## @knitr style, eval=TRUE, echo=FALSE, results='asis'
BiocStyle::latex()


## @knitr include=FALSE
library(knitr)
opts_chunk$set(tidy=FALSE)


## @knitr Homo.sapiens
library(Homo.sapiens)
columns(Homo.sapiens)


## @knitr Homo.sapiens2
keytypes(Homo.sapiens) 


## @knitr Homo.sapiens3
k <- head(keys(Homo.sapiens,keytype="ENTREZID"))
k


## @knitr Homo.sapiens4
result <- select(Homo.sapiens, keys=k, 
                 columns=c("TXNAME","TXSTART","TXSTRAND"), 
                 keytype="ENTREZID")
head(result)


## @knitr URI Example
   uri <- 'http://www.uniprot.org/uniprot/?query='
   ids <- c('P13368', 'Q6GZX4')
   idStr <- paste(ids, collapse="+or+")
   format <- '&format=tab'
   fullUri <- paste0(uri,idStr,format)
   read.delim(fullUri)


## @knitr web service code
getUniprotGoodies  <- function(query, columns)
{
    ## query and columns start as a character vectors
    qstring <- paste(query, collapse="+or+")
    cstring <- paste(columns, collapse=",")
    uri <- 'http://www.uniprot.org/uniprot/?query='
    fullUri <- paste0(uri,qstring,'&format=tab&columns=',cstring)
    dat <- read.delim(fullUri, stringsAsFactors=FALSE)
    ## now remove things that were not in the specific original query...
    dat <- dat[dat[,1] %in% query,]
    dat
}


## @knitr xml_tree,eval=FALSE
## library(XML)
## uri <- "http://www.uniprot.org/uniprot/?query=P13368+or+Q6GZX4&format=xml"
## xml <- xmlTreeParse(uri, useInternalNodes=TRUE)


## @knitr xml_namespace,eval=FALSE
## defs <- xmlNamespaceDefinitions(xml, recurisve=TRUE)
## defs


## @knitr xml_namespace_struct,eval=FALSE
## ns <- structure(sapply(defs, function(x) x$uri), names=names(defs))


## @knitr xml_namespace2,eval=FALSE
## entry <- getNodeSet(xml, "//ns:entry", "ns")
## xmlSize(entry)


## @knitr xml_xmlAttrs,eval=FALSE
## nms <- xpathSApply(xml, "//ns:entry/ns:name", xmlValue, namespaces="ns")
## attrs <- xpathApply(xml, "//ns:entry", xmlAttrs, namespaces="ns")
## names(attrs) <- nms
## attrs


## @knitr xml_xmlChildren,eval=FALSE
## fun1 <- function(elt) unique(names(xmlChildren(elt)))
## xpathApply(xml, "//ns:entry", fun1, namespaces="ns")


## @knitr xml_feature_type,eval=FALSE
## Q6GZX4 <- "//ns:entry[ns:accession='Q6GZX4']/ns:feature"
## xmlSize(getNodeSet(xml, Q6GZX4, namespaces="ns"))
## 
## P13368 <- "//ns:entry[ns:accession='P13368']/ns:feature"
## xmlSize(getNodeSet(xml, P13368, namespaces="ns"))


## @knitr xml_feature_type2,eval=FALSE
## path <- "//ns:feature"
## unique(xpathSApply(xml, path, xmlGetAttr, "type", namespaces="ns"))


## @knitr xml_feature_type_P13368,eval=FALSE
## path <- "//ns:entry[ns:accession='P13368']/ns:feature[@type='sequence conflict']"
## data.frame(t(xpathSApply(xml, path, xmlAttrs, namespaces="ns")))


## @knitr xml_sequence,eval=FALSE
## library(Biostrings)
## path <- "//ns:entry/ns:sequence"
## seqs <- xpathSApply(xml, path, xmlValue, namespaces="ns")
## aa <- AAStringSet(unlist(lapply(seqs, function(elt) gsub("\n", "", elt)),
##     use.names=FALSE))
## names(aa) <- nms
## aa


## @knitr WebServiceObject
setClass("uniprot", representation(name="character"),
         prototype(name="uniprot"))


## @knitr makeInstanceWebServiceObj
    uniprot <- new("uniprot")


## @knitr onLoad2,eval=FALSE
## .onLoad <- function(libname, pkgname)
## {
##     ns <- asNamespace(pkgname)
##     uniprot <- new("uniprot")
##     assign("uniprot", uniprot, envir=ns)
##     namespaceExport(ns, "uniprot")
## }


## @knitr keytypeUniprot
setMethod("keytypes", "uniprot",function(x){return("UNIPROT")})
uniprot <- new("uniprot")
keytypes(uniprot)


## @knitr keytypeUniprot2
setMethod("columns", "uniprot", 
          function(x){return(c("ID", "SEQUENCE", "ORGANISM"))})
columns(uniprot)


## @knitr webServiceSelect
.select <- function(x, keys, columns){
    colsTranslate <- c(id='ID', sequence='SEQUENCE', organism='ORGANISM')
    columns <- names(colsTranslate)[colsTranslate %in% columns]
    getUniprotGoodies(query=keys, columns=columns)
}
setMethod("select", "uniprot", 
    function(x, keys, columns, keytype)
{
    .select(keys=keys, columns=columns)
})
select(uniprot, keys=c("P13368","P20806"), columns=c("ID","ORGANISM"))


## @knitr classicConn,results='hide'
drv <- SQLite()
library("org.Hs.eg.db")
con_hs <- dbConnect(drv, dbname=system.file("extdata", "org.Hs.eg.sqlite",
                        package = "org.Hs.eg.db"))
con_hs
dbDisconnect(con_hs)


## @knitr ourConn
require(hom.Hs.inp.db)
str(hom.Hs.inp.db)


## @knitr ourConn2
hom.Hs.inp.db$conn
## or better we can use a helper function to wrap this:
AnnotationDbi:::dbConn(hom.Hs.inp.db)
## or we can just call the provided convenience function 
## from when this package loads:
hom.Hs.inp_dbconn()


## @knitr dbListTables
con <- AnnotationDbi:::dbConn(hom.Hs.inp.db)
head(dbListTables(con))
dbListFields(con, "Mus_musculus")


## @knitr dbGetQuery
dbGetQuery(con, "SELECT * FROM metadata")


## @knitr dbListTables2
head(dbListTables(con))


## @knitr dbListFields2
dbListFields(con, "Apis_mellifera")


## @knitr dbGetQuery2
head(dbGetQuery(con, "SELECT * FROM Apis_mellifera"))


## @knitr Anopheles,eval=FALSE
## head(dbGetQuery(con, "SELECT * FROM Anopheles_gambiae"))
## ## Then only retrieve human records
## ## Query: SELECT * FROM Anopheles_gambiae WHERE species='HOMSA'
## head(dbGetQuery(con, "SELECT * FROM Anopheles_gambiae WHERE species='HOMSA'"))
## dbDisconnect(con)


## @knitr getMetadata, echo=FALSE
library(hom.Hs.inp.db)
hom.Hs.inp_dbInfo()


## @knitr referenceClass,eval=FALSE
## .InparanoidDb <-
##     setRefClass("InparanoidDb", contains="AnnotationDb")


## @knitr onLoad,eval=FALSE
## sPkgname <- sub(".db$","",pkgname)
## db <- loadDb(system.file("extdata", paste(sPkgname,
##                ".sqlite",sep=""), package=pkgname, lib.loc=libname),
##                packageName=pkgname)
## dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"InparanoidDb")
## ns <- asNamespace(pkgname)
## assign(dbNewname, db, envir=ns)
## namespaceExport(ns, dbNewname)


## @knitr columns,eval=FALSE
## .cols <- function(x)
## {
##     con <- AnnotationDbi:::dbConn(x)
##     list <- dbListTables(con)
##     ## drop unwanted tables
##     unwanted <- c("map_counts","map_metadata","metadata")
##     list <- list[!list %in% unwanted]
##     ## Then just to format things in the usual way
##     list <- toupper(list)
##     dbDisconnect(con)
##     list
## }
## 
## ## Then make this into a method
## setMethod("columns", "InparanoidDb", .cols(x))
## ## Then we can call it
## columns(hom.Hs.inp.db)


## @knitr keytypes,eval=FALSE
## setMethod("keytypes", "InparanoidDb", .cols(x))
## ## Then we can call it
## keytypes(hom.Hs.inp.db)
## 
## ## refactor of .cols
## .getLCcolnames <- function(x)
## {
##     con <- AnnotationDbi:::dbConn(x)
##     list <- dbListTables(con)
##     ## drop unwanted tables
##     unwanted <- c("map_counts","map_metadata","metadata")
##     list <- list[!list %in% unwanted]
##     dbDisconnect(con)
##     list
## }
## .cols <- function(x)
## {
##     list <- .getLCcolnames(x)
##     ## Then just to format things in the usual way
##     toupper(list)
## }
## ## Test:
## columns(hom.Hs.inp.db)
## 
## ## new helper function:
## .getTableNames <- function(x)
## {
##     LC <- .getLCcolnames(x)
##     UC <- .cols(x)
##     names(UC) <- LC
##     UC
## }
## .getTableNames(hom.Hs.inp.db)


## @knitr keys,eval=FALSE
## .keys <- function(x, keytype)
## {
##     ## translate keytype back to table name
##     tabNames <- .getTableNames(x)
##     lckeytype <- names(tabNames[tabNames %in% keytype])
##     ## get a connection
##     con <- AnnotationDbi:::dbConn(x)
##     sql <- paste("SELECT inp_id FROM",lckeytype, "WHERE species!='HOMSA'")
##     res <- dbGetQuery(con, sql)
##     res <- as.vector(t(res))
##     dbDisconnect(con)
##     res
## }
## 
## setMethod("keys", "InparanoidDb", .keys(x, keytype))
## ## Then we can call it
## keys(hom.Hs.inp.db, "TRICHOPLAX_ADHAERENS")


## @knitr dbDisconnect
   dbDisconnect(con)


## @knitr makeNewDb
drv <- dbDriver("SQLite")
dbname <- file.path(tempdir(), "myNewDb.sqlite")
con <- dbConnect(drv, dbname=dbname)


## @knitr exampleFrame
data = data.frame(id=c(1,2,9),
                  string=c("Blue",
                           "Red",
                           "Green"),
                  stringsAsFactors=FALSE)


## @knitr exercise2
dbGetQuery(con, "CREATE Table genePheno (id INTEGER, string TEXT)")


## @knitr LabelledPreparedQueries
names(data) <- c("id","string")
sql <- "INSERT INTO genePheno VALUES ($id, $string)"
dbBeginTransaction(con)
dbGetPreparedQuery(con, sql, bind.data = data)
dbCommit(con)


## @knitr ATTACH
db <- system.file("extdata", "TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite", 
                  package="TxDb.Hsapiens.UCSC.hg19.knownGene")
dbGetQuery(con, sprintf("ATTACH '%s' AS db",db))


## @knitr ATTACHJoin
  sql <- "SELECT * FROM db.gene AS dbg, 
          genePheno AS gp WHERE dbg.gene_id=gp.id"
  res <- dbGetQuery(con, sql)
  res


## @knitr SessionInfo, echo=FALSE
sessionInfo()