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


-- | Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl
--   
--   BiobaseHTTP provides functions to interface the Bioinformatics REST
--   services - Entrez Ensembl
--   
--   NCBI Entrez provides multiple different databases and eutils.
--   
--   For more information on Entrez refer to:
--   <a>http://www.ncbi.nlm.nih.gov/gquery/</a>.
--   
--   Information on the webservice can be found at:
--   <a>http://www.ncbi.nlm.nih.gov/books/NBK25497/</a>. If you plan to
--   include the library in a tool, register it as explained <a>here</a>.
--   
--   Information on ENSEMBL genomes API can be found here:
--   <a>http://rest.ensemblgenomes.org/</a>.
--   
--   BiobaseHTTP is the successor of the deprecated EntrezHTTP library.
@package BiobaseHTTP
@version 1.2.0


-- | Interface for Ensembl
module Biobase.Ensembl.HTTP
startXRefSession :: Text -> Text -> IO (Either String [EnsemblEntry])
requestGOTermsWithGeneIds :: [Text] -> IO [(Text, [Text])]
requestUniProtWithGeneIds :: [Text] -> IO [(Text, Text)]
data EnsemblEntry
EnsemblEntry :: Maybe Text -> Maybe Text -> Maybe Text -> Maybe Text -> Maybe Text -> [Text] -> Maybe Text -> Maybe Text -> Maybe Text -> EnsemblEntry
[display_id] :: EnsemblEntry -> Maybe Text
[primary_id] :: EnsemblEntry -> Maybe Text
[version] :: EnsemblEntry -> Maybe Text
[description] :: EnsemblEntry -> Maybe Text
[dbname] :: EnsemblEntry -> Maybe Text
[synonyms] :: EnsemblEntry -> [Text]
[info_text] :: EnsemblEntry -> Maybe Text
[info_type] :: EnsemblEntry -> Maybe Text
[db_display_name] :: EnsemblEntry -> Maybe Text


-- | Data structures for Entrez HTTP queries
module Biobase.Entrez.HTTPData

-- | 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
newtype 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
newtype 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 GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezSearch
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezSearch
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.TranslationStack
instance GHC.Show.Show Biobase.Entrez.HTTPData.TranslationStack
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.TermSet
instance GHC.Show.Show Biobase.Entrez.HTTPData.TermSet
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezGeneSummary
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezGeneSummary
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezGeneDocSummary
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezGeneDocSummary
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezGenomicInfo
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezGenomicInfo
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezSummary
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezSummary
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezDocSum
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezDocSum
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.SummaryItem
instance GHC.Show.Show Biobase.Entrez.HTTPData.SummaryItem
instance GHC.Classes.Eq Biobase.Entrez.HTTPData.EntrezHTTPQuery
instance GHC.Show.Show Biobase.Entrez.HTTPData.EntrezHTTPQuery


-- | 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 Biobase.Entrez.HTTP

-- | 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