@base <http://www.w3.org/2005/04/swls/gsk3b/pathwayView>

@prefix	dc:			<http://purl.org/dc/elements/1.1/>
@prefix	hs:			<http://haystack.lcs.mit.edu/schemata/haystack#>
@prefix	ozone:		<http://haystack.lcs.mit.edu/schemata/ozone#>
@prefix	task:		<http://haystack.lcs.mit.edu/schemata/task#>
@prefix	applet:		<http://haystack.lcs.mit.edu/schemata/ozoneapplet#>
@prefix	slide:		<http://haystack.lcs.mit.edu/schemata/ozoneslide#> 
@prefix	vc:			<http://haystack.lcs.mit.edu/ui/viewContainer#> 
@prefix	layout:		<http://haystack.lcs.mit.edu/schemata/layout#>
@prefix	summary:	<http://haystack.lcs.mit.edu/ui/summaryView#> 
@prefix	data:		<http://haystack.lcs.mit.edu/schemata/dataProvider#>
@prefix op:			<http://haystack.lcs.mit.edu/schemata/operation#>
@prefix	modeless:	<http://haystack.lcs.mit.edu/schemata/ozonemodeless#>
@prefix	create:		<http://haystack.lcs.mit.edu/programs/create#> 
@prefix	marble:		<http://haystack.lcs.mit.edu/ui/marble#>
@prefix	cv:			<http://haystack.lcs.mit.edu/ui/collectionView#> 
@prefix	metadata:	<http://haystack.lcs.mit.edu/ui/metadataEditor#> 
@prefix help:		<http://haystack.lcs.mit.edu/programs/help#>
@prefix	lensui:		<http://haystack.lcs.mit.edu/ui/lens#> 
@prefix graph:		<http://haystack.lcs.mit.edu/programs/graphExplorer#>
@prefix	vowl:		<http://haystack.lcs.mit.edu/schemata/vowl#> 
@prefix biopax:		<http://www.biopax.org/release/biopax-level1.owl#>
@prefix opdata:		<http://haystack.lcs.mit.edu/data/operations#>
@prefix dnd:		<http://haystack.lcs.mit.edu/schemata/dnd#>
@prefix gsk:		<http://www.w3.org/2005/04/swls/gsk3b/gsk#>
@prefix ls:			<http://www.w3.org/2005/04/swls/ls-ont-1.0#>
@prefix topicview:	<http://www.w3.org/2005/04/swls/gsk3b/topicView#>
@prefix :			<http://www.w3.org/2005/04/swls/gsk3b/pathwayView#>

add { biopax:pathway
	hs:possibleClassView				cv:ListView ;
	hs:possibleClassView				cv:ReportView ;
	hs:possibleClassView				graph:CollectionGraphExplorerView ;
	cv:listDataSourceSpecification ${
		rdf:type			data:SortingListSource ;
		data:sortDataSource ${ rdf:type summary:TitleSource } ;
		ozone:dataSource	:query
	} ;
	cv:naturalDataSourceSpecification	:query ;
	cv:setDataSourceSpecification		:query ;
	vowl:titleSourcePredicate			biopax:NAME
}

add { biopax:protein
	hs:classView				:IconSummaryView2 ;
#	ozone:icon		<http://haystack.lcs.mit.edu/data/ozone/icons/types/dna.gif> ;
	ozone:icon		<http://haystack.lcs.mit.edu/data/ozone/icons/types/protein.gif> ;
	vowl:titleSourcePredicate	biopax:NAME
}

add { :query
	rdf:type				data:RDFQuerySetSource ;
	data:existentials		@( ?x ?y ) ;
	data:targetExistential	?x ;
	data:statement ${
		data:subjectDataSource	data:underlyingSource ;
		data:predicate		biopax:PATHWAY-COMPONENTS ;
		data:object			?y
	} ;
	data:statement ${
		data:subject	?y ;
		data:predicate	biopax:PARTICIPANTS ;
		data:object		?x
	}
}

add { :predicateSet
	rdf:type	graph:CollectionPredicateSet ;
	rdf:type	graph:PredicateSet ;
	dc:title	"BioPAX pathway arrows" ;
	hs:member	biopax:NEXT-STEP ;
	hs:member	:pointingTo ;
	hs:member ${
		rdf:type				data:RDFQueryAspect ;
		data:sourceExistential	?s ;
		data:targetExistential	?t ;
		rdfs:label				"" ;
		data:existentials		@( ?s ?t ?type ) ;
		data:statement ${
			data:subject	?type ;
			data:predicate	biopax:LEFT ;
			data:object		?s
		} ;
		data:statement ${
			data:subject	?type ;
			data:predicate	biopax:RIGHT ;
			data:object		?t
		}
	}
}

add { graph:basicPredicateSetsDataSource hs:member :predicateSet }

add {
	:iconSummaryViewPart2
		rdf:type				ozone:Part ;
		rdf:type				ozone:ViewPart ;
		rdf:type				ozone:IconViewPart ;
		ozone:viewDomain		:IconSummaryView2 ;
		ozone:template ${
			rdf:type		ozone:MultiplexPartContainer ;
			ozone:children @(
				:normalIcon
				:redIcon
			) ;
			ozone:dataSource ${
				rdf:type			data:MappingSource ;
				data:domain			@( "true" ) ;
				data:range			@( :redIcon ) ;
				data:default		:normalIcon ;
				ozone:dataSource ${
					rdf:type			data:LiteralPropertySource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		:indicated
				}
			}
		} ;
		hs:javaImplementation	${ rdf:type hs:JavaClass ; hs:className	"edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" } 
}

add { :normalIcon
	rdf:type			slide:Block ;
	slide:borderWidth	"1" ;
	slide:borderColor	"gray" ;
	slide:bgcolor		"white" ;
	slide:color			"darkestGray" ;
	slide:margin		"2" ;
	slide:width			"140" ;
	slide:height		"33" ;
	slide:valign		"center" ;
	slide:child			:iconBody
}

add { :redIcon
	rdf:type			slide:Block ;
	slide:borderWidth	"1" ;
	slide:borderColor	"gray" ;
	slide:bgcolor		"red" ;
	slide:color			"darkestGray" ;
	slide:margin		"2" ;
	slide:width			"140" ;
	slide:height		"33" ;
	slide:child			:iconBody
}

add { :iconBody
	rdf:type			slide:ColumnSet;
	slide:pack			"right" ;
	slide:children		@(
		${	rdf:type			slide:ColumnSet;
			slide:children @(
				${	rdf:type			slide:Block ;
					slide:background	<http://www.w3.org/2005/04/swls/gsk3b/dna.png> ;
					slide:width			"20" ;
					slide:height		"28" ;
					slide:child			slide:space
				}
				${	rdf:type		slide:Block ;
					slide:marginX	"6" ;
					slide:marginY	"1" ;
					slide:valign	"center" ;
					slide:child ${
						rdf:type		slide:Paragraph ;
						slide:fontSize	"8" ;
						slide:children @(
							${	rdf:type			ozone:ViewContainer ;
								ozone:dataSource	data:underlyingSource ;
								ozone:viewPartClass	ozone:InlineViewPart
							}
						)
					}
				}
			)
		}
		${	rdf:type		slide:Block ;
			slide:width		"10" ;
			slide:valign	"top" ;
			slide:child		:colorBarArea
		}
	)
}

add { :colorBarArea
	rdf:type		ozone:MultiplexPartContainer ;
	ozone:children @(
		slide:space
		:colorBarDisplay
	) ;
	ozone:dataSource ${
		rdf:type			data:MappingSource ;
		data:domain			@( "true" ) ;
		data:range			@( :colorBarDisplay ) ;
		data:default		slide:space ;
		ozone:dataSource ${
			rdf:type			data:LiteralPropertySource ;
			ozone:dataSource	data:secondUnderlyingSource ;
			data:predicate		:showSNPBars
		}
	}
}

add { :colorBarDisplay
	rdf:type			layout:Layout ;
	ozone:dataSource ${
		rdf:type				data:RDFQuerySetSource ;
		data:existentials		@( ?uniprot ?snpset ?snp ) ;
		data:targetExistential	?snp ;
		data:statement ${
			data:subjectDataSource	data:underlyingSource ;
			data:predicate			ls:xref ;
			data:object				?uniprot
		} ;
		data:statement ${
			data:subject			?snpset ;
			data:predicate			ls:studying ;
			data:object				?uniprot
		} ;
		data:statement ${
			data:subject			?snpset ;
			data:predicate			ls:indivSNP ;
			data:object				?snp
		}
	} ;
	layout:layoutConstraint ${ 
		rdf:type				layout:RowStackerConstraint ;
		ozone:viewPartClass		:ColorBarViewPart ;
		layout:emptyPartData	:blank ;
		layout:morePartData		:blank ;
		layout:sortBy ${
			rdf:type			data:SortingListSource ;
			data:sortDataSource ${ rdf:type summary:TitleSource }
		}
	}
}

add { :blank
	rdf:type		slide:Block ;
	slide:width		"0" ;
	slide:height	"0" ;
	slide:child		slide:space
}

add { :snpColorBarViewPart
	rdf:type				ozone:Part ;
	rdf:type				ozone:ViewPart ;
	rdf:type				:ColorBarViewPart ;
	ozone:viewDomain		:SNPColorBarView ;
	ozone:template ${
		rdf:type				slide:Block ;
		slide:borderTopWidth	"2" ;
		slide:borderTopColor	"#8800ff" ;
		slide:height			"4" ;
		slide:width				"10" ;
		ozone:tooltip			"Click for SNP details" ;
		slide:child ${
			rdf:type		slide:Text ;
			slide:text		"" ;
			ozone:onClick	:showSNPPopup
		}
	} ;
	hs:javaImplementation	${ rdf:type hs:JavaClass ; hs:className	"edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" } 
}

method :showSNPPopup
	= modelessChild ${
		rdf:type			slide:Block ;
		slide:alignX		"left" ;
		slide:fontBold		"false" ;
		slide:fontFamily	"Tahoma, Arial, Times New Roman" ;
		slide:fontSize		"8" ;
		slide:bgcolor		"white" ;
		slide:color			"#3B5377" ;
		slide:borderWidth	"2" ;
		slide:borderColor	"#8800ff" ;
		slide:margin		"5" ;
		slide:width			"150" ;
		slide:child			${
			rdf:type				ozone:ViewContainer ;
			ozone:viewPartClass		:PopupViewPart ;
			ozone:initialResource	(data:getUnderlying)
		}
	}

	= chooser ${
		rdf:type		modeless:Modeless ;
		modeless:child	modelessChild
	}

	importjava "org.eclipse.swt.widgets" Display
	= point ((Display.getDefault).getCursorLocation)

	(__context__.getProperty modeless:modelessCreator).createModelessPart chooser point __context__

add { ls:RefSNP
	hs:classView	:SNPColorBarView ;
	hs:classView	:SNPPopupView
}

add { :snpPopupViewPart
	rdf:type				ozone:Part ;
	rdf:type				ozone:ViewPart ;
	rdf:type				:PopupViewPart ;
	ozone:viewDomain		:SNPPopupView ;
	ozone:template ${
		rdf:type	slide:Paragraph ;
		slide:children @(
			${	rdf:type		slide:Text ;
				slide:fontBold	"true" ;
				slide:text		"SNP details"
			}
			slide:line
			slide:newLine
			${	rdf:type		slide:Text ;
				slide:fontBold	"true" ;
				ozone:dataSource ${
					rdf:type			data:LiteralPropertySource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		ls:changedBase
				}
			}
			slide:space
			${	rdf:type	slide:Text ;
				slide:text	"->"
			}
			slide:space
			${	rdf:type		slide:Text ;
				slide:fontBold	"true" ;
				ozone:dataSource ${
					rdf:type			data:LiteralPropertySource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		ls:changedBaseTo
				}
			}
			slide:space
			${	rdf:type	slide:Text ;
				slide:text	"on chromosome"
			}
			slide:space
			${	rdf:type		slide:Text ;
				slide:fontBold	"true" ;
				ozone:dataSource ${
					rdf:type			data:LiteralPropertySource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		ls:location
				}
			}
			slide:space
			${	rdf:type	slide:Text ;
				slide:text	"at"
			}
			slide:space
			${	rdf:type		slide:Text ;
				slide:fontBold	"true" ;
				ozone:dataSource ${
					rdf:type			data:LiteralPropertySource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		ls:locationOnChromosome
				}
			}
			slide:space
			${	rdf:type		slide:Text ;
				slide:text		"[more]" ;
				ozone:onClick	ozone:underlyingHyperlink
			}
		)
	} ;
	hs:javaImplementation	${ rdf:type hs:JavaClass ; hs:className	"edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" } 
}

################################################################################
# Pathway explorer view

add { :predicateSet
	rdf:type	graph:CollectionPredicateSet ;
	rdf:type	graph:PredicateSet ;
	dc:title	"BioPAX pathway arrows" ;
	hs:member	biopax:NEXT-STEP ;
	hs:member ${
		rdf:type				data:RDFQueryAspect ;
		data:sourceExistential	?s ;
		data:targetExistential	?t ;
		rdfs:label				"" ;
		data:existentials		@( ?s ?t ?type ) ;
		data:statement ${
			data:subject	?type ;
			data:predicate	biopax:LEFT ;
			data:object		?s
		} ;
		data:statement ${
			data:subject	?type ;
			data:predicate	biopax:RIGHT ;
			data:object		?t
		}
	}
}

add { <http://www.biopax.org/release/biopax-level1.owl#pathway> hs:classView :CollectionGraphExplorerView }

add { :collectionGraphExplorerViewPart
	rdf:type				ozone:SWTPart ;
	rdf:type				ozone:Part ;
	rdf:type				ozone:ViewPart ;
	rdf:type				ozone:InteractiveViewPart ;
	ozone:viewDomain		:CollectionGraphExplorerView ;
	vc:toolbarCaption		"Pathway view" ;
	ozone:template ${
		rdf:type			ozone:DataProviderHost ;
		ozone:hostedDataProvider ${
			rdf:type			data:ResourcePropertySource ;
			ozone:dataSource	data:viewInstanceSource ;
			data:predicate		:selectedPredicateSet
		} ;
		ozone:propertyName	:selectedPredicateSetDataSource ;
		ozone:propertyName	:target ;
		slide:child ${
			rdf:type			graph:GraphExplorerContainerPart ;
			marble:graphExplorerDataSource ${
				rdf:type				graph:CollectionGraphExplorerSource ;
				marble:extraDataSource ${
					rdf:type			data:MergeSetSource ;
					ozone:dataSource	cv:setDataSource ;
					ozone:dataSource ${
						rdf:type			data:PredicateSetSource ;
						ozone:dataSource	data:underlyingSource ;
						data:predicate		:extra
					}
				} ; 
				marble:relationships ${
					rdf:type		data:PredicateSetSource ;
					data:subject	:predicateSet ;
					data:predicate	hs:member
				}
#[				 ${
					rdf:type	data:SetProviderConstructorSource ;
					ozone:dataSource ${
						rdf:type				data:RDFQuerySetSource ;
						data:existentials		@( ?x ?y ) ;
						data:extract			"true" ;
						data:targetExistential	?x ;
						data:statement ${
							data:subjectDataSource	:selectedPredicateSetDataSource ;
							data:predicate		rdf:type ;
							data:object			?y
						} ;
						data:statement ${
							data:subject		?y ;
							data:predicate		:dataSourceSpecification ;
							data:object			?x
						}
					}
				}]#
			} ;
			slide:child ${
				rdf:type			layout:Layout ;
				ozone:dataSource	${
					rdf:type		data:DAMLListSource ;
					data:damlList	@( :graphExplorerGraphPane :bottomPane )
				} ;
				layout:layoutConstraint ${
					rdf:type			layout:RowSplitterConstraint ;
					layout:pack			"last" ;
					layout:constraint	${ layout:element :bottomPane ; layout:dimension "100" }
				}
			}
		}
	} ;
	hs:javaImplementation	${ rdf:type hs:JavaClass ; hs:className "edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" }
}

add { :bottomPane
	rdf:type			slide:Block ;
	slide:borderWidth	"1" ;
	slide:border		"1" ;
	slide:margin		"10" ;
	slide:fontSize		"11" ;
	slide:child ${
		rdf:type	slide:Paragraph ;
		slide:children @(
			${	rdf:type				ozone:ViewContainer ;
				ozone:viewPartClass		ozone:InlineViewPart ;
				ozone:initialResource	:dropTarget
			}
			slide:newLine
			slide:space
			slide:newLine
			${	rdf:type		slide:Text ;
				slide:text		"Click here to find and add SNP data to the display." ;
				ozone:onClick	:addSNP
			}
			slide:newLine
			slide:space
			slide:newLine
			${	rdf:type		slide:Text ;
				slide:text		"Click here to reset the pathway display. (Afterwards, click Refresh on toolbar to complete reset.)" ;
				ozone:onClick	:reset
			}
		)
	}
}

method :addSNP
	= x (data:getUnderlying)
	replace x :showSNPBars ?x "true"

method :reset
	= x (data:getUnderlying)
	remove x :extra ?x
	remove ?x :indicated "true"
	remove x :showSNPBars ?x

add { :dropTarget
	dc:title		"Drop targets here to merge them into the pathway display." ;
	rdf:type		:DropTarget
}

add { :Dot
	hs:classView	:DotIconView
}

add { :pointingTo
	rdfs:label		""
}

add { :dotIconViewPart
	rdf:type				ozone:SWTPart ;
	rdf:type				ozone:Part ;
	rdf:type				ozone:IconViewPart ;
	rdf:type				ozone:ViewPart ;
	ozone:viewDomain		:DotIconView ;
	hs:javaImplementation	${ rdf:type hs:JavaClass ; hs:className	"edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" } ;
	ozone:template ${
		rdf:type			slide:Block ;
		slide:width			"33" ;
		slide:bgcolor		"#e0dfe3" ;
		slide:borderWidth	"1" ;
		slide:borderColor	"gray" ;
		slide:margin		"1" ;
		slide:child ${
			rdf:type			ozone:ViewContainer ;
			ozone:dataSource ${
				rdf:type			data:ResourcePropertySource ;
				ozone:dataSource	data:underlyingSource ;
				data:predicate		:original
			} ;
			ozone:viewPartClass	:DotViewPart
		}
	}
}

add { :dragParam
	rdf:type			op:Parameter ;
	rdf:type			daml:ObjectProperty ;
	rdf:type			dnd:DragParameter ;
	op:required			"true" ;
	rdfs:range			ls:Target
}

add { :dropParam
	rdf:type			op:Parameter ;
	rdf:type			daml:ObjectProperty ;
	rdf:type			dnd:DropParameter ;
	op:required			"true" ;
	rdfs:range			:DropTarget
}

method :addToDrop :dragParam = dragParam :dropParam = dropParam ;
rdf:type			dnd:DNDOperation ;
rdf:type			op:Operation
	= thingToAdd dragParam[0]
	= pathway (data:getSecondUnderlying)
	= results (query { thingToAdd ls:xref ?x ?y ls:xref ?x } @(?y))
	for x in results
		if (!= thingToAdd x[0])
			add { x[0] :indicated "true" ; :target thingToAdd }
			for y in (query { thingToAdd ls:for ?x })
				= dot ${
					rdf:type	:Dot ;
					:original	y[0] ;
					:pointingTo	x[0]
				}
				add { pathway 
					:extra	dot
				}
				
				for z in (query { ?target ls:for y[0] ?target ls:xref ?uniprot ?other ls:xref ?uniprot } @(?other))
					add { dot :pointingTo z[0] }
			return

add { :selectedPredicateSetDataSource
	rdf:type		data:ContextHostedResourceSource ;
	data:property	:selectedPredicateSetDataSource
}

add { :extraNodesDataSource
	rdf:type			data:PredicateSetSource ;
	ozone:dataSource	data:viewInstanceSource ;
	data:predicate		:extraNode
}

add { :graphExplorerGraphPane
	rdf:type	marble:Diagram ;
	ozone:dataSource ${
		rdf:type		marble:ContextHostedSetSource ;
		data:property	marble:graphExplorerDataProvider
	} ;
	marble:arcDataSource ${
		rdf:type	graph:GraphExplorerArcSetSource
	} ;
	layout:focus ${
		rdf:type		data:ContextHostedResourceSource ;
		data:property	layout:focus
	}
}

add { :basicPredicateSetsDataSource
	rdf:type		data:PredicateSetSource ;
	data:subject	:basicPredicateSetsDataSource ;
	data:predicate	hs:member ;
	hs:member		:schemaPredicateSet ;
	hs:member		:ontologyPredicateSet
}