paup.cxx File Reference

#include "input_format.h"
#include "reader.h"
#include "paup.h"
#include "ali.h"

Include dependency graph for paup.cxx:

Go to the source code of this file.

Functions
static void	paup_verify_name (char *&Str)
static void	paup_print_line (const Seq &seq, int offset, int first_line, Writer &write)
static void	paup_print_headerstart (Writer &write)
static void	paup_print_header_counters (Writer &write)
static void	paup_print_header_counters (Writer &write, int total_seq, int maxsize)
static void	paup_print_header (const Paup &paup, Writer &write)
void	to_paup (const FormattedFile &in, const char *outf)

Function Documentation

static void paup_verify_name ( char *&  Str )

static

Definition at line 6 of file paup.cxx.

References str0len(), and TOKENSIZE.

Referenced by to_paup().

static void paup_print_line ( const Seq &  seq, int  offset, int  first_line, Writer &  write  )

static

Definition at line 26 of file paup.cxx.

References Seq::get_id(), Seq::get_len(), Seq::get_seq(), length, Writer::out(), Writer::outf(), and SEQLINE.

Referenced by to_paup().

static void paup_print_headerstart ( Writer &  write )

static

Definition at line 63 of file paup.cxx.

References Writer::out(), Writer::outf(), and today_date().

Referenced by paup_print_header(), and to_paup().

static void paup_print_header_counters ( Writer &  write )

static

Definition at line 70 of file paup.cxx.

References Writer::outf().

Referenced by paup_print_header(), and to_paup().

static void paup_print_header_counters ( Writer &  write, int  total_seq, int  maxsize  )

static

Definition at line 73 of file paup.cxx.

References Writer::outf().

static void paup_print_header ( const Paup &  paup, Writer &  write  )

static

Definition at line 77 of file paup.cxx.

References Paup::equate, Paup::gap, Writer::out(), Writer::outf(), paup_print_header_counters(), and paup_print_headerstart().

Referenced by to_paup().

void to_paup	(	const FormattedFile &	in,
		const char *	outf
	)

Definition at line 88 of file paup.cxx.

References ARB_strdup(), ca_assert, FileWriter::expect_written(), Alignment::get(), Alignment::get_count(), FileWriter::get_FILE(), Alignment::get_len(), Alignment::get_max_len(), Alignment::getSeqPtr(), is_input_format(), NEXUS, FileWriter::out(), paup_print_header(), paup_print_header_counters(), paup_print_headerstart(), paup_print_line(), paup_verify_name(), read_alignment(), seq, FileWriter::seq_done(), SEQLINE, throw_conversion_not_supported(), and FormattedFile::type().

Referenced by convert().