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mapgd
0.4
A program for the Maximum-likelihood analysis of population genomic data.
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An interface for reading and writing data specified outside of mapgd. More...
#include <external-file.h>


Public Member Functions | |
| void | open (const char *, const std::ios_base::openmode &) |
| ! The function that opens a External_file (if file). | |
| External_file & | write (const External_data &) |
| Writes a row to the file and advances one row. More... | |
| External_file & | read (External_data &) |
| Reads a row from the file and advances one row. More... | |
Public Member Functions inherited from Base_file | |
| const std::fstream::openmode & | openmode () |
| returns the open mode. | |
| const std::string & | filename () |
| returns the filename. | |
| Base_file () | |
| returns the concatenated flag. More... | |
| void | open_no_extention (const char *, const std::ios::openmode &) |
| The function that opens a indexed_file (if file). | |
| void | open (const std::ios::openmode &) |
| Opens a Base_file to the cin/cout. | |
| void | open (std::iostream *, const std::ios_base::openmode &) |
| Opens a Base_file to an istream. | |
| void | open (std::istream *, const std::ios_base::openmode &) |
| Opens a Base_file to an istream. | |
| void | open (std::ostream *, const std::ios_base::openmode &) |
| Opens a Base_file to an istream. | |
| std::istream * | get_in (void) |
| returns the istream. | |
| std::ostream * | get_out (void) |
| returns the ostream. | |
| void | close (void) |
| Close iostreams, writes tail, etc. | |
| void | close_table (void) |
| Ends table w/o closing iostreams. | |
| bool | is_open (void) const |
| Returns true iff Base_file is open. | |
| bool | table_is_open (void) const |
| Returns true iff a table is open in Base_file. | |
| bool | binary (void) const |
| Returns true iff a table is open in binary mode. | |
| Data * | read_header (void) |
| Returns a pointer to a new instance of the derived data class. | |
| void | write_header (const Data *) |
| void | write_header (const File_index &, const Data *) |
| Base_file & | read (Data *) |
| Reads from the istream. | |
| Base_file & | read (File_index &, Indexed_data *) |
| Base_file & | write (const Data *) |
| Writes to the ostream. | |
| Base_file & | write (File_index &, const Indexed_data *) |
| void | seek (const std::streampos &pos) |
| sets in and out (for reading and writing) to position pos. | |
| void | seekg (const std::streampos &pos) |
| sets in (for reading) to position pos. | |
| void | seekp (const std::streampos &pos) |
| sets out (for writing) to position pos. | |
| void | seek (std::streampos pos, std::ios_base::seekdir way) |
| TODO. | |
| void | seekg (std::streampos off, std::ios_base::seekdir way) |
| TODO. | |
| void | seekp (std::streampos off, std::ios_base::seekdir way) |
| TODO. | |
| std::streampos | tellp (void) |
| Tells streampos of out (writing) | |
| std::streampos | tellg (void) |
| Tells streampos of in (reading) | |
| void | set_delim (const char &) |
| Sets the delimiter that separates columns. Only used in text mode. | |
| const char & | get_delim (void) const |
| Gets the delimiter that separates columns. Only used in text mode. | |
| size_t | size (void) const |
| Returns the number of rows in the file. More... | |
| bool | eof (void) |
| bool | indexed (void) const |
| bool | concatenated (void) |
| bool | check_concatenated (void) |
| bool | check_compressed (void) |
Protected Member Functions | |
| void | read_binary (External_data &) |
| Read file in binary mode. | |
| void | write_binary (const External_data &) |
| Write in binary mode. | |
| virtual void | read_text (External_data &) |
| virtual void | write_text (const External_data &) |
| Read file in text mode. | |
Additional Inherited Members | |
Protected Attributes inherited from Base_file | |
| bool | open_ |
| indicates whether the iostream opened succesfully | |
| bool | table_open_ |
| indicates whether the header has been read successfully | |
| bool | concatenated_ |
| indicates whether multiple tables are included in the file | |
| bool | compressed_ |
| indicates whether the input/output stream is compressed. | |
| char | delim_column_ |
| The delimiter which separates columns. | |
| bool | read_ |
| File is open for reading. | |
| bool | write_ |
| File is open for writing. | |
| bool | binary_ |
| Binary mode flag. | |
| bool | try_binary_ |
| Attempt to set binary mode flag. | |
| bool | indexed_ |
| Indexed mode flag. | |
| std::istream * | in_ |
| All data is read from in. | |
| std::ostream * | out_ |
| All data is written is written to out. | |
| Tmp_buffer | buffer_ |
| a buffer which can be rewound. | |
| std::fstream | file_ |
| The file to read data from. | |
| igzstream | gzin_ |
| compressed istream. | |
| ogzstream | gzout_ |
| compressed ostream. | |
| std::ios::openmode | openmode_ |
| stores information about the mode in which the file was opened. | |
| std::string | filename_ |
| The name of the file if opened. | |
An interface for reading and writing data specified outside of mapgd.
Because we do not know the interanl structure of the external data, we ...
in the table, which must store a pair of IDs retrived by the get_id0() and get_id1() member functions. Additionally, data types must return a name for the table in the database where the data may be stored with member function table_name(), and must name the columns of the table with cannonical data types listed in the file ?. This allows data to easily be transfered into and out of a database. Finally...
| External_file& External_file< External_data >::read | ( | External_data & | ) |
Reads a row from the file and advances one row.
Returns the class.
| External_file& External_file< External_data >::write | ( | const External_data & | ) |
Writes a row to the file and advances one row.
Returns the ostream.
1.8.6