### basica functions.
 
 # getMatrices
 # returns a list with the PWM matrices.
 # filter: name of PWM to obtain.
 # matrices are returned as 'matrix' object (before was 'pwm' object (MotIV package) but now I am 
 # moving to standard bioconductor classes and methods.
 getMatrices = function (filter, dbname = NULL) 
 {
   if (missing(filter)) 
     sql = "SELECT * FROM matrix"
   else {
     filter = paste("('", paste(filter, collapse = "','"), 
                    "')", sep = "")
     sql = paste("SELECT * FROM matrix WHERE pwm_id IN", filter)
   }
   tmp = .getSQLresult(sql, dbname = dbname)
   ids = unique(tmp$pwm_id)
   res = lapply(ids, function(id) {
     sel = tmp$pwm_id == id
     tmp2 = t(tmp[sel, c("A", "C", "G", "T")])
     colnames(tmp2) = 1:ncol(tmp2)
     tmp2
   })
   names(res) = ids
   res
 }
 
 
 getAnnotations = function(filter, dbname = NULL) {	
 	if(missing(filter))
 		sql = "SELECT * FROM pwm"
 	else {
 		filter = paste("('", paste(filter, collapse = "','"), "')", sep = "")
 		sql = paste("SELECT * FROM pwm WHERE pwm_id IN", filter)
 	}
 
 	.getSQLresult(sql, dbname = dbname)
 }
 
 getMaps = function(filter, dbname = NULL) {	
 	if(missing(filter))
 		sql = "SELECT * FROM map"
 	else {
 		filter = paste("('", paste(filter, collapse = "','"), "')", sep = "")
 		sql = paste("SELECT * FROM map WHERE pwm_id IN", filter)
 	}
 
 	.getSQLresult(sql, dbname = dbname)
 }
 
 getOrthologs = function (filter, organism, dbname = NULL) 
 {
   sql = paste("SELECT * FROM ortholog", sep = "")
   if (!missing(organism))
     sql = paste(sql, " WHERE map_organism='", organism, "'", sep = "")
   if (!missing(filter)) {
     filter = paste("('", paste(filter, collapse = "','"), "')", sep = "")
     sql = paste(sql, "AND entrezgene IN", filter)
   }
   .getSQLresult(sql, dbname = dbname)
 }
 
 getTFclass = function(dbname = NULL) {
   sql = "SELECT * FROM tfclass"
   .getSQLresult(sql, dbname = dbname)
 }
 
 .getDefaultDb = function() {
 	system.file("db/database.db", package = "rTRM")
 }
 
 .getSQLresult = function(sql, drv = "SQLite", dbname = NULL) {
 	if(is.null(dbname))
 		dbname = .getDefaultDb()
 	
 	drv <- dbDriver(drv)
 	con = dbConnect(drv, dbname = dbname)
 	res = dbSendQuery(con, sql)
 	r = fetch(res, n = -1)
 	dbClearResult(res)
 	dbDisconnect(con)
 	r
 }
 
 
 ######## utility functions.
 
 # getOrthologFromMatrix
 # returns a vector with with corresponding entrezgene ids for the
 # target organism from a list of motif ids.
 getOrthologFromMatrix = function(filter, organism = "human", dbname = NULL) {
   m = getMaps(filter, dbname = dbname)
   o = unique(getOrthologs(m$entrezgene, organism = organism)$map_entrezgene)
   o[o != ""]
 }
 
 # get corresponding motifs for entrezgene ids.
 getMotifsFromEntrezgene = function(e, organism) {
   o = getOrthologs(organism = organism)
   e_map = unique(o$entrezgene[o$map_entrezgene == e])
   m = getMaps()
   m$pwm_id[m$entrezgene %in% e_map]
 }
 
 # get corresponding motifs from entrezgene symbol
 getMotifsFromSymbol = function(s, organism) {

   map=.getMapFromOrg(organism)
   res=select(map,keys=s,columns="ENTREZID",keytype="ALIAS")
   e=unique(na.omit(res$ENTREZID))

   
   o = getOrthologs(organism = organism)
   e_map = unique(o$entrezgene[o$map_entrezgene == e])
   m = getMaps()
   m$pwm_id[m$entrezgene %in% e_map]
 }