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 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: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: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:complexType name="AAMatrixObsRow" abstract="false">
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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: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:complexType name="AASeqMatrix" abstract="false">
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A matrix of rows with amino acid data as sequence strings.
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<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="AAMatrixSeqRow"/>
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<xs:complexType name="AAObsMatrix" abstract="false">
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<xs:documentation>
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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="AAMatrixObsRow"/>
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</xs:complexType>
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<xs:complexType name="ProteinSeqs" abstract="false">
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An amino acid characters block consisting of granular cells preceded by metadata.
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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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<!--
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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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<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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<xs:element name="char" type="RestrictionChar" 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: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: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: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:complexType name="RestrictionSeqMatrix" abstract="false">
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A matrix of rows with seq strings of type restriction.
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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="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:complexContent>
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</xs:complexType>
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<xs:complexType name="RestrictionSeqs" abstract="false">
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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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