R/AllClasses.R

In rangeMapper: A platform for the study of macroecology of life history traits

	
# Class definitions
	# rangeMapStart
	# rangeMap
	# rangeFiles
	# gridSize
	# rangeMapProcess
	# rangeMapSave
	# bioSaveFile
	# bioSaveDataFrame
	# MapImport
	# rangeMapFetch
	# SpatialPixelsRangeMap
	# rangeMapRemove


setClass("rangeMapStart", 
		representation(
			dir = "character", 
			file = "character", 
			skeleton = "list",
			overwrite = "logical"
			), 
		prototype(
			file = paste("rangeMapperProj",format(Sys.time(), "%Y-%m-%d_%H-%M-%S.sqlite"), sep = "_"),
			skeleton = 	list(
		create = 
		c(	"CREATE TABLE version (ver CHAR)", 
			"CREATE TABLE proj4string (p4s CHAR)", 
			"CREATE TABLE gridSize(gridSize FLOAT)", 
			"CREATE TABLE bbox(xmin FLOAT,xmax FLOAT,ymin FLOAT,ymax FLOAT)", 
			"CREATE TABLE canvas (x FLOAT,y FLOAT,id INT)", 
			"CREATE TABLE ranges (id INT,bioid CHAR)",
			"CREATE TABLE metadata_ranges (bioid CHAR)"

		),
		index = 
		c(  "CREATE INDEX IF NOT EXISTS   id_canvas ON canvas (id)", 
			"CREATE INDEX IF NOT EXISTS   id_ranges ON ranges (id)", 
			"CREATE INDEX IF NOT EXISTS   bioid_ranges ON ranges (bioid)",
			"CREATE INDEX IF NOT EXISTS   bioid_metadata_ranges ON metadata_ranges (bioid)")
		), 
		overwrite = FALSE
		), 
		
		validity = function(object) {
		if(!file.exists(object@dir)) stop("'dir' should be set and point to a valid location.")
		}
	)
	

setClass("rangeMap", 
		representation(
			CON = "SQLiteConnection", 
			VERSION = "character",   			
			ID = "character",         			
			BIOID = "character",         		
			PROJ4STRING = "character",   			
			GRIDSIZE = "character",   			
			BBOX = "character",   			
			METADATA_RANGES = "character",   	
			CANVAS = "character",   			
			RANGES = "character", 				
			BIO = "character", 					
			MAP = "character" 					
			),
		prototype(
			VERSION = "version",         
			ID = "id",         
			BIOID = "bioid",         
			PROJ4STRING = "proj4string",   			
			GRIDSIZE = "gridsize",   			
			BBOX = "bbox", 
			METADATA_RANGES = "metadata_ranges",  
			CANVAS = "canvas",   
			RANGES = "ranges", 
			BIO = "BIO_", 
			MAP = "MAP_"
			), 
		
		validity = function(object) {
		
		if ( ! init_extensions(object@CON)) warning("Aggregate functions provided by RSQLite.extfuns packages not available!")
		
		if ( ! all( .dbtable.exists(object@CON, object@PROJ4STRING),
				  .dbtable.exists(object@CON, object@METADATA_RANGES),
				  .dbtable.exists(object@CON, object@GRIDSIZE),
				  .dbtable.exists(object@CON, object@BBOX),
				  .dbtable.exists(object@CON, object@CANVAS),
				  .dbtable.exists(object@CON, object@RANGES) ) ) stop ("Corrupt rangeMapper project!")
		
		# projVer = try(sqliteQuickSQL(object@CON, paste("SELECT * FROM", object@VERSION) )$ver, silent = TRUE)
		# if(inherits(projVer, "try-error")) projVer = "0.0-0"
		
		# curVer  = packageDescription("rangeMapper")$Version 		
		# if(compareVersion(curVer,  projVer) == 1)
			# message("This project was created with rangeMapper ", projVer)
		
		}	
	)

setClass("rangeFiles", 
		representation(
		dir = "character",
		ogr = "logical", 
		polygons.only = "logical") , 
		prototype(
		dir = "",
		ogr = TRUE, 
		polygons.only = TRUE), 
		validity = function(object) {
		if(!file.exists(object@dir)) stop("'dir' should be set and point to a valid location.")
		
		}
	)
	
	
setClass("gridSize", 
		representation(
		gridSize = "numeric"	
			), 
		
		contains = "rangeMap", 
		
		validity = function(object)	{
			if(!.is.empty(object@CON, object@GRIDSIZE)) stop("The grid size was allready set!")
			if(.is.empty(object@CON, object@BBOX)) stop("There is no bouding box!")

		},
	)
	
# class only used for validity checks
setClass("rangeMapProcess", 
		contains = "rangeMap", 
		
		validity = function(object)	{
					if(!.is.empty(object@CON, object@RANGES)) stop(paste(dQuote(object@RANGES), "table is not empty!"))
		}
)	

setClass("rangeMapSave", 
		representation(
			biotab    = "character", 
			biotrait  = "character",
			tableName = "character",
			subset    = "list"), 
			
		contains = "rangeMap", 
		
		validity = function(object)	{
		# the new table should not exist
			if(.dbtable.exists(object@CON, paste(object@MAP, object@tableName, sep = "") ) ) 
				stop(paste(sQuote(object@tableName), " already exists."))
			
			if(.dbtable.exists(object@CON, paste(object@BIO, object@tableName, sep = "") ) ) 
				stop( paste(sQuote(object@tableName), " already exists."))	
			
		}
	)

	
	
setClass("bioSaveFile", representation(loc = "character", sep = "character"), 
							contains = "rangeMapSave", 
							prototype( sep = ";", 
									  tableName = "unknown"
							
							), 
							validity = function(object) {
							if(!file.exists(object@loc)) stop(paste(sQuote(object@loc), "is not a valid file"))


							}
		)	
	
	
setClass("bioSaveDataFrame", representation(loc = "data.frame"), 
							contains = "rangeMapSave", 
							validity = function(object) {

							}
		)	
	
	
	
	
setClass("MapImport", representation(path = "character"), 
							contains = "rangeMapSave", 
 
							validity = function(object) {
							
							if(!file.exists(object@path)) stop(paste(sQuote(object@path), "is not a valid path.") ) 	
							if(!require("raster")) stop("package raster is not available")

							} 

		)

setClass("rangeMapFetch", representation(
					tableName    = "character"), 
				    contains = "rangeMap", 
	
					validity = function(object)	{
						mapNam =paste(object@MAP, object@tableName, sep = "") 
						
						invalidNam = sapply(mapNam, FUN = function(x) !.dbtable.exists(object@CON, x) )
						
						if( any(invalidNam) )
						  stop(paste(sQuote(names(invalidNam[invalidNam] )), "is not a valid MAP!\n"))
						
						# check if empty map
						mapvar = sapply(mapNam, function(x)
									setdiff(sqliteQuickSQL(object@CON, paste("pragma table_info(", x, ")"))$name, object@ID ) )
						
						sql = paste("select count (", mapvar, ") FROM", mapNam)
						isempty = sapply(sql, function(x) sqliteQuickSQL(object@CON,  x)[, 1] ) < 1
						
						if(any(isempty))
						 stop(paste(sQuote(mapNam[isempty]), "is an empty MAP!\n"))
			}
	)

setClass("SpatialPixelsRangeMap", representation(
					mapvar    = "character"), 
				    contains  = "SpatialPixelsDataFrame",
	
					validity = function(object)	{
					return(TRUE)
					}
	)

setClass("rangeMapRemove", representation(
						tableName = "character", 
						tablePrefix = "character"						 
						), 
						 contains = "rangeMap",
						 
						validity = function(object)	{
									if(object@PROJ4STRING%in%object@tableName |
									   object@BBOX%in%object@tableName|
									   object@GRIDSIZE%in%object@tableName|
									   object@CANVAS%in%object@tableName|
									   object@CANVAS%in%object@tableName)
						stop( paste(object@PROJ4STRING,",", object@BBOX, ",",object@GRIDSIZE,",",
										object@CANVAS, "or", 
										object@RANGES, "table(s) cannot be removed!"))

			}
	)