bio-nexml 0.0.1
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- data/Gemfile +15 -0
- data/Gemfile.lock +24 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +47 -0
- data/Rakefile +55 -0
- data/TODO.txt +6 -0
- data/VERSION +1 -0
- data/bio-nexml.gemspec +126 -0
- data/extconf.rb +2 -0
- data/lib/bio-nexml.rb +0 -0
- data/lib/bio.rb +321 -0
- data/lib/bio/db/nexml.rb +109 -0
- data/lib/bio/db/nexml/mapper.rb +113 -0
- data/lib/bio/db/nexml/mapper/framework.rb +157 -0
- data/lib/bio/db/nexml/mapper/inflection.rb +99 -0
- data/lib/bio/db/nexml/mapper/repository.rb +59 -0
- data/lib/bio/db/nexml/matrix.rb +1046 -0
- data/lib/bio/db/nexml/parser.rb +622 -0
- data/lib/bio/db/nexml/schema/README.txt +21 -0
- data/lib/bio/db/nexml/schema/abstract.xsd +159 -0
- data/lib/bio/db/nexml/schema/characters/README.txt +1 -0
- data/lib/bio/db/nexml/schema/characters/abstractcharacters.xsd +361 -0
- data/lib/bio/db/nexml/schema/characters/characters.xsd +22 -0
- data/lib/bio/db/nexml/schema/characters/continuous.xsd +190 -0
- data/lib/bio/db/nexml/schema/characters/dna.xsd +282 -0
- data/lib/bio/db/nexml/schema/characters/protein.xsd +280 -0
- data/lib/bio/db/nexml/schema/characters/restriction.xsd +239 -0
- data/lib/bio/db/nexml/schema/characters/rna.xsd +283 -0
- data/lib/bio/db/nexml/schema/characters/standard.xsd +261 -0
- data/lib/bio/db/nexml/schema/external/sawsdl.xsd +21 -0
- data/lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd +177 -0
- data/lib/bio/db/nexml/schema/external/xlink.xsd +75 -0
- data/lib/bio/db/nexml/schema/external/xml.xsd +145 -0
- data/lib/bio/db/nexml/schema/meta/README.txt +2 -0
- data/lib/bio/db/nexml/schema/meta/annotations.xsd +100 -0
- data/lib/bio/db/nexml/schema/meta/meta.xsd +294 -0
- data/lib/bio/db/nexml/schema/nexml.xsd +104 -0
- data/lib/bio/db/nexml/schema/taxa/README.txt +2 -0
- data/lib/bio/db/nexml/schema/taxa/taxa.xsd +39 -0
- data/lib/bio/db/nexml/schema/trees/README.txt +2 -0
- data/lib/bio/db/nexml/schema/trees/abstracttrees.xsd +135 -0
- data/lib/bio/db/nexml/schema/trees/network.xsd +113 -0
- data/lib/bio/db/nexml/schema/trees/tree.xsd +149 -0
- data/lib/bio/db/nexml/schema/trees/trees.xsd +36 -0
- data/lib/bio/db/nexml/taxa.rb +147 -0
- data/lib/bio/db/nexml/trees.rb +663 -0
- data/lib/bio/db/nexml/writer.rb +265 -0
- data/test/data/nexml/test.xml +69 -0
- data/test/test_bio-nexml.rb +17 -0
- data/test/unit/bio/db/nexml/tc_factory.rb +119 -0
- data/test/unit/bio/db/nexml/tc_mapper.rb +78 -0
- data/test/unit/bio/db/nexml/tc_matrix.rb +551 -0
- data/test/unit/bio/db/nexml/tc_parser.rb +21 -0
- data/test/unit/bio/db/nexml/tc_taxa.rb +118 -0
- data/test/unit/bio/db/nexml/tc_trees.rb +370 -0
- data/test/unit/bio/db/nexml/tc_writer.rb +633 -0
- metadata +253 -0
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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targetNamespace="http://www.nexml.org/2009"
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xmlns="http://www.nexml.org/2009"
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elementFormDefault="qualified">
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<xs:annotation>
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<xs:documentation>
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This module aggregates the subclass definitions for the different
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datatypes "<a href="../continuous">continuous</a>",
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"<a href="../dna">dna</a>", "<a href="../protein">protein</a>",
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"<a href="../restriction">restriction</a>", "<a href="../rna">rna</a>"
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and "<a href="../standard">standard</a>".
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</xs:documentation>
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</xs:annotation>
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<xs:include schemaLocation="continuous.xsd"/>
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<xs:include schemaLocation="dna.xsd"/>
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<xs:include schemaLocation="protein.xsd"/>
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<xs:include schemaLocation="restriction.xsd"/>
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<xs:include schemaLocation="rna.xsd"/>
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<xs:include schemaLocation="standard.xsd"/>
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</xs:schema>
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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: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 continuous-valued character data, such as
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length or width measurements. In a verbose notation, this data
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is represented as the "state" attribute of the <cell>
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element. In a compact notation, the same data is represented as
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a sequence of space-separated floating point numbers.
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</xs:documentation>
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</xs:annotation>
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<xs:include schemaLocation="abstractcharacters.xsd"/>
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<xs:simpleType name="ContinuousToken">
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<xs:restriction base="xs:float"/>
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</xs:simpleType>
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<xs:complexType name="ContinuousChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#ContinuousCharacter">
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<xs:annotation>
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<xs:documentation>
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A concrete implementation of the char element, which requires
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only an id attribute.
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</xs:documentation>
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<xs:appinfo>Continuous_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="states" type="xs:IDREF" use="prohibited"/>
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<xs:attribute name="codon" type="CodonPosition" use="prohibited"/>
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<xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
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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="ContinuousFormat" abstract="false">
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<xs:annotation>
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<xs:documentation>
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The ContinuousFormat class is the container of continuous 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="char" type="ContinuousChar" 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="ContinuousObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#ContinuousStateDatum">
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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 a continuous
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observation.
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</xs:documentation>
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<xs:appinfo>Continuous_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="ContinuousToken"/>
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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="ContinuousSeq">
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<xs:annotation>
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<xs:documentation>
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This is a simple type that specifies
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a list of xs:float characters.
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</xs:documentation>
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</xs:annotation>
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<!--<xs:list itemType="xs:float"/>-->
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<xs:restriction base="AbstractTokenList"/>
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</xs:simpleType>
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<xs:complexType name="ContinuousMatrixSeqRow" 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 continuous data as character sequences.
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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="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="ContinuousSeq"/>
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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="ContinuousMatrixObsRow" 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 continuous data as granular obervations.
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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="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="ContinuousObs"/>
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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="ContinuousSeqMatrix" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A matrix of rows with seq strings of type continuous.
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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="ContinuousMatrixSeqRow"/>
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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="ContinuousObsMatrix" 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="ContinuousMatrixObsRow"/>
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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="ContinuousSeqs" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A continuous characters block consisting of float 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="ContinuousFormat"/>
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<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="ContinuousSeqMatrix"/>
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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="ContinuousCells" abstract="false">
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<xs:annotation>
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<xs:documentation>
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A continuous characters block consisting of granular cells preceded by metadata.
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</xs:documentation>
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</xs:annotation>
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<xs:complexContent>
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<xs:restriction base="AbstractCells">
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<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="ContinuousFormat"/>
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<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="ContinuousObsMatrix"/>
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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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@@ -0,0 +1,282 @@
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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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<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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15
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that all character matrices must implement. The subclasses
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defined here apply to DNA 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 U). 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="DNAToken">
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<xs:annotation>
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<xs:documentation>
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The DNAToken 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="[ABCDGHKMNRSTVWXY\-\?]"/>
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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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<xs:complexType name="DNAMapping">
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<xs:annotation>
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<xs:documentation>An IUPAC ambiguity mapping.</xs:documentation>
|
|
44
|
+
</xs:annotation>
|
|
45
|
+
<xs:complexContent>
|
|
46
|
+
<xs:restriction base="AbstractMapping"/>
|
|
47
|
+
</xs:complexContent>
|
|
48
|
+
</xs:complexType>
|
|
49
|
+
|
|
50
|
+
<xs:complexType name="DNAState">
|
|
51
|
+
<xs:annotation>
|
|
52
|
+
<xs:documentation>
|
|
53
|
+
This is a concrete implementation of the state element, which requires
|
|
54
|
+
a symbol element, in this case restricted to DNAToken, i.e. a single IUPAC nucleotide
|
|
55
|
+
symbol, and optional mapping elements to refer to other states.
|
|
56
|
+
</xs:documentation>
|
|
57
|
+
</xs:annotation>
|
|
58
|
+
<xs:complexContent>
|
|
59
|
+
<xs:restriction base="AbstractState">
|
|
60
|
+
<xs:sequence minOccurs="1" maxOccurs="1"/>
|
|
61
|
+
<xs:attribute name="symbol" type="DNAToken" use="required"></xs:attribute>
|
|
62
|
+
</xs:restriction>
|
|
63
|
+
</xs:complexContent>
|
|
64
|
+
</xs:complexType>
|
|
65
|
+
|
|
66
|
+
<xs:complexType name="DNAUncertainStateSet">
|
|
67
|
+
<xs:annotation>
|
|
68
|
+
<xs:documentation>
|
|
69
|
+
The AbstractState type is the superclass for a state definition.
|
|
70
|
+
The element encloses a required AbstractSymbol element that in restricted concrete
|
|
71
|
+
subclasses must be of a sensible type such as a single IUPAC character. It may
|
|
72
|
+
enclose zero or more AbstractMapping elements to resolve ambiguities.
|
|
73
|
+
</xs:documentation>
|
|
74
|
+
</xs:annotation>
|
|
75
|
+
<xs:complexContent>
|
|
76
|
+
<xs:restriction base="AbstractUncertainStateSet">
|
|
77
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
78
|
+
<xs:element name="member" type="DNAMapping" minOccurs="0" maxOccurs="unbounded"/>
|
|
79
|
+
</xs:sequence>
|
|
80
|
+
<xs:attribute name="symbol" type="DNAToken" use="required"></xs:attribute>
|
|
81
|
+
</xs:restriction>
|
|
82
|
+
</xs:complexContent>
|
|
83
|
+
</xs:complexType>
|
|
84
|
+
|
|
85
|
+
<xs:complexType name="DNAPolymorphicStateSet">
|
|
86
|
+
<xs:annotation>
|
|
87
|
+
<xs:documentation>
|
|
88
|
+
The AbstractState type is the superclass for a state definition.
|
|
89
|
+
The element encloses a required AbstractSymbol element that in restricted concrete
|
|
90
|
+
subclasses must be of a sensible type such as a single IUPAC character. It may
|
|
91
|
+
enclose zero or more AbstractMapping elements to resolve ambiguities.
|
|
92
|
+
</xs:documentation>
|
|
93
|
+
</xs:annotation>
|
|
94
|
+
<xs:complexContent>
|
|
95
|
+
<xs:restriction base="AbstractPolymorphicStateSet">
|
|
96
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
97
|
+
<xs:element name="member" type="DNAMapping" minOccurs="0" maxOccurs="unbounded"/>
|
|
98
|
+
<xs:element name="uncertain_state_set" type="DNAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
|
|
99
|
+
</xs:sequence>
|
|
100
|
+
<xs:attribute name="symbol" type="DNAToken" use="required"></xs:attribute>
|
|
101
|
+
</xs:restriction>
|
|
102
|
+
</xs:complexContent>
|
|
103
|
+
</xs:complexType>
|
|
104
|
+
|
|
105
|
+
<xs:complexType name="DNAStates">
|
|
106
|
+
<xs:annotation>
|
|
107
|
+
<xs:documentation>
|
|
108
|
+
A container for a set of states.
|
|
109
|
+
</xs:documentation>
|
|
110
|
+
</xs:annotation>
|
|
111
|
+
<xs:complexContent>
|
|
112
|
+
<xs:restriction base="AbstractStates">
|
|
113
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
114
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
115
|
+
<xs:element name="state" type="DNAState" minOccurs="0" maxOccurs="unbounded"/>
|
|
116
|
+
<xs:element name="polymorphic_state_set" type="DNAPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/>
|
|
117
|
+
<xs:element name="uncertain_state_set" type="DNAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
|
|
118
|
+
</xs:sequence>
|
|
119
|
+
</xs:restriction>
|
|
120
|
+
</xs:complexContent>
|
|
121
|
+
</xs:complexType>
|
|
122
|
+
|
|
123
|
+
<xs:complexType name="DNAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideResidueCharacter">
|
|
124
|
+
<xs:annotation>
|
|
125
|
+
<xs:documentation>
|
|
126
|
+
A concrete implementation of the AbstractChar element. In this implementation
|
|
127
|
+
there is no reference to explicitly defined states, as we use the IUPAC standard.
|
|
128
|
+
There may be a CodonPosition ("codon") attribute, and there must be an identifier
|
|
129
|
+
("id") that is of type xs:nonNegativeInteger to define the column number.
|
|
130
|
+
</xs:documentation>
|
|
131
|
+
<xs:appinfo>Nucleotide_Character</xs:appinfo>
|
|
132
|
+
</xs:annotation>
|
|
133
|
+
<xs:complexContent>
|
|
134
|
+
<xs:restriction base="AbstractChar">
|
|
135
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
136
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
137
|
+
</xs:sequence>
|
|
138
|
+
<xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
|
|
139
|
+
<xs:attribute name="states" type="xs:IDREF" use="required"/>
|
|
140
|
+
<xs:attribute name="codon" type="CodonPosition" use="optional"/>
|
|
141
|
+
<xs:attribute name="id" type="xs:ID" use="required"/>
|
|
142
|
+
</xs:restriction>
|
|
143
|
+
</xs:complexContent>
|
|
144
|
+
</xs:complexType>
|
|
145
|
+
|
|
146
|
+
<xs:complexType name="DNAFormat" abstract="false">
|
|
147
|
+
<xs:annotation>
|
|
148
|
+
<xs:documentation> The DNAFormat class is the container of DNA column definitions.
|
|
149
|
+
</xs:documentation>
|
|
150
|
+
</xs:annotation>
|
|
151
|
+
<xs:complexContent>
|
|
152
|
+
<xs:restriction base="AbstractFormat">
|
|
153
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
154
|
+
<xs:element name="states" type="DNAStates" minOccurs="1" maxOccurs="unbounded"/>
|
|
155
|
+
<xs:element name="char" type="DNAChar" minOccurs="1" maxOccurs="unbounded"/>
|
|
156
|
+
</xs:sequence>
|
|
157
|
+
</xs:restriction>
|
|
158
|
+
</xs:complexContent>
|
|
159
|
+
</xs:complexType>
|
|
160
|
+
|
|
161
|
+
<xs:complexType name="DNAObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideStateDatum">
|
|
162
|
+
<xs:annotation>
|
|
163
|
+
<xs:documentation>
|
|
164
|
+
This is a single cell in a matrix containing a nucleotide observation.
|
|
165
|
+
</xs:documentation>
|
|
166
|
+
<xs:appinfo>Nucleotide_State_Datum</xs:appinfo>
|
|
167
|
+
</xs:annotation>
|
|
168
|
+
<xs:complexContent>
|
|
169
|
+
<xs:restriction base="AbstractObs">
|
|
170
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
171
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
172
|
+
</xs:sequence>
|
|
173
|
+
<xs:attribute name="char" use="required" type="xs:IDREF"/>
|
|
174
|
+
<xs:attribute name="state" use="required" type="xs:IDREF"/>
|
|
175
|
+
</xs:restriction>
|
|
176
|
+
</xs:complexContent>
|
|
177
|
+
</xs:complexType>
|
|
178
|
+
|
|
179
|
+
<xs:simpleType name="DNASeq">
|
|
180
|
+
<xs:annotation>
|
|
181
|
+
<xs:documentation> This is a simple type that specifies a sequence of DNA characters,
|
|
182
|
+
following IUPAC single character symbols for nucleotides (and ambiguities).
|
|
183
|
+
</xs:documentation>
|
|
184
|
+
</xs:annotation>
|
|
185
|
+
<xs:restriction base="AbstractSeq">
|
|
186
|
+
<xs:pattern value="[\-\?ABCDGHKMNRSTVWXY\s]*"/>
|
|
187
|
+
</xs:restriction>
|
|
188
|
+
</xs:simpleType>
|
|
189
|
+
|
|
190
|
+
<xs:complexType name="DNAMatrixSeqRow" abstract="false">
|
|
191
|
+
<xs:annotation>
|
|
192
|
+
<xs:documentation> This is a row in a matrix of DNA data containing raw sequence data. </xs:documentation>
|
|
193
|
+
</xs:annotation>
|
|
194
|
+
<xs:complexContent>
|
|
195
|
+
<xs:restriction base="AbstractSeqRow">
|
|
196
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
197
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
198
|
+
<xs:element name="seq" minOccurs="1" maxOccurs="1" type="DNASeq"/>
|
|
199
|
+
</xs:sequence>
|
|
200
|
+
</xs:restriction>
|
|
201
|
+
</xs:complexContent>
|
|
202
|
+
</xs:complexType>
|
|
203
|
+
|
|
204
|
+
<xs:complexType name="DNAMatrixObsRow" abstract="false">
|
|
205
|
+
<xs:annotation>
|
|
206
|
+
<xs:documentation> This is a row in a matrix of DNA data containing granular observations. </xs:documentation>
|
|
207
|
+
</xs:annotation>
|
|
208
|
+
<xs:complexContent>
|
|
209
|
+
<xs:restriction base="AbstractObsRow">
|
|
210
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
211
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
212
|
+
<xs:element name="cell" minOccurs="1" maxOccurs="unbounded" type="DNAObs"/>
|
|
213
|
+
</xs:sequence>
|
|
214
|
+
</xs:restriction>
|
|
215
|
+
</xs:complexContent>
|
|
216
|
+
</xs:complexType>
|
|
217
|
+
|
|
218
|
+
<xs:complexType name="DNASeqMatrix" abstract="false">
|
|
219
|
+
<xs:annotation>
|
|
220
|
+
<xs:documentation>
|
|
221
|
+
A matrix of rows with seq strings of type DNA.
|
|
222
|
+
</xs:documentation>
|
|
223
|
+
</xs:annotation>
|
|
224
|
+
<xs:complexContent>
|
|
225
|
+
<xs:restriction base="AbstractSeqMatrix">
|
|
226
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
227
|
+
<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="DNAMatrixSeqRow"/>
|
|
228
|
+
</xs:sequence>
|
|
229
|
+
</xs:restriction>
|
|
230
|
+
</xs:complexContent>
|
|
231
|
+
</xs:complexType>
|
|
232
|
+
|
|
233
|
+
<xs:complexType name="DNAObsMatrix" abstract="false">
|
|
234
|
+
<xs:annotation>
|
|
235
|
+
<xs:documentation>
|
|
236
|
+
A matrix of rows with single character observations.
|
|
237
|
+
</xs:documentation>
|
|
238
|
+
</xs:annotation>
|
|
239
|
+
<xs:complexContent>
|
|
240
|
+
<xs:restriction base="AbstractObsMatrix">
|
|
241
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
242
|
+
<xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="DNAMatrixObsRow"/>
|
|
243
|
+
</xs:sequence>
|
|
244
|
+
</xs:restriction>
|
|
245
|
+
</xs:complexContent>
|
|
246
|
+
</xs:complexType>
|
|
247
|
+
|
|
248
|
+
<xs:complexType name="DnaSeqs" abstract="false">
|
|
249
|
+
<xs:annotation>
|
|
250
|
+
<xs:documentation>
|
|
251
|
+
A DNA characters block consisting of sequences preceded by metadata.
|
|
252
|
+
</xs:documentation>
|
|
253
|
+
</xs:annotation>
|
|
254
|
+
<xs:complexContent>
|
|
255
|
+
<xs:restriction base="AbstractSeqs">
|
|
256
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
257
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
258
|
+
<xs:element name="format" minOccurs="1" maxOccurs="1" type="DNAFormat"/>
|
|
259
|
+
<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="DNASeqMatrix"/>
|
|
260
|
+
</xs:sequence>
|
|
261
|
+
</xs:restriction>
|
|
262
|
+
</xs:complexContent>
|
|
263
|
+
</xs:complexType>
|
|
264
|
+
|
|
265
|
+
<xs:complexType name="DnaCells" abstract="false">
|
|
266
|
+
<xs:annotation>
|
|
267
|
+
<xs:documentation>
|
|
268
|
+
A DNA characters block consisting of granular cells preceded by metadata.
|
|
269
|
+
</xs:documentation>
|
|
270
|
+
</xs:annotation>
|
|
271
|
+
<xs:complexContent>
|
|
272
|
+
<xs:restriction base="AbstractCells">
|
|
273
|
+
<xs:sequence minOccurs="1" maxOccurs="1">
|
|
274
|
+
<xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/>
|
|
275
|
+
<xs:element name="format" minOccurs="1" maxOccurs="1" type="DNAFormat"/>
|
|
276
|
+
<xs:element name="matrix" minOccurs="1" maxOccurs="1" type="DNAObsMatrix"/>
|
|
277
|
+
</xs:sequence>
|
|
278
|
+
</xs:restriction>
|
|
279
|
+
</xs:complexContent>
|
|
280
|
+
</xs:complexType>
|
|
281
|
+
|
|
282
|
+
</xs:schema>
|