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mapgd
0.4
A program for the Maximum-likelihood analysis of population genomic data.
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Public Member Functions | |
| void | open (const char *, const std::ios_base::openmode &) |
| ! The function that opens a Data_file (if file). | |
| void | open_extention (const char *, const std::ios_base::openmode &) |
| ! Doesn't check extension. | |
| void | open_from (Base_file &) |
| ! Appends to a file. More... | |
| void | open_header (Base_file &) |
| Opens a header for a Flat_file. More... | |
| Data_file & | write (const Data &) |
| Writes a row to the file and advances one row. More... | |
| Data_file & | read (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 (Data &) |
| Read file in binary mode. | |
| void | write_binary (const Data &) |
| Write in binary mode. | |
| virtual void | read_text (Data &) |
| virtual void | write_text (const Data &) |
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. | |
! Appends to a file.
If there is a table open, it is immediately closed. This is because the information that follows may no longer be from the previous class, and the column labels need to changed accordingly. If the Flat_file was not opened in concatenate to disk, then make a new file with the extension T::file_name is created.
Opens a header for a Flat_file.
This method opens a file to the same i/o stream as Base_file iff Base_file is not associated with a file, and creates a file with the extension T:file_name otherwise. Base_file is not closed. This can result in data between the Base_file and the . . . being interspersed, potentially corrupting the file.
Reads a row from the file and advances one row.
Returns the class.
Writes a row to the file and advances one row.
Returns the ostream.
1.8.6