<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+ <xs:complexType name="rangeType">
+ <xs:annotation>
+ <xs:documentation>Specify positions and/or regions on the principle dimension of some associated vamsas objects
+ TODO: this is abstract. should provide context to scope the range of ids for each use</xs:documentation>
+ <xs:documentation>Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings
+ </xs:documentation></xs:annotation>
+ <!-- Do we really need this - a position could be just a seg with start=end and inclusive=true -->
+ <xs:choice>
+ <xs:element name="pos" maxOccurs="unbounded" minOccurs="1">
+ <xs:annotation><xs:documentation>a position within the associated object's coordinate system</xs:documentation></xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="i" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seg" maxOccurs="unbounded" minOccurs="1">
+ <xs:annotation><xs:documentation>a region from start to end, with flag for inclusivity of terminii</xs:documentation></xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ <xs:attribute name="inclusive" type="xs:boolean" use="required"><xs:annotation><xs:documentation>when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2</xs:documentation></xs:annotation></xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:complexType>
<xs:element name="VAMSAS">
+ <xs:annotation><xs:documentation>contains unassociated trees and a number of analysis sets</xs:documentation></xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
+ <xs:annotation>
+ <xs:documentation> Properties. Generally, these are mutable so an application should check them each time. This may change depending on the context of the property</xs:documentation>
+ </xs:annotation>
<xs:element name="Tree">
<xs:complexType>
+ <xs:annotation><xs:documentation>Contains a named collection of trees TODO: define way of referencing leaves of global tree for any sequence/alignment object</xs:documentation></xs:annotation>
<xs:sequence>
<xs:element name="title" type="xs:string" minOccurs="0"/>
<xs:element name="newick" maxOccurs="unbounded">
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="title" type="xs:string" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
+ <xs:element ref="vamsas:property" maxOccurs="unbounded" minOccurs="0"/>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="property">
+ <xs:complexType><xs:simpleContent>
+ <xs:annotation><xs:documentation>Named and typed property string</xs:documentation></xs:annotation>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
+ </xs:extension>
+ </xs:simpleContent></xs:complexType>
+ </xs:element>
+ <xs:complexType name="rangeAnnotation">
+ <xs:annotation>
+ <xs:documentation>provenance contains source of annotation</xs:documentation>
+ <xs:documentation>polymorphism for having collection of single points,
+ or ordered set of regions with polarity (start.lt.end or end.lt.start)</xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeType">
+ <xs:sequence>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="status" type="xs:string" minOccurs="0"/>
+ <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:Provenance" maxOccurs="1" minOccurs="1"/>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation>
+ <xs:documentation>Note:These are mutable so an application should check them each time.</xs:documentation>
+ </xs:annotation></xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional">
+ <xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="group" type="xs:string" use="optional">
+ <xs:annotation><xs:documentation>Annotation with the same non-empty group name are grouped together</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="type" type="xs:string" use="required"/>
+ <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
+ <xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:element name="param"><xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Specifies a named and typed value used to perform some data transformation.
+ </xs:documentation>
+ <xs:documentation>
+ LATER: experiment with xml validation of property set prototypes for services</xs:documentation></xs:annotation>
+ <xs:simpleContent>
+ <xs:annotation><xs:documentation>Named and typed property string</xs:documentation></xs:annotation>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType></xs:element>
+ <xs:element name="input"><xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Selects all or part of a collection of vamsas objects as a named input to some transformation process.
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeType">
+ <xs:attribute name="name" type="xs:string" use="required"></xs:attribute>
+ <xs:attribute name="objRef" type="xs:IDREF" use="optional"><xs:annotation><xs:documentation>Reference Frame for rangeType specfication</xs:documentation></xs:annotation></xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
+
<xs:element name="Provenance">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Defines the origin and series of operations applied directly to the object that references it.
+ </xs:documentation>
+ </xs:annotation>
<xs:sequence>
<xs:element name="entry" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="User" type="xs:string"/>
- <xs:element name="Action" type="xs:string"/>
- <xs:element name="Date" type="xs:date"/>
+ <xs:element name="User" type="xs:string"><xs:annotation><xs:documentation>Who</xs:documentation></xs:annotation></xs:element>
+ <xs:element name="App" type="xs:string"><xs:annotation><xs:documentation>With which application</xs:documentation></xs:annotation></xs:element>
+ <xs:element name="Action" type="xs:string"><xs:annotation><xs:documentation>Did what</xs:documentation></xs:annotation></xs:element>
+ <xs:element name="Date" type="xs:date"><xs:annotation><xs:documentation>When</xs:documentation></xs:annotation></xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>additional information</xs:documentation></xs:annotation></xs:element>
+ <xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>parameter for the action</xs:documentation></xs:annotation></xs:element>
+ <xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>bioinformatic objects input to action</xs:documentation></xs:annotation></xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:element>
<xs:element name="DataSet">
<xs:complexType>
+ <xs:annotation><xs:documentation>A collection of sequences, alignments, trees and other things.</xs:documentation></xs:annotation>
<xs:sequence>
<xs:element name="Sequence" maxOccurs="unbounded">
<xs:complexType>
+ <xs:annotation><xs:documentation>a primary or secondary sequence record from which all other sequences may be derived</xs:documentation></xs:annotation>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
<xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
<xs:attribute name="source" type="xs:string"/>
<xs:attribute name="version" type="xs:string"/>
<xs:attribute name="accessionId" type="xs:string"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="required"/>
- <xs:attribute name="dictionary" type="xs:string"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="dictionary" type="xs:string" use="required"><xs:annotation><xs:documentation>symbol class for sequence</xs:documentation></xs:annotation></xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="status" type="xs:string" minOccurs="0"/>
- <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:Provenance" maxOccurs="1" minOccurs="1"/>
- </xs:sequence>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="end" type="xs:integer" use="required"/>
- <xs:attribute name="begin" type="xs:integer" use="required"/>
- <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:annotation><xs:documentation>Annotate over positions and regions of dataset sequences</xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeAnnotation"/>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
+ <xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
+ <xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
+ </xs:annotation><xs:complexContent>
+ <xs:extension base="vamsas:rangeAnnotation"></xs:extension>
+ </xs:complexContent></xs:complexType></xs:element>
<xs:element name="AlignmentAnnotations" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
<xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:sequence>
+ <xs:element name="AlignmentSequenceFeatures" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType><xs:annotation>
+ <xs:documentation>Annotate over positions and regions of the ungapped sequences in the alignment</xs:documentation>
+ <xs:documentation>TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference</xs:documentation>
+ </xs:annotation><xs:complexContent>
+ <xs:extension base="vamsas:rangeAnnotation"></xs:extension>
+ </xs:complexContent></xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
<xs:attribute name="refid" type="xs:IDREF" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation>
+ <xs:documentation>typical properties may be alignment score objects </xs:documentation>
+ </xs:annotation></xs:element>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
<xs:attribute name="gapChar" type="xs:string" use="required"/>
<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
<xs:complexType>
+ <xs:annotation><xs:documentation>per-site symbolic and/or quantitative annotation</xs:documentation>
+ <xs:documentation>SecondaryStructure and display character (from Jalview) have been subsumed into the glyph element</xs:documentation></xs:annotation>
<xs:sequence>
- <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="secondaryStructure" minOccurs="0">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:length value="1"/>
- </xs:restriction>
- </xs:simpleType>
+
+ <xs:element name="description" type="xs:string" minOccurs="0">
+ <xs:annotation><xs:documentation>Free text at this position</xs:documentation></xs:annotation>
+ </xs:element>
+ <xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation><xs:documentation>Discrete symbol - possibly graphically represented</xs:documentation></xs:annotation>
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="dict" type="xs:string" default="utf8" use="optional">
+ <xs:annotation><xs:documentation>specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here</xs:documentation>
+ <xs:documentation>TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified</xs:documentation></xs:annotation></xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
</xs:element>
- <xs:element name="value" type="xs:float" minOccurs="0"/>
+ <xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation><xs:documentation>Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions
+ </xs:documentation></xs:annotation></xs:element>
</xs:sequence>
- <xs:attribute name="position" type="xs:integer" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="position" type="xs:integer" use="required"><xs:annotation><xs:documentation>position with respect to the coordinate frame defined by a rangeType specification</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="after" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true means the annotation element appears between the specified position and the next</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:complexType name="SequenceType">
<xs:sequence>
<xs:element name="sequence" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>additional typed properties</xs:documentation></xs:annotation></xs:element>
</xs:sequence>
<xs:attribute name="start" type="xs:integer" use="required"/>
<xs:attribute name="end" type="xs:integer" use="required"/>
</xs:complexType>
<xs:element name="ApplicationData">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation>Data specific to a particular type and version of vamsas application</xs:documentation>
+ </xs:annotation>
<xs:complexContent>
<xs:extension base="vamsas:appData">
<xs:sequence>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:appData">
+ <xs:annotation><xs:documentation>Data available to just a particular user</xs:documentation></xs:annotation>
<xs:attribute name="fullname" type="xs:string" use="required"/>
<xs:attribute name="organization" type="xs:string" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element name="Common" maxOccurs="1" minOccurs="0">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData"> </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Instance" maxOccurs="unbounded" minOccurs="0">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:annotation>
+ <xs:documentation>Data available to just a specific instance of the application</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="urn" type="xs:string" use="required"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
</xs:sequence>
<xs:attribute name="version" type="xs:string" use="required"/>
<xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="urn" type="xs:string" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element name="Attachment">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:annotation>
+ <xs:documentation>General data container to attach a typed data object to any vamsas object</xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="compressed" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true implies data will be decompresses with Zip before presenting to application</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>Type of arbitrary data - TODO: decide format - use (extended) MIME types ?</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="objectref" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object the arbitrary data is associated with</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional"> <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
<xs:complexType name="appData">
<xs:choice>
<xs:element name="data" type="xs:base64Binary"/>
git://source.jalview.org / vamsas.git / commitdiff