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* RAA.H
*/
#ifndef _RAA_H_
#define _RAA_H_
/**
* @mainpage
*
* Network access to sequence databases (embl, genbank, swissprot, and others).
*
* These classes provides network access to several nucleotide and protein sequence databases
* structured for multi-criteria retrieval under the ACNUC system as described in
* <a href=http://dx.doi.org/10.1016/j.biochi.2007.07.003>Remote access to ACNUC nucleotide
* and protein sequence databases at PBIL</a>.
*
* The list of available databases is <a href=http://pbil.univ-lyon1.fr/databases/acnuc/banques_raa.php>here</a>.
* EMBL and GenBank are daily updated; SwissProt (it is in fact UniProt and includes SwissProt and trEMBL)
* is updated at each partial release; EMBLwgs is updated at each full release (that is, quarterly).
*
*
*/
extern "C" {
#include "RAA_acnuc.h"
}
#include <string>
#include <Bpp/Seq/Sequence.h>
#include <Bpp/Seq/Alphabet.all>
#include "RaaList.h"
#include "RaaSpeciesTree.h"
#include "RaaSeqAttributes.h"
namespace bpp
{
/**
* @brief Identifies an annotation line in a database.
*/
class RaaAddress {
friend class RAA;
int div;
raa_long faddr;
public:
/**
* @brief Gives the rank of the database file containing this annotation line.
*/
int getDiv() {return div; };
/**
* @brief Gives, as a 64-bit int value, the offset of this annotation line within its database file.
*/
raa_long getAddr() {return faddr; };
};
/**
* @brief Network access to sequence databases (embl, genbank, swissprot, and others).
*
* The list of available databases is <a href=http://pbil.univ-lyon1.fr/databases/acnuc/banques_raa.php>here</a>.
*
* Access can be done to single sequences from their name or accession number
* or to lists of sequences matching a query combining several retrieval criteria.
* Any fragment of any sequence defined by coordinates or by feature table entries
* can be retrieved. Access to sequence annotations is possible. Concurrent access
* to several databases is possible.
*
* Access is possible to database entries and also to subsequences, i.e., one or more fragments
* of one or more parent sequences defined by a feature table entry.
* Subsequences are named by adding an extension (e.g., .PE1) to the name of their parent sequence.
*/
class RAA {
friend class RaaList;
public:
/**
* @name Opening/closing database connections.
*
* @{
*/
/**
* @brief Direct constructor: opens a network connection to a database.
*
* @param dbname The database name (e.g., "embl", "genbank", "swissprot").
* @param port The IP port number of the server (the default value is a safe choice; make sure that no
* firewall blocks outbound connections on this port).
* @param server The IP name of the server (the default value is a safe choice).
* @throw int An error code as follows:\n
* 1: incorrect server name\n
* 2: cannot create connection with server\n
* 3: unknown database name\n
* 4: database is currently not available for remote connection\n
* 7: not enough memory
*/
RAA(const std::string &dbname, int port = 5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int);
/**
* @brief Direct constructor: opens a network connection to a database server, without specifying a database.
*
* Typical usage is to ask with knownDatabases() for the list of served databases, and then to open the chosen
* database with openDatabase().
*
* @param port The IP port number of the server (the default value is a safe choice; make sure that no
* firewall blocks outbound connections on this port).
* @param server The IP name of the server (the default value is a safe choice).
* @throw int An error code as follows:\n
* 1: incorrect server name\n
* 2: cannot create connection with server\n
* 7: not enough memory
*/
RAA(int port=5558, const std::string &server = "pbil.univ-lyon1.fr") throw(int);
/**
* @brief Destructor: closes both the database access, if any, and the network connection.
*/
~RAA();
/**
* @brief Opens a database from its name.
*
* @param dbname The database name (e.g., "embl", "genbank", "swissprot").
* @param getpasswordf NULL, or, for a password-protected database, pointer to a password-providing function
* that returns the password as a writable static char string.
* @param p NULL, or pointer to data transmitted as argument of getpasswordf.
* @return 0 if OK, or an error code as follows:\n
* 3: unknown database name\n
* 4: database is currently not available for remote connection\n
* 5: a database was previously opened on this RAA object and not closed\n
* 6: incorrect password for password-protected database\n
* 7: not enough memory
*/
int openDatabase(const std::string &dbname, char *(*getpasswordf)(void *) = NULL, void *p = NULL);
/**
* @brief Closes a database connection.
* Allows to later open another database with openDatabase() using the same RAA object.
*/
void closeDatabase();
/**
* @brief Computes the list of names and descriptions of databases served by the server.
* Typically used after creation of an RAA object without database and before openDatabase() call.
*
* @return The number of served databases.
* @param name Vector of database names. Any of these names can be used
* in openDatabase() calls.
* @param description Vector of database descriptions. A description can
* begin with "(offline)" to mean the database is currently not available.
*/
int knownDatabases(std::vector<std::string> &name, std::vector<std::string> &description);
/** @} */
/**
* @name Access to sequence data and annotations.
*
* @{
*/
/**
* @brief Returns several attributes of a sequence from its name or accession number.
*
* @param name_or_accno A sequence name or accession number. Case is not significant.
* @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence.
*/
RaaSeqAttributes *getAttributes(const std::string &name_or_accno);
/**
* @brief Returns several attributes of a sequence from its database rank.
*
* @param seqrank The database rank of a sequence.
* @return Several attributes (length, species, etc..., see: RaaSeqAttributes) of a sequence,
* or NULL if seqrank is not a valid database sequence rank.
*/
RaaSeqAttributes *getAttributes(int seqrank);
/**
* @brief Returns a database sequence identified by name or accession number.
*
* Because nucleotide database sequences can be several megabases in length, the maxlength argument
* avoids unexpected huge sequence downloads.
*
* @param name_or_accno A sequence name or accession number. Case is not significant.
* @param maxlength The maximum sequence length beyond which the function returns NULL.
* @return The database sequence including a one-line comment, or NULL if name_or_accno
* does not match any sequence or if the sequence length exceeds maxlength.
*/
Sequence *getSeq(const std::string &name_or_accno, int maxlength=100000);
/**
* @brief Returns a sequence identified by its database rank.
*
* Because nucleotide database sequences can be several megabases in length, the maxlength argument
* avoids unexpected huge sequence downloads.
*
* @param seqrank The database rank of a sequence.
* @param maxlength The maximum sequence length beyond which the function returns NULL.
* @return The database sequence including a one-line comment, or NULL if seqrank
* does not match any sequence or if the sequence length exceeds maxlength.
*/
Sequence *getSeq(int seqrank, int maxlength=100000);
/**
* @brief Returns any part of a sequence identified by its database rank.
*
* @param seqrank The database rank of a sequence.
* @param first The first desired position within the sequence (1 is the smallest valid value).
* @param length The desired number of residues (can be larger than what exists in the sequence).
* @param sequence Filled upon return with requested sequence data.
* @return The length of returned sequence data, or 0 if impossible.
*/
int getSeqFrag(int seqrank, int first, int length, std::string &sequence);
/**
* @brief Returns any part of a sequence identified by its name or accession number.
*
* @param name_or_accno The name or accession number of a sequence. Case is not significant.
* @param first The first desired position within the sequence (1 is the smallest valid value).
* @param length The desired number of residues (can be larger than what exists in the sequence).
* @param sequence Filled upon return with requested sequence data.
* @return The length of returned sequence data, or 0 if impossible.
*/
int getSeqFrag(const std::string &name_or_accno, int first, int length, std::string &sequence);
/**
* @brief Returns the first annotation line of the sequence of given database rank.
*
* @param seqrank Database rank of a sequence.
* @return The first annotation line of this sequence (without terminal \\n).
*/
std::string getFirstAnnotLine(int seqrank);
/**
* @brief Returns the next annotation line after that previously read, or NULL if the end of the
* database file was reached.
*
* @return The next annotation line after that previously read (without terminal \\n).
*/
std::string getNextAnnotLine();
/**
* @brief Returns information identifying the position of the last read annotation line.
*
* @return Information identifying the position of the last read annotation line.
*/
RaaAddress getCurrentAnnotAddress();
/**
* @brief Returns the annotation line at the given address.
*
* @param address Information identifying the position of an annotation line
* typically obtained from a previous call to getCurrentAnnotAddress().
* @return The annotation line at that position (in static memory, without terminal \\n).
*/
std::string getAnnotLineAtAddress(RaaAddress address);
/**
* @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
*
* @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
* corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
* @return The complete protein translation of this CDS, using the genetic code suggested
* by the sequence annotations and with a one-line comment, or NULL if seqrank does not match a CDS
* or if not enough memory.
* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
* exception when translated to protein.
*/
Sequence *translateCDS(int seqrank) throw(BadCharException);//TODO add comment to Sequence
/**
* @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
*
* @param name The name of a protein-coding sequence. It can be either a subsequence
* corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
* @return The complete protein translation of this CDS, using the genetic code suggested
* by the sequence annotations and with a one-line comment, or NULL if name does not match a CDS or
* if not enough memory.
* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
* exception when translated to protein.
*/
Sequence *translateCDS(const std::string &name) throw(BadCharException);
/**
* @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence.
*
* @param seqrank The database rank of a protein-coding sequence. It can be either a subsequence
* corresponding to a CDS feature table entry, or a sequence if all of it belongs to the CDS.
* @return The amino acid corresponding to the start codon of this sequence, using the
* adequate initiation-codon-specific genetic code.
*/
char translateInitCodon(int seqrank);
/** @} */
/**
* @name Creation of lists of sequences, species or keywords.
*
* @{
*/
/**
* @brief Returns the list of database elements (often sequences) matching a query.
*
* Query examples:\n k=ribosomal protein L14 \n sp=felis catus and t=cds
* @param query A retrieval query following the syntax described
* <a href=http://pbil.univ-lyon1.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE>here</a>.
* @param listname A name to be given to the resulting list. Case is not significant. If a list with same
* name already exists, it is replaced by the new list.
* @return The resulting list of matching database elements.
* @throw string If error, the string is a message describing the error cause.
*/
RaaList *processQuery(const std::string &query, const std::string &listname) throw(std::string);
/**
* @brief Creates an empty list with specified name.
*
* @param listname A name to be given to the resulting list. Case is not significant.
* @param kind Nature of the resulting list. One of RaaList::LIST_SEQUENCES, RaaList::LIST_KEYWORDS,
* RaaList::LIST_SPECIES.
* @return The resulting list, unless an exception was raised.
* @throw int 3: a list with same name already existed; it is left unchanged.\n
* 4: the server cannot create more lists.
*/
RaaList *createEmptyList(const std::string &listname, const std::string &kind=RaaList::LIST_SEQUENCES) throw(int);
/**
* @brief Deletes a list and calls its destructor.
*
* @param list An RaaList object.
*/
void deleteList(RaaList *list);
/** @} */
/**
* @name Access to feature table-defined sequences (nucleotide databases only).
*
* @{
*/
/**
* @brief Computes the list of subsequences of a given sequence corresponding to a given feature key with
* optional annotation string matching.
*
* This function allows to retrieve all features of the given sequence corresponding to a given feature key
* and whose annotation optionally contains a given string. \n
* Example:\n
* getDirectFeature("AE005174", "tRNA", "mytrnas", "anticodon: TTG")\n
* retrieves all tRNA features present in the feature table of sequence AE005174 that contain the string
* "anticodon: TTG" in their annotations, and puts that in a sequence list called "mytrnas". This function is
* meaningful with nucleotide sequence databases only (not with protein databases).
*
* @param seqname The name of a database sequence. Case is not significant.
* @param featurekey A feature key (e.g., CDS, tRNA, ncRNA) that must be directly accessible, that is, one of those
* returned by listDirectFeatureKeys(). Case is not significant.
* @param listname The name to give to the resulting sequence list.
* @param matching An optional string required to be present in the feature's annotations. Case is not significant.
* @return The list of subsequences of <i>seqname</i> that correspond to the specified feature key and, optionally, whose
* annotation contains the matching string, or NULL if no matching sequence exists.
*/
RaaList *getDirectFeature(const std::string &seqname, const std::string &featurekey, const std::string &listname,
const std::string &matching = "");
/**
* @brief Gives all feature keys of the database that can be directly accessed.
*
* These feature keys (e.g., CDS, rRNA, tRNA) can be used with function getDirectFeature(). This function is
* meaningful with nucleotide sequence databases only (not with protein databases).
*
* @return A string vector listing all feature keys of the database that can be directly accessed.
*/
std::vector<std::string> listDirectFeatureKeys();
/**
* @brief Gives all feature keys of the database.
*
* These feature keys (e.g., CDS, conflict, misc_feature) can be used with function prepareGetAnyFeature(). This function is
* meaningful with nucleotide sequence databases only (not with protein databases).
*
* @return A string vector listing all feature keys of the database.
*/
std::vector<std::string> listAllFeatureKeys();
/**
* @brief Starts extraction of all features of a specified key present in the feature table of a database sequence.
*
* A database sequence can contain many instances of a given feature key in its feature table. Thus, feature extraction
* is done by first preparing the desired feature extraction, and by then successively extracting features
* by getNextFeature() calls until no more exist in the feature table or until a call to interruptGetAnyFeature() is done.
* Any successful prepareGetAnyFeature() call must be followed by getNextFeature() calls until
* it returns NULL or by a call to interruptGetAnyFeature(); any call to other RAA member functions in between is prohibited.
*
* @param seqrank The database rank of a sequence.
* @param featurekey Any feature key (direct or not) defined in
* <a href=http://www.ebi.ac.uk/embl/WebFeat/>EMBL/GenBank/DDBJ feature tables</a>. These are also returned by listAllFeatureKeys().
* @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature().
* @throw string A message indicating the cause of the error.
*/
void *prepareGetAnyFeature(int seqrank, const std::string &featurekey) throw(std::string);
/**
* @brief Successively returns features specified in a previous prepareGetAnyFeature() call.
*
* This function must be called repetitively until it returns NULL or until function interruptGetAnyFeature() is called.
* Features are processed in their order of appearance in the feature table.
* @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
* @return A sequence corresponding to one of the features specified in the prepareGetAnyFeature() call, or NULL
* if no more such feature exists.
*/
Sequence *getNextFeature(void *opaque);
/**
* @brief Terminates a features extraction session initiated by a prepareGetAnyFeature() call before getNextFeature() call
* returned NULL.
*
* @param opaque A pointer returned by a previous prepareGetAnyFeature() call.
*/
void interruptGetAnyFeature(void *opaque);
/** @} */
/**
* @name Browsing database species and keywords.
*
* @{
*/
/**
* @brief Loads the database's full species tree classification.
*
* This call takes a few seconds to run on large databases because much data get downloaded from the server.
*
* @param showprogress If true, progress information gets sent to stdout.
* @return An object allowing work with the full species tree (see RaaSpeciesTree), or NULL if error.
*/
RaaSpeciesTree *loadSpeciesTree(bool showprogress=true);
/**
* @brief Frees the memory occupied by the species tree classification.
*
* @param tree An object previously returned by a loadSpeciesTree() call. It is deleted upon return.
*/
void freeSpeciesTree(RaaSpeciesTree *tree);
/**
* @brief Initializes pattern-matching in database keywords. Matching keywords are then returned by successive nextMatchingKeyword() calls.
*
* @param pattern A pattern-matching string using @ as wildcard (example: RNA\@polymerase\@).
* Case is not significant.
* @return The maximum length of any database keyword.
*/
int keywordPattern(const std::string &pattern);
/**
* @brief Finds next matching keyword in database.
*
* @param matching Set to the next matching keyword upon return.
* @return The database rank of the next matching keyword, or 0 if no more matching keyword.
*/
int nextMatchingKeyword(std::string &matching);
/** @} */
protected:
raa_db_access *raa_data;
private:
RaaAddress current_address;
int current_kw_match;
std::string *kw_pattern;
Sequence *getSeq_both(const std::string &name_or_accno, int rank, int maxlength);
};
} //end of namespace bpp.
#endif // _RAA_H_
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