\name{UCSCTableQuery-class}
\docType{class}

\alias{UCSCTableQuery-class}

% Accessors:
\alias{browserSession,UCSCTableQuery-method}
\alias{browserSession<-}
\alias{browserSession<-,UCSCTableQuery,UCSCSession-method}
\alias{trackName}
\alias{trackName,UCSCTableQuery-method}
\alias{trackName<-}
\alias{trackName<-,UCSCTableQuery-method}
\alias{tableName}
\alias{tableName,UCSCTableQuery-method}
\alias{tableName<-}
\alias{tableName<-,UCSCTableQuery-method}
\alias{range,UCSCTableQuery-method}
\alias{range<-,UCSCTableQuery-method}
\alias{names,UCSCTableQuery-method}
\alias{names<-,UCSCTableQuery-method}
\alias{trackNames,UCSCTableQuery-method}
\alias{ucscSchema}
\alias{ucscSchema,UCSCTableQuery-method}

% Query execution
\alias{tableNames}
\alias{tableNames,UCSCTableQuery-method}
\alias{getTable}
\alias{getTable,UCSCTableQuery-method}
\alias{track}
\alias{track,UCSCTableQuery-method}

% Constructor:
\alias{ucscTableQuery}
\alias{ucscTableQuery,UCSCSession-method}

% Show:
\alias{show,UCSCTableQuery-method}

\title{Querying UCSC Tables}
\description{The UCSC genome browser is backed by a large database,
  which is exposed by the Table Browser web interface. Tracks are
  stored as tables, so this is also the mechanism for retrieving tracks. The
  \code{UCSCTableQuery} class represents a query against the Table
  Browser. Storing the query fields in a formal class facilitates
  incremental construction and adjustment of a query.} 

\details{
  There are five supported fields for a table query:
  \describe{
    \item{session}{The \code{\linkS4class{UCSCSession}} instance from
      the tables are retrieved. Although all sessions are based on the
      same database, the set of user-uploaded tracks, which are represented
      as tables, is not the same, in general.
    }
    \item{trackName}{The name of a track from which to retrieve a
      table. Each track can have multiple tables. Many times there is a
      primary table that is used to display the track, while the other
      tables are supplemental. Sometimes, tracks are displayed by
      aggregating multiple tables. If \code{NULL}, search for a primary
      table across all of the tracks (will not find secondary tables).
    }
    \item{tableName}{The name of the specific table to retrieve. May be
      \code{NULL}, in which case the behavior depends on how the query
      is executed, see below.
    }
    \item{range}{A genome identifier, a
      \code{\link[GenomicRanges]{GRanges}} or 
      a \code{\link[IRanges]{IntegerRangesList}} indicating
      the portion of the table to retrieve, in genome coordinates.
      Simply specifying the genome string is the easiest way to download
      data for the entire genome, and \code{\link{GRangesForUCSCGenome}}
      facilitates downloading data for e.g. an entire chromosome.
    }
    \item{names}{Names/accessions of the desired features}
  } 

  A common workflow for querying the UCSC database is to create an
  instance of \code{UCSCTableQuery} using the \code{ucscTableQuery}
  constructor, invoke \code{tableNames} to list the available tables for
  a track, and finally to retrieve the desired table either as a
  \code{data.frame} via \code{getTable} or as a track
  via \code{track}. See the examples.

  The reason for a formal query class is to facilitate multiple queries
  when the differences between the queries are small. For example, one
  might want to query multiple tables within the track and/or same
  genomic region, or query the same table for multiple regions. The
  \code{UCSCTableQuery} instance can be incrementally adjusted for each
  new query. Some caching is also performed, which enhances performance. 
}

\section{Constructor}{
  \describe{
    \item{}{
      \code{ucscTableQuery(x, track, range = seqinfo(x), table = NULL,
        names = NULL)}: Creates a \code{UCSCTableQuery} with the
        \code{UCSCSession} given as \code{x} and the track name given by
        the single string \code{track}. \code{range} should be a genome
        string identifier, a \code{GRanges} instance or
        \code{IntegerRangesList} instance, and it effectively defaults to
        \code{genome(x)}. If the genome is missing, it is taken from the
        session. The table name is given by
        \code{table}, which may be a single string or
        \code{NULL}. Feature names, such as gene identifiers, may be
        passed via \code{names} as a character vector.
    }
  }
}

\section{Executing Queries}{
  Below, \code{object} is a \code{UCSCTableQuery} instance.
  
  \describe{
    \item{}{
      \code{track(object)}:
      Retrieves the indicated table as a track, i.e. a \code{GRanges}
      object. Note that not all tables are available as tracks.
    }
    \item{}{
      \code{getTable(object)}: Retrieves the indicated table as a
      \code{data.frame}. Note that not all tables are output in
      parseable form, and that UCSC will truncate responses if they
      exceed certain limits (usually around 100,000 records). The safest
      (and most efficient) bet for large queries is to download the file
      via FTP and query it locally.
    }
    \item{}{
      \code{tableNames(object)}: Gets the names of the tables available
      for the session, track and range specified by the query.
    }
  }
}

\section{Accessor methods}{
  In the code snippets below, \code{x}/\code{object} is a
  \code{UCSCTableQuery} object.

  \describe{
    \item{}{\code{browserSession(object)},
      \code{browserSession(object) <- value}:
      Get or set the \code{UCSCSession} to query.
    }
    \item{}{\code{trackName(x)}, \code{trackName(x) <- value}: Get or
      set the single string indicating the track containing the table of
      interest.
    }
    \item{}{\code{trackNames(x)}}{List the names of the tracks available
        for retrieval for the assigned genome.}
    \item{}{\code{tableName(x)}, \code{tableName(x) <- value}: Get or
      set the single string indicating the name of the table to
      retrieve. May be \code{NULL}, in which case the table is
      automatically determined.
    }
    \item{}{\code{range(x)}, \code{range(x) <- value}: Get or set the
      \code{GRanges} indicating the portion of the table to retrieve in
      genomic coordinates. Any missing information, such as the genome
      identifier, is filled in using \code{range(browserSession(x))}. It
      is also possible to set the genome identifier string or
      a \code{IntegerRangesList}.
    }
    \item{}{\code{names(x)}, \code{names(x) <- value}: Get or set the
      names of the features to retrieve. If \code{NULL}, this filter is
      disabled.
    }
    \item{}{\code{ucscSchema(x)}: Get
      the \code{\linkS4class{UCSCSchema}} object describing the selected table.}
  }
}

\author{ Michael Lawrence }

\examples{
\dontrun{
session <- browserSession()
genome(session) <- "mm9"
trackNames(session) ## list the track names
## choose the Conservation track for a portion of mm9 chr1
query <- ucscTableQuery(session, "Conservation",
                        GRangesForUCSCGenome("mm9", "chr12",
                                             IRanges(57795963, 57815592)))
## list the table names
tableNames(query)
## get the phastCons30way track
tableName(query) <- "phastCons30way"
## retrieve the track data
track(query)  # a GRanges object
## get a data.frame summarizing the multiple alignment
tableName(query) <- "multiz30waySummary"
getTable(query)

genome(session) <- "hg18"
query <- ucscTableQuery(session, "snp129",
                        names = c("rs10003974", "rs10087355", "rs10075230"))
ucscSchema(query)
getTable(query)
}
}

\keyword{methods}
\keyword{classes}
