/** null * @return CMLAttribute */ public CMLAttribute getDictRefAttribute() { return (CMLAttribute) getAttribute("dictRef"); } /** null
/** A set of ids representing the base of a link. * For a partial mapping where a number of 'to' elements are known to link to a number of 'from' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'to' elements and n 'from' elements but that the precise links are unknown. The semantics of the reference are the same as for 'to' and all the elements must be of the same type (which can be specified with 'toType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'fromSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. * * @return CMLAttribute */ public CMLAttribute getToSetAttribute() { return (CMLAttribute) getAttribute("toSet"); } /** A set of ids representing the base of a link.
/** Role of the object. * How the object functions or its position in the architecture. No controlled vocabulary. * @return CMLAttribute */ public CMLAttribute getRoleAttribute() { return (CMLAttribute) getAttribute("role"); } /** Role of the object.
/** null * @return CMLAttribute */ public CMLAttribute getIdAttribute() { return (CMLAttribute) getAttribute("id"); } /** null
/** The target of one or more links. * No description * @return CMLAttribute */ public CMLAttribute getToAttribute() { return (CMLAttribute) getAttribute("to"); } /** The target of one or more links.
/** The type of the base of a link. * The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type. * This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types. * * @return CMLAttribute */ public CMLAttribute getFromTypeAttribute() { return (CMLAttribute) getAttribute("fromType"); } /** The type of the base of a link.
/** The base of one or more links. * On link elements the value is the single id of an element within the document or context specified in map@fromRef attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'to' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'fromSet'. * @return CMLAttribute */ public CMLAttribute getFromAttribute() { return (CMLAttribute) getAttribute("from"); } /** The base of one or more links.
/** null * @return CMLAttribute */ public CMLAttribute getRefAttribute() { return (CMLAttribute) getAttribute("ref"); } /** null
/** A set of ids representing the base of a link. * For a partial mapping where a number of 'from' elements are known to link to a number of 'to' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'from' elements and n 'to' elements but that the precise links are unknown. The semantics of the reference are the same as for 'from' and all the elements must be of the same type (which can be specified with 'fromType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'toSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. * * @return CMLAttribute */ public CMLAttribute getFromSetAttribute() { return (CMLAttribute) getAttribute("fromSet"); } /** A set of ids representing the base of a link.
/** The context for the 'from' links in a map. * A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id. * This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context. * * @return CMLAttribute */ public CMLAttribute getFromContextAttribute() { return (CMLAttribute) getAttribute("fromContext"); } /** The context for the 'from' links in a map.
/** A title on an element. * No controlled value. * @return CMLAttribute */ public CMLAttribute getTitleAttribute() { return (CMLAttribute) getAttribute("title"); } /** A title on an element.
/** The type of the base of a link. * * The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type. * This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types. * * @return CMLAttribute */ public CMLAttribute getToTypeAttribute() { return (CMLAttribute) getAttribute("toType"); } /** The type of the base of a link.
/** The context for the 'from' links in a map. * A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id. * This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context. * * @return CMLAttribute */ public CMLAttribute getToContextAttribute() { return (CMLAttribute) getAttribute("toContext"); } /** The context for the 'from' links in a map.
/** address of a resource. * Links to another element in the same or other file. For dictionary/@dictRef requires the prefix and the physical URI * address to be contained within the same file. We can anticipate that * better mechanisms will arise - perhaps through XMLCatalogs. * At least it works at present. * @return CMLAttribute */ public CMLAttribute getHrefAttribute() { return (CMLAttribute) getAttribute("href"); } /** address of a resource.
/** The type of the link. * No description * @return CMLAttribute */ public CMLAttribute getLinkTypeAttribute() { return (CMLAttribute) getAttribute("linkType"); } /** The type of the link.
/** A reference to a convention. * There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements, * so that a convention for molecule would by default extend to its bond and atom children. This can be overwritten * if necessary by an explicit convention. * It may be useful to create conventions with namespaces (e.g. iupac:name). * Use of convention will normally require non-STMML semantics, and should be used with * caution. We would expect that conventions prefixed with "ISO" would be useful, * such as ISO8601 for dateTimes. * There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed. * @return CMLAttribute */ public CMLAttribute getConventionAttribute() { return (CMLAttribute) getAttribute("convention"); } /** A reference to a convention.