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## es.upm.gib.eutilsrdfwrapper.eutils
Class EUtilsWrapper

    java.lang.Object
      es.upm.gib.eutilsrdfwrapper.eutils.EUtilsWrapper

    public class EUtilsWrapper

extends java.lang.Object

Methods for accessing the eutils functionality

Field Summary
`static java.lang.String` | `RETMAX_FOR_SEARCHES`

Constructor Summary
`EUtilsWrapper()`

Method Summary
`static org.jdom.Document` | `dbList()` Returns a document with Entrez Databases
`static java.net.URL` | `efetch(java.lang.String db, java.lang.String id, DoubleElement... args)` Responds to a list of UIDs in a given database with the corresponding data records in a specified format.
`static java.net.URL` | `efetch(java.lang.String db, java.lang.String query_key, java.lang.String WebEnv, DoubleElement... args)` Responds to a list of UIDs in a given database with the corresponding data records in a specified format.
`static java.net.URL` | `egquery(java.lang.String term)` Responds to a text eSearch with the number of records matching the eSearch in each Entrez database.
`static java.net.URL` | `einfo(DoubleElement<java.lang.String,java.lang.String>... database)` Provides the number of records indexed in each elem1 of a given database, the date of the last update of the database, and the available links from the database to other Entrez databases.
`static java.net.URL` | `elink(java.lang.String db, java.lang.String dbfrom, java.lang.String cmd, java.util.List<java.lang.String> id, DoubleElement... args)` Responds to a list of UIDs in a given database with either a list of related UIDs (and relevancy scores) in the same database or a list of linked UIDs in another Entrez database; checks for the existence of a specified link from a list of one or more UIDs; creates a hyperlink to the primary LinkOut provider for a specific UID and database, or lists LinkOut URLs and retrieved for multiple UIDs.
`static java.net.URL` | `elink(java.lang.String db, java.lang.String dbfrom, java.lang.String cmd, java.lang.String query_key, java.lang.String WebEnv, DoubleElement... args)` Responds to a list of UIDs in a given database with either a list of related UIDs (and relevancy scores) in the same database or a list of linked UIDs in another Entrez database; checks for the existence of a specified link from a list of one or more UIDs; creates a hyperlink to the primary LinkOut provider for a specific UID and database, or lists LinkOut URLs and retrieved for multiple UIDs.
`static java.net.URL` | `epost(java.lang.String db, java.util.List<java.lang.String> id, DoubleElement... webEnv)` Accepts a list of UIDs from a given database, stores the set on the History Server, and responds with a eSearch key and web environment for the uploaded dataset.
`static java.net.URL` | `esearch(java.lang.String db, java.lang.String term, DoubleElement... args)` Responds to a text eSearch with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the eSearch.
`static java.net.URL` | `espell(java.lang.String db, java.lang.String term)` Retrieves spelling suggestions for a text eSearch in a given database.
`static java.net.URL` | `esummary(java.lang.String db, java.lang.String id, DoubleElement... args)` Responds to a list of UIDs from a given database with the corresponding document summaries.
`static java.net.URL` | `esummary(java.lang.String db, java.lang.String query_key, java.lang.String WebEnv, DoubleElement... args)` Responds to a list of UIDs from a given database with the corresponding document summaries.
`static InternalQueryState` | `generateInitialInternalQueryState(ConceptsQuery query)` Launches the query for the first database and related databases in the concepts query and creates the initial internal query state
`static java.util.List<java.util.List<java.lang.String>>` | `getResults(ConceptsQuery originalQuery, InternalQueryState internalQueryState, java.util.List<java.util.List<java.lang.String>> varNames, CacheMap<java.lang.String,org.jdom.Document> resultCache)` Retrieves a set of results from ArrayExpress, performing the necessary efetch operations with the already available query keys from a given internal query state
`static boolean` | `hasResults(InternalQueryState array)`
`static FourElements<java.lang.String,java.lang.String,java.lang.Integer,java.util.List<java.lang.String>>` | `initialSearch(java.lang.String database, java.lang.String term)` Generates the URL for the initial search and launches the query
`static org.jdom.Document` | `launchQuery(java.net.URL url)`
`static FourElements<java.lang.String,java.lang.String,java.lang.Integer,java.util.List<java.lang.String>>` | `launchSearch(java.lang.String database, java.lang.String term, java.lang.String webenv, java.lang.String querykey)`
`static InternalQueryState` | `myNextInternalQueryState(InternalQueryState iqs, ConceptsQuery query)` It is assumed that at least one element in the given internal query state can move forward

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### RETMAX_FOR_SEARCHES

    public static final java.lang.String RETMAX_FOR_SEARCHES

See Also:
  Constant Field Values

Constructor Detail

### EUtilsWrapper

    public EUtilsWrapper()

Method Detail

### dbList

    public static org.jdom.Document dbList()

  Returns a document with Entrez Databases

  Returns:
    XML document with Entrez Databases

### einfo

    public static java.net.URL einfo(DoubleElement<java.lang.String,java.lang.String>... database)

  Provides the number of records indexed in each elem1 of a given database, the date of the last update of the database, and the available links from the database to other Entrez databases.

  Provides a list of the names of all valid Entrez databases, if no db parameter is provider Provides statistics for a single database, including lists of indexing fields and available link names

  Parameters:
    `database` - Optional Parameters Target database about which to gather statistics. Value must be a valid Entrez database name
  Returns:
    a url to the XML for the eSearch

### esearch

    public static java.net.URL esearch(java.lang.String db,
                                       java.lang.String term,
                                       DoubleElement... args)

  Responds to a text eSearch with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the eSearch.

  Provides a list of UIDs matching a text eSearch Posts the results of a search on the History server Downloads all UIDs from a dataset stored on the History server Combines or limits UID datasets stored on the History server Sorts sets of UIDs

  Parameters:
    `db` - Database to search. Value must be a valid Entrez database name (default = pubmed).
    `term` - Entrez text eSearch. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search elem1 descriptions and tags. Search fields and tags are database specific.
    `args` - Optional Parameters – History Server usehistory: When usehistory is set to 'y', ESearch will post the UIDs resulting from the search operation onto the History server so that they can be used directly in a subsequent E-utility call. Also, usehistory must be set to 'y' for ESearch to interpret eSearch key values included in term or to accept a WebEnv as input. WebEnv: Web environment string returned from a previous ESearch, EPost or ELink call. When provided, ESearch will post the results of the search operation to this pre-existing WebEnv, thereby appending the results to the existing environment. In addition, providing WebEnv allows eSearch keys to be used in term so that previous search sets can be combined or limited. As described above, if WebEnv is used, usehistory must be set to 'y'. query_key: Integer eSearch key returned by a previous ESearch, EPost or ELink call. When provided, ESearch will find the intersection of the set specified by query_key and the set retrieved by the eSearch in term (i.e. joins the two with AND). For query_key to function, WebEnv must be assigned an existing WebEnv string and usehistory must be set to 'y'. Values for eSearch keys may also be provided in term if they are preceeded by a '#' (%23 in the URL). While only one query_key parameter can be provided to ESearch, any number of eSearch keys can be combined in term. Also, if eSearch keys are provided in term, they can be combined with OR or NOT in addition to AND. – Retrieval retstart: Sequential index of the first UID in the retrieved set to be shown in the XML output (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of UIDs retrieved from a search. retmax: Total number of UIDs from the retrieved set to be shown in the XML output (default=20). By default, ESearch only includes the first 20 UIDs retrieved in the XML output. If usehistory is set to 'y', the remainder of the retrieved set will be stored on the History server; otherwise these UIDs are lost. Increasing retmax allows more of the retrieved UIDs to be included in the XML output, up to a maximum of 100,000 records. To retrieve more than 100,000 UIDs, submit multiple esearch requests while incrementing the elem2 of retstart. rettype: Retrieval type. There are two allowed values for ESearch: 'uilist' (default), which displays the standard XML output, and 'count', which displays only the tag. elem1: Search elem1. If used, the entire search term will be limited to the specified Entrez elem1. – Dates datetype: Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype. reldate: When reldate is set to an integer n, the search returns only those items that have a date specified by datetype within the last n days. mindate, maxdate: Date range used to limit a search result by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.
  Returns:
    a url to the XML for the eSearch

### epost

    public static java.net.URL epost(java.lang.String db,
                                     java.util.List<java.lang.String> id,
                                     DoubleElement... webEnv)

  Accepts a list of UIDs from a given database, stores the set on the History Server, and responds with a eSearch key and web environment for the uploaded dataset.

  ,, Uploads a list of UIDs to the Entrez History server Appends a list of UIDs to an existing set of UID lists attached to a Web Environment

  Parameters:
    `db` - Database containing the UIDs in the input list. The elem2 must be a valid Entrez database name (default = pubmed).
    `id` - UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to epost, but if more than about 200 UIDs are to be posted, the request should be made using the HTTP POST method.
    `webEnv` - Optional Parameters Web Environment. If provided, this parameter specifies the Web Environment that will receive the UID list sent by post. EPost will create a new eSearch key associated with that Web Environment. Usually this webEnv elem2 is obtained from the output of a previous ESearch, EPost or ELink call. If no webEnv parameter is provided, EPost will create a new Web Environment and post the UID list to query_key 1.
  Returns:
    a url to the XML for the eSearch

### esummary

    public static java.net.URL esummary(java.lang.String db,
                                        java.lang.String id,
                                        DoubleElement... args)

  Responds to a list of UIDs from a given database with the corresponding document summaries.

  Returns document summaries (DocSums) for a list of input UIDs Returns DocSums for a set of UIDs stored on the Entrez History server

  Parameters:
    `db` - Database from which to retrieve DocSums. The elem2 must be a valid Entrez database name (default = pubmed).
    `id` - UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to ESummary, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.
    `args` - Optional Parameters – Retrieval retstart: Sequential index of the first DocSum to be retrieved (default=1, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of DocSums from the input set. retmax: Total number of DocSums from the input set to be retrieved, up to a maximum of 10,000. If the total set is larger than this maximum, the elem2 of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax.
  Returns:
    a url to the XML for the eSearch

### esummary

    public static java.net.URL esummary(java.lang.String db,
                                        java.lang.String query_key,
                                        java.lang.String WebEnv,
                                        DoubleElement... args)

  Responds to a list of UIDs from a given database with the corresponding document summaries.

  Returns document summaries (DocSums) for a list of input UIDs Returns DocSums for a set of UIDs stored on the Entrez History server

  Parameters:
    `db` - Database from which to retrieve DocSums. The elem2 must be a valid Entrez database name (default = pubmed).
    `query_key` - This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ESummary. Query keys are obtained from the output of previous ESearch, EPost or ELink calls. The query_key parameter must be used in conjunction with WebEnv.
    `WebEnv` - This parameter specifies the Web Environment that contains the UID list to be provided as input to ESummary. Usually this WebEnv elem2 is obtained from the output of a previous ESearch, EPost or ELink call. The WebEnv parameter must be used in conjunction with query_key.
    `args` - Optional Parameters – Retrieval retstart: Sequential index of the first DocSum to be retrieved (default=1, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of DocSums from the input set. retmax: Total number of DocSums from the input set to be retrieved, up to a maximum of 10,000. If the total set is larger than this maximum, the elem2 of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax.
  Returns:
    a url to the XML for the eSearch

### elink

    public static java.net.URL elink(java.lang.String db,
                                     java.lang.String dbfrom,
                                     java.lang.String cmd,
                                     java.util.List<java.lang.String> id,
                                     DoubleElement... args)

  Responds to a list of UIDs in a given database with either a list of related UIDs (and relevancy scores) in the same database or a list of linked UIDs in another Entrez database; checks for the existence of a specified link from a list of one or more UIDs; creates a hyperlink to the primary LinkOut provider for a specific UID and database, or lists LinkOut URLs and retrieved for multiple UIDs.

  Returns UIDs linked to an input set of UIDs in either the same or a different Entrez database Returns UIDs linked to other UIDs in the same Entrez database that match an Entrez eSearch Checks for the existence of Entrez links for a set of UIDs within the same database Lists the available links for a UID Lists LinkOut URLs and retrieved for a set of UIDs Lists hyperlinks to primary LinkOut providers for a set of UIDs Creates hyperlinks to the primary LinkOut provider for a single UID

  Parameters:
    `db` - Database from which to retrieve UIDs. The elem2 must be a valid Entrez database name (default = pubmed) This is the destination database for the link operation.
    `dbfrom` - Database containing the input UIDs. The elem2 must be a valid Entrez database name (default = pubmed). This is the origin database of the link operation. If db and dbfrom are set to the same database elem2, then ELink will return computational neighbors within that database. Please see the full list of Entrez links for available computational neighbors. Computational neighbors have linknames that begin with dbname_dbname (examples: protein_protein, pcassay_pcassay_activityneighbor).
    `cmd` - ELink command mode. The command mode specified which function ELink will perform. Some optional parameters only function for certain values of &cmd (see below). cmd=neighbor (default): ELink returns a set of UIDs in db linked to the input UIDs in dbfrom. cmd=neighbor_score: ELink returns a set of UIDs within the same database as the input UIDs along with computed similarity scores. cmd=neighbor_history: ELink posts the output UIDs to the Entrez History server and returns a query_key and WebEnv corresponding to the location of the output set. cmd=acheck: ELink lists all links available for a set of UIDs. cmd=ncheck: ELink checks for the existence of links within the same database for a set of UIDs. These links are equivalent to setting db and dbfrom to the same elem2. cmd=lcheck: Elink checks for the existence of external links (LinkOuts) for a set of UIDs. cmd=llinks: For each input UID, ELink lists the URLs and retrieved for the LinkOut providers that are not libraries. cmd=llinkslib: For each input UID, ELink lists the URLs and retrieved for all LinkOut providers including libraries. cmd=prlinks: ELink lists the primary LinkOut provider for each input UID, or links directly to the LinkOut provider's web site for a single UID if retmode is set to ref.
    `id` - UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by dbfrom. There is no set maximum for the number of UIDs that can be passed to ELink, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method. If more than one id parameter is provided, ELink will perform a separate link operation for the set of UIDs specified by each id parameter. This effectively accomplishes "one-to-one" links and preserves the connection between the input and output UIDs.
    `args` - Optional Parameters - Limiting the Output Set of Links linkname: Name of the Entrez link to retrieve. Every link in Entrez is given a name of the form dbfrom_db_subset. The values of subset vary depending on the values of dbfrom and db. Many dbfrom/db combinations have no subset values. See the list of Entrez links for a listing of all available linknames. When linkname is used, only the links with that name will be retrieved. The linkname parameter only functions when cmd is set to neighbor or neighbor_history. term: Entrez eSearch used to limit the output set of linked UIDs. The eSearch in the term parameter will be applied after the link operation, and only those UIDs matching the eSearch will be returned by ELink. The term parameter only functions when db and dbfrom are set to the same database elem2. holding: Name of LinkOut provider. Only URLs for the LinkOut provider specified by holding will be returned. The elem2 provided to holding should be the abbreviation of the LinkOut provider's name found in the tag of the ELink XML output when cmd is set to llinks or llinkslib. The holding parameter only functions when cmd is set to llinks or llinkslib. - Dates datetype: Type of date used to limit a link operation. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype. reldate: When reldate is set to an integer n, ELink returns only those items that have a date specified by datetype within the last n days. mindate, maxdate: Date range used to limit a link operation by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.
  Returns:
    a url to the XML for the eSearch

### elink

    public static java.net.URL elink(java.lang.String db,
                                     java.lang.String dbfrom,
                                     java.lang.String cmd,
                                     java.lang.String query_key,
                                     java.lang.String WebEnv,
                                     DoubleElement... args)

  Responds to a list of UIDs in a given database with either a list of related UIDs (and relevancy scores) in the same database or a list of linked UIDs in another Entrez database; checks for the existence of a specified link from a list of one or more UIDs; creates a hyperlink to the primary LinkOut provider for a specific UID and database, or lists LinkOut URLs and retrieved for multiple UIDs.

  Returns UIDs linked to an input set of UIDs in either the same or a different Entrez database Returns UIDs linked to other UIDs in the same Entrez database that match an Entrez eSearch Checks for the existence of Entrez links for a set of UIDs within the same database Lists the available links for a UID Lists LinkOut URLs and retrieved for a set of UIDs Lists hyperlinks to primary LinkOut providers for a set of UIDs Creates hyperlinks to the primary LinkOut provider for a single UID

  Parameters:
    `db` - Database from which to retrieve UIDs. The elem2 must be a valid Entrez database name (default = pubmed) This is the destination database for the link operation.
    `dbfrom` - Database containing the input UIDs. The elem2 must be a valid Entrez database name (default = pubmed). This is the origin database of the link operation. If db and dbfrom are set to the same database elem2, then ELink will return computational neighbors within that database. Please see the full list of Entrez links for available computational neighbors. Computational neighbors have linknames that begin with dbname_dbname (examples: protein_protein, pcassay_pcassay_activityneighbor).
    `cmd` - ELink command mode. The command mode specified which function ELink will perform. Some optional parameters only function for certain values of &cmd (see below). cmd=neighbor (default): ELink returns a set of UIDs in db linked to the input UIDs in dbfrom. cmd=neighbor_score: ELink returns a set of UIDs within the same database as the input UIDs along with computed similarity scores. cmd=neighbor_history: ELink posts the output UIDs to the Entrez History server and returns a query_key and WebEnv corresponding to the location of the output set. cmd=acheck: ELink lists all links available for a set of UIDs. cmd=ncheck: ELink checks for the existence of links within the same database for a set of UIDs. These links are equivalent to setting db and dbfrom to the same elem2. cmd=lcheck: Elink checks for the existence of external links (LinkOuts) for a set of UIDs. cmd=llinks: For each input UID, ELink lists the URLs and retrieved for the LinkOut providers that are not libraries. cmd=llinkslib: For each input UID, ELink lists the URLs and retrieved for all LinkOut providers including libraries. cmd=prlinks: ELink lists the primary LinkOut provider for each input UID, or links directly to the LinkOut provider's web site for a single UID if retmode is set to ref.
    `query_key` - Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ELink. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The query_key parameter must be used in conjunction with WebEnv.
    `WebEnv` - Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ELink. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The query_key parameter must be used in conjunction with WebEnv.
    `args` - Optional Parameters - Limiting the Output Set of Links linkname: Name of the Entrez link to retrieve. Every link in Entrez is given a name of the form dbfrom_db_subset. The values of subset vary depending on the values of dbfrom and db. Many dbfrom/db combinations have no subset values. See the list of Entrez links for a listing of all available linknames. When linkname is used, only the links with that name will be retrieved. The linkname parameter only functions when cmd is set to neighbor or neighbor_history. term: Entrez eSearch used to limit the output set of linked UIDs. The eSearch in the term parameter will be applied after the link operation, and only those UIDs matching the eSearch will be returned by ELink. The term parameter only functions when db and dbfrom are set to the same database elem2. holding: Name of LinkOut provider. Only URLs for the LinkOut provider specified by holding will be returned. The elem2 provided to holding should be the abbreviation of the LinkOut provider's name found in the tag of the ELink XML output when cmd is set to llinks or llinkslib. The holding parameter only functions when cmd is set to llinks or llinkslib. - Dates datetype: Type of date used to limit a link operation. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype. reldate: When reldate is set to an integer n, ELink returns only those items that have a date specified by datetype within the last n days. mindate, maxdate: Date range used to limit a link operation by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.
  Returns:
    a url to the XML for the eSearch

### egquery

    public static java.net.URL egquery(java.lang.String term)

  Responds to a text eSearch with the number of records matching the eSearch in each Entrez database.

  Provides the number of records retrieved in all Entrez databases by a single text eSearch.

  Parameters:
    `term` - Entrez text eSearch. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search elem1 descriptions and tags. Search fields and tags are database specific.
  Returns:
    a url to the XML for the eSearch

### espell

    public static java.net.URL espell(java.lang.String db,
                                      java.lang.String term)

  Retrieves spelling suggestions for a text eSearch in a given database.

  Provides spelling suggestions for terms within a single text eSearch in a given database.

  Parameters:
    `db` - Database to search. Value must be a valid Entrez database name (default = pubmed).
    `term` - Entrez text eSearch. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search elem1 descriptions and tags. Search fields and tags are database specific.
  Returns:
    a url to the XML for the eSearch

### efetch

    public static java.net.URL efetch(java.lang.String db,
                                      java.lang.String id,
                                      DoubleElement... args)

  Responds to a list of UIDs in a given database with the corresponding data records in a specified format.

  Returns formatted data records for a list of input UIDs Returns formatted data records for a set of UIDs stored on the Entrez History server

  Parameters:
    `db` - Database from which to retrieve records. The elem2 must be a valid Entrez database name (default = pubmed). Currently EFetch does not support all Entrez databases.
    `id` - UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by db. There is no set maximum for the number of UIDs that can be passed to EFetch, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.
    `args` - Optional Parameters - Retrieval retmode: Retrieval mode. This parameter specifies the data format of the records returned, such as plain text, HMTL or XML. See Table 1 (http://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.chapter4_table1/?report=objectonly) for a full list of allowed values for each database. rettype: Retrieval type. This parameter specifies the record view returned, such as Abstract or MEDLINE from PubMed, or GenPept or FASTA from protein. Please see Table 1 for a full list of allowed values for each database. retstart: Sequential index of the first record to be retrieved (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of records from the input set. retmax: Total number of records from the input set to be retrieved, up to a maximum of 10,000. Optionally, for a large set the elem2 of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax. - Sequence Databases strand: Strand of DNA to retrieve. Available values are "1" for the plus strand and "2" for the minus strand. seq_start: First sequence base to retrieve. The elem2 should be the integer coordinate of the first desired base, with "1" representing the first base of the seqence. seq_stop: Last sequence base to retrieve. The elem2 should be the integer coordinate of the last desired base, with "1" representing the first base of the seqence. complexity: Data content to return. Many sequence records are part of a larger data structure or "blob", and the complexity parameter determines how much of that blob to return. For example, an mRNA may be stored together with its protein product. The available values are as follows: Value of complexity Data returned for each requested GI 0 entire blob 1 bioseq 2 minimal bioseq-set 3 minimal nuc-prot 4 minimal pub-set
  Returns:
    a url to the XML for the eSearch

### efetch

    public static java.net.URL efetch(java.lang.String db,
                                      java.lang.String query_key,
                                      java.lang.String WebEnv,
                                      DoubleElement... args)

  Responds to a list of UIDs in a given database with the corresponding data records in a specified format.

  Returns formatted data records for a list of input UIDs Returns formatted data records for a set of UIDs stored on the Entrez History server

  Parameters:
    `db` - Database from which to retrieve records. The elem2 must be a valid Entrez database name (default = pubmed). Currently EFetch does not support all Entrez databases.
    `query_key` - This integer specifies which of the UID lists attached to the given Web Environment will be used as input to EFetch. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The query_key parameter must be used in conjunction with WebEnv.
    `WebEnv` - Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to EFetch. Usually this WebEnv elem2 is obtained from the output of a previous ESearch, EPost or ELink call. The WebEnv parameter must be used in conjunction with query_key.
    `args` - Optional Parameters - Retrieval retmode: Retrieval mode. This parameter specifies the data format of the records returned, such as plain text, HMTL or XML. See Table 1 (http://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.chapter4_table1/?report=objectonly) for a full list of allowed values for each database. rettype: Retrieval type. This parameter specifies the record view returned, such as Abstract or MEDLINE from PubMed, or GenPept or FASTA from protein. Please see Table 1 for a full list of allowed values for each database. retstart: Sequential index of the first record to be retrieved (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with retmax to download an arbitrary subset of records from the input set. retmax: Total number of records from the input set to be retrieved, up to a maximum of 10,000. Optionally, for a large set the elem2 of retstart can be iterated while holding retmax constant, thereby downloading the entire set in batches of size retmax. - Sequence Databases strand: Strand of DNA to retrieve. Available values are "1" for the plus strand and "2" for the minus strand. seq_start: First sequence base to retrieve. The elem2 should be the integer coordinate of the first desired base, with "1" representing the first base of the seqence. seq_stop: Last sequence base to retrieve. The elem2 should be the integer coordinate of the last desired base, with "1" representing the first base of the seqence. complexity: Data content to return. Many sequence records are part of a larger data structure or "blob", and the complexity parameter determines how much of that blob to return. For example, an mRNA may be stored together with its protein product. The available values are as follows: Value of complexity Data returned for each requested GI 0 entire blob 1 bioseq 2 minimal bioseq-set 3 minimal nuc-prot 4 minimal pub-set
  Returns:
    a url to the XML for the eSearch

### launchQuery

    public static org.jdom.Document launchQuery(java.net.URL url)

### initialSearch

    public static FourElements<java.lang.String,java.lang.String,java.lang.Integer,java.util.List<java.lang.String>> initialSearch(java.lang.String database,
                                                                                                                                   java.lang.String term)

  Generates the URL for the initial search and launches the query

  Parameters:
    `database` - RELLENAR
    `term` - RELLENAR
  Returns:
    Elemento doble que contiene la variable de entorno web y la querykey de la búsqueda

### launchSearch

    public static FourElements<java.lang.String,java.lang.String,java.lang.Integer,java.util.List<java.lang.String>> launchSearch(java.lang.String database,
                                                                                                                                  java.lang.String term,
                                                                                                                                  java.lang.String webenv,
                                                                                                                                  java.lang.String querykey)

  Parameters:
    `database` - RELLENAR
    `term` - RELLENAR
    `webenv` - RELLENAR
    `querykey` - RELLENAR
  Returns:
    devuelve la querykey

### getResults

    public static java.util.List<java.util.List<java.lang.String>> getResults(ConceptsQuery originalQuery,
                                                                              InternalQueryState internalQueryState,
                                                                              java.util.List<java.util.List<java.lang.String>> varNames,
                                                                              CacheMap<java.lang.String,org.jdom.Document> resultCache)

  Retrieves a set of results from ArrayExpress, performing the necessary efetch operations with the already available query keys from a given internal query state

  Parameters:
    `originalQuery` - original concepts query, in case the result tree needs to be rebuilt
    `internalQueryState` - internal query state with the stored query keys
    `varNames` - names of variables in the query, grouped by database
    `resultCache` - cache of results
  Returns:
    a set of result rows

### generateInitialInternalQueryState

    public static InternalQueryState generateInitialInternalQueryState(ConceptsQuery query)

  Launches the query for the first database and related databases in the concepts query and creates the initial internal query state

  Parameters:
    `query` - the concepts query issued by the user
  Returns:
    the initial internal query state

### hasResults

    public static boolean hasResults(InternalQueryState array)

### myNextInternalQueryState

    public static InternalQueryState myNextInternalQueryState(InternalQueryState iqs,
                                                              ConceptsQuery query)

  It is assumed that at least one element in the given internal query state can move forward

  Parameters:
    `iqs` - original internal query state that must be updated with the next configuration
    `query` - original query
  Returns:
    the new internal query state

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