AAToken" 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="AAUncertainStateSet">
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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="AAMapping" minOccurs="0" maxOccurs="unbounded"/>
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</xs:sequence>
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<xs:attribute name="symbol" type="AAToken" 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="AAMapping">
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<xs:annotation>
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<xs:documentation>An IUPAC ambiguity mapping.</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="AAState">
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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 DNAToken, 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="AAToken" 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="AAObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueStateDatum">
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<xs:annotation>
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<xs:documentation>
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This is a single cell in a matrix containing
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an amino acid observation.
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</xs:documentation>
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<xs:appinfo>Amino_Acid_State_Datum</xs:appinfo>
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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="AASeq">
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<xs:annotation>
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<xs:documentation>
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This is a simple type that specifies a sequence of amino acid characters,
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following IUPAC single character symbols for aa (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="[\*\-\?ABCDEFGHIKLMNPQRSTUVWXYZ\s]*"/>
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</xs:restriction>
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</xs:simpleType>
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<xs:complexType name="AAMatrixSeqRow" abstract="false">
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<xs:annotation>
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<xs:documentation> This is a row in a matrix of amino acid 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="AASeq"/>
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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="AAMatrixObsRow" abstract="false">
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<xs:annotation>
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<xs:documentation> This is a row in a matrix of amino acid 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="AAObs"/>
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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="AASeqMatrix" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A matrix of rows with amino acid data as sequence strings.
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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="AAMatrixSeqRow"/>
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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="AAObsMatrix" 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="AAMatrixObsRow"/>
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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="ProteinSeqs" abstract="false">
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<xs:annotation>
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<xs:documentation>
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An amino acid characters block consisting of sequences preceded by metadata.
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</xs:documentation>
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An amino acid characters block consisting of granular cells preceded by metadata.
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema
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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: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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schemaLocation="http://www.w3.org/2001/xml.xsd"/>-->
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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 restriction site 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 0 or 1. In a compact
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notation, the same data is represented as a sequence of tokens (whitespace is allowed but has no meaning).
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A restriction site matrix only has presence (1) or absence (0), so
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state definitions and ambiguity mappings are omitted.
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<xs:documentation>A standard character ambiguity mapping.</xs:documentation>
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-->
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<xs:documentation> This is a concrete implementation of the state element, which requires
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a symbol element, in this case restricted to integers, and optional mapping
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elements to refer to other states. </xs:documentation>
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A container for a set of states.
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A concrete implementation of the char element,
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which only requires a unique identifier.
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<xs:attribute name="codon" type="CodonPosition" use="prohibited"/>
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<xs:complexType name="RestrictionFormat" abstract="false">
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<xs:documentation> The RestrictionFormat class is the container of restriction column definitions.
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<xs:element name="states" type="RestrictionStates" minOccurs="1" maxOccurs="unbounded"/>
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This is a single cell in a matrix containing a
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restriction site observation.
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<xs:attribute name="char" use="required" type="xs:IDREF"/>
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<xs:simpleType name="RestrictionSeq">
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This is a simple type that specifies a
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sequence of restriction site characters.
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</xs:documentation>
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<xs:restriction base="xs:string">
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<xs:pattern value="[01\s]*"></xs:pattern>
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</xs:simpleType>
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<xs:complexType name="RestrictionMatrixSeqRow" abstract="false">
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<xs:documentation>
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This is a row in a matrix of restriction
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site data as character sequences.
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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="RestrictionSeq"/>
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</xs:restriction>
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<xs:complexType name="RestrictionMatrixObsRow" abstract="false">
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<xs:annotation>
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<xs:documentation>
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This is a row in a matrix of restriction
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site data as granular obervations.
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</xs:documentation>
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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="RestrictionObs"/>
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</xs:sequence>
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<xs:complexType name="RestrictionSeqMatrix" abstract="false">
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<xs:annotation>
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A matrix of rows with seq strings of type restriction.
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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="RestrictionMatrixSeqRow"/>
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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="RestrictionObsMatrix" 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="RestrictionMatrixObsRow"/>
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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="RestrictionSeqs" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A restriction site characters block
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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="RestrictionFormat"/>
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<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="RestrictionSeqMatrix"/>
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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="RestrictionCells" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A standard characters block consisting
|
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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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<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="RestrictionFormat"/>
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<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="RestrictionObsMatrix"/>
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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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