-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Libary to interface with the NCBI Entrez REST service.
--   
@package EntrezHTTP
@version 1.0.0


-- | Data structures for Entrez HTTP queries
module Bio.EntrezHTTPData

-- | Input datastructure for EntrezHTTP. Program is the selected eutility
--   (e.g efetch, esearch), database is the selected Entrez database
--   (nucleotide) and query the query string.
data EntrezHTTPQuery
EntrezHTTPQuery :: Maybe String -> Maybe String -> String -> EntrezHTTPQuery
program :: EntrezHTTPQuery -> Maybe String
database :: EntrezHTTPQuery -> Maybe String
query :: EntrezHTTPQuery -> String

-- | Data structure for Entrez summary result
data EntrezSummary
EntrezSummary :: [EntrezDocSum] -> EntrezSummary
documentSummaries :: EntrezSummary -> [EntrezDocSum]
data EntrezDocSum
EntrezDocSum :: String -> [SummaryItem] -> EntrezDocSum
summaryId :: EntrezDocSum -> String
summaryItems :: EntrezDocSum -> [SummaryItem]
data SummaryItem
SummaryItem :: String -> String -> String -> SummaryItem
itemName :: SummaryItem -> String
itemType :: SummaryItem -> String
itemContent :: SummaryItem -> String

-- | Gene doc summary
data EntrezGeneSummary
EntrezGeneSummary :: [EntrezGeneDocSummary] -> EntrezGeneSummary
geneSummaries :: EntrezGeneSummary -> [EntrezGeneDocSummary]
data EntrezGeneDocSummary
EntrezGeneDocSummary :: String -> String -> String -> String -> String -> String -> EntrezGenomicInfo -> EntrezGeneDocSummary
geneId :: EntrezGeneDocSummary -> String
geneName :: EntrezGeneDocSummary -> String
geneStatus :: EntrezGeneDocSummary -> String
geneCurrentID :: EntrezGeneDocSummary -> String
geneGeneticSource :: EntrezGeneDocSummary -> String
geneOtherAliases :: EntrezGeneDocSummary -> String
geneGenomicInfo :: EntrezGeneDocSummary -> EntrezGenomicInfo
data EntrezGenomicInfo
EntrezGenomicInfo :: String -> Int -> Int -> Int -> EntrezGenomicInfo
chrAccVer :: EntrezGenomicInfo -> String
chrStart :: EntrezGenomicInfo -> Int
chrStop :: EntrezGenomicInfo -> Int
exonCount :: EntrezGenomicInfo -> Int

-- | Data structure for Entrez search result
data EntrezSearch
EntrezSearch :: Int -> Int -> Int -> [Int] -> [TranslationStack] -> String -> EntrezSearch
count :: EntrezSearch -> Int
retMax :: EntrezSearch -> Int
retStart :: EntrezSearch -> Int
searchIds :: EntrezSearch -> [Int]
translationStack :: EntrezSearch -> [TranslationStack]
queryTranslation :: EntrezSearch -> String
data TranslationStack
TranslationStack :: [TermSet] -> String -> TranslationStack
termSets :: TranslationStack -> [TermSet]
operation :: TranslationStack -> String
data TermSet
TermSet :: String -> String -> Int -> String -> TermSet
term :: TermSet -> String
field :: TermSet -> String
termCount :: TermSet -> Int
explode :: TermSet -> String
instance Show EntrezHTTPQuery
instance Eq EntrezHTTPQuery
instance Show SummaryItem
instance Eq SummaryItem
instance Show EntrezDocSum
instance Eq EntrezDocSum
instance Show EntrezSummary
instance Eq EntrezSummary
instance Show EntrezGenomicInfo
instance Eq EntrezGenomicInfo
instance Show EntrezGeneDocSummary
instance Eq EntrezGeneDocSummary
instance Show EntrezGeneSummary
instance Eq EntrezGeneSummary
instance Show TermSet
instance Eq TermSet
instance Show TranslationStack
instance Eq TranslationStack
instance Show EntrezSearch
instance Eq EntrezSearch


-- | Interface for the NCBI Entrez REST webservice.
--   
--   The entrezHTTP function provides a interface to the NCBI Entrez REST
--   service.
--   
--   A series of different eutilites and databases are provided by the REST
--   interface. Response depends on the combination of eutil and database,
--   as well requested returntype. Specific combinations have wrapper
--   functions with corresponding parsing functions included (see Usage
--   example).
--   
--   If you use this libary in a tool, please read <a>A General
--   Introduction to the E-utilities</a> carefully and register your tool
--   at eutilities@ncbi.nlm.nih.gov. You can append your registration info
--   generated with the included buildRegistration function to your query.
--   
--   <h2>Usage example:</h2>
--   
--   Retrieve a nucleotide sequence for Escherichia coli
--   
--   <pre>
--   nucleotideFasta &lt;- fetchNucleotideString "NC_000913.3" 50 1000 "+" Nothing
--   </pre>
module Bio.EntrezHTTP

-- | Function for querying the NCBI entrez REST interface. Input
--   EntrezHTTPQuery datatype is used to select database, program of
--   interest and contains the query string. Please note that query strings
--   containing whitespace or special characters need to be urlencoded. The
--   response format and content depends on the query type, the output
--   therefore provided as String.
entrezHTTP :: EntrezHTTPQuery -> IO String

-- | Retrieve sequence for gene symbol (e.g. yhfA) from accession number
--   (e.g. NC_000913.3) and if available entrez registration
--   (toolname,devemail)
retrieveGeneSymbolFasta :: String -> String -> Maybe (String, String) -> IO String

-- | Fetches sequence strings from the nucleotide database. nucleotideId
--   can be a NCBI accession number or gene id. Strand is 1 in case of plus
--   strand (forward) or 2 minus (reverse) strand, the setStrand function
--   can be used for conversion.
fetchNucleotideString :: String -> Int -> Int -> Int -> Maybe (String, String) -> IO String

-- | Wrapper function for eutils that accept a list of querys (e.g. a list
--   of gene ids) that ensures that only chunks of 20 queries are sent per
--   request. Sending to long queries otherwise results in a serverside
--   exception.
retrieveElementsEntrez :: [a] -> ([a] -> IO b) -> IO [b]
portionListElements :: [a] -> Int -> [[a]]

-- | Read entrez fetch for taxonomy database into a simplyfied datatype
--   Result of e.g: <a>http://eutils.ncbi.nlm.nih</a>.
readEntrezTaxonSet :: String -> [Taxon]

-- | Read entrez fetch for taxonomy database into a simplyfied datatype
--   Result of e.g:
--   <a>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&amp;id=1406860</a>
readEntrezSimpleTaxons :: String -> [SimpleTaxon]
readEntrezParentIds :: String -> [Int]

-- | Read entrez summary from internal haskell string
readEntrezSummaries :: String -> [EntrezSummary]

-- | Read entrez summary from internal haskell string
readEntrezSearch :: String -> [EntrezSearch]

-- | Builds Entrez registration String that has to be appended to query key
buildRegistration :: String -> String -> String

-- | Builds Entrez registration String if present
maybeBuildRegistration :: Maybe (String, String) -> String
setStrand :: String -> Int
convertCoordinatesToStrand :: Int -> Int -> Int