#include <TreeWrite.h>
#include <TreeNode.h>
#include <arb_strbuf.h>
#include <arb_file.h>
#include <xml.hxx>

Include dependency graph for TreeWrite.cxx:

Macros
#define	tree_assert(cond) arb_assert(cond)

Functions
void	replace_by_underscore (char str, const char toReplace)

bool	isQuoteChar (char c)

bool	whole_label_quoted (const char *label, size_t length)

char	first_non_ascii_char (const char *label)

static GB_ERROR	export_tree_label (const char label, FILE out, LabelQuoting qmode)

void	indentTo (int indent, FILE *out)

static GB_ERROR	export_tree_node_print (GBDATA gb_main, FILE out, TreeNode tree, const char tree_name, bool pretty, int indent, const TreeLabeler &labeler, bool save_branchlengths, bool save_bootstraps, bool save_groupnames, LabelQuoting qmode)

string	buildNodeIdentifier (const string &parent_id, int &son_counter)

static const char *	export_tree_node_print_xml (GBDATA gb_main, TreeNode tree, double my_length, const char *tree_name, const TreeLabeler &labeler, bool skip_folded, const string &parent_id, int &parent_son_counter)

GB_ERROR	TREE_write_XML (GBDATA gb_main, const char db_name, const char tree_name, const TreeLabeler &labeler, bool skip_folded, const char path)

static char *	complete_newick_comment (const char *comment)

GB_ERROR	TREE_write_Newick (GBDATA gb_main, const char tree_name, const TreeLabeler &labeler, bool save_branchlengths, bool save_bootstraps, bool save_groupnames, bool pretty, LabelQuoting quoteMode, const char *path)

static void	export_tree_node_print_remove (char *str)

static void	export_tree_rek (TreeNode tree, FILE out, bool export_branchlens, bool dquot)

GB_ERROR	TREE_export_tree (GBDATA , FILE out, TreeNode *tree, bool triple_root, bool export_branchlens, bool dquot)

Macro Definition Documentation

#define tree_assert ( cond ) arb_assert(cond)

Definition at line 19 of file TreeWrite.cxx.

Referenced by complete_newick_comment(), export_tree_label(), export_tree_node_print_xml(), and TREE_write_Newick().

Function Documentation

void replace_by_underscore	(	char *	str,
		const char *	toReplace
	)

inline

Definition at line 21 of file TreeWrite.cxx.

Referenced by export_tree_label().

bool isQuoteChar ( char c )

inline

Definition at line 29 of file TreeWrite.cxx.

Referenced by whole_label_quoted().

bool whole_label_quoted	(	const char *	label,
		size_t	length
	)

inline

Definition at line 30 of file TreeWrite.cxx.

References isQuoteChar().

Referenced by export_tree_label().

char first_non_ascii_char ( const char * label )

inline

Definition at line 40 of file TreeWrite.cxx.

Referenced by export_tree_label().

static GB_ERROR export_tree_label	(	const char *	label,
		FILE *	out,
		LabelQuoting	qmode
	)

static

Definition at line 49 of file TreeWrite.cxx.

References ARB_strduplen(), error(), first_non_ascii_char(), fputc(), fputs(), GBS_global_string(), LABEL_ACCEPT_NON_ASCII, LABEL_DOUBLE_QUOTES, LABEL_FORCE_QUOTES, LABEL_FORCE_REPLACE, LABEL_SINGLE_QUOTES, NULp, replace_by_underscore(), safeCharIndex(), tree_assert, and whole_label_quoted().

Referenced by export_tree_node_print().

void indentTo	(	int	indent,
		FILE *	out
	)

inline

Definition at line 123 of file TreeWrite.cxx.

Referenced by export_tree_node_print().

static GB_ERROR export_tree_node_print	(	GBDATA *	gb_main,
		FILE *	out,
		TreeNode *	tree,
		const char *	tree_name,
		bool	pretty,
		int	indent,
		const TreeLabeler &	labeler,
		bool	save_branchlengths,
		bool	save_bootstraps,
		bool	save_groupnames,
		LabelQuoting	qmode
	)

static

Definition at line 130 of file TreeWrite.cxx.

References arb_assert, error(), export_tree_label(), fputc(), fputs(), TreeNode::gb_node, GBS_global_string(), GBS_global_string_copy(), TreeNode::get_remark(), group, TreeNode::has_group_info(), indentTo(), TreeNode::is_leaf(), TreeNode::keelTarget(), label, TreeNode::leftlen, NULp, TreeNode::parse_bootstrap(), REMARK_BOOTSTRAP, REMARK_NONE, REMARK_OTHER, TreeNode::rightlen, and TreeLabeler::speciesLabel().

Referenced by TREE_write_Newick().

string buildNodeIdentifier	(	const string &	parent_id,
		int &	son_counter
	)

inline

Definition at line 200 of file TreeWrite.cxx.

References GBS_global_string().

Referenced by export_tree_node_print_xml().

static const char* export_tree_node_print_xml	(	GBDATA *	gb_main,
		TreeNode *	tree,
		double	my_length,
		const char *	tree_name,
		const TreeLabeler &	labeler,
		bool	skip_folded,
		const string &	parent_id,
		int &	parent_son_counter
	)

static

Definition at line 206 of file TreeWrite.cxx.

References buildNodeIdentifier(), error(), GB_entry(), TreeNode::gb_node, GB_read_byte(), GBS_global_string(), GBS_global_string_copy(), GBT_count_leafs(), TreeNode::is_leaf(), TreeNode::leftlen, TreeNode::name, NULp, TreeNode::parse_bootstrap(), REMARK_BOOTSTRAP, REMARK_NONE, REMARK_OTHER, TreeNode::rightlen, TreeLabeler::speciesLabel(), and tree_assert.

Referenced by TREE_write_XML().

GB_ERROR TREE_write_XML	(	GBDATA *	gb_main,
		const char *	db_name,
		const char *	tree_name,
		const TreeLabeler &	labeler,
		bool	skip_folded,
		const char *	path
	)

Definition at line 283 of file TreeWrite.cxx.

References ARB_date_string(), error(), export_tree_node_print_xml(), GB_await_error(), GB_entry(), GB_export_errorf(), GB_read_string(), GBT_find_tree(), GBT_link_tree(), GBT_read_tree(), NULp, and ta.

Referenced by tree_save_cb().

static char* complete_newick_comment ( const char * comment )

static

Definition at line 323 of file TreeWrite.cxx.

References GBS_strstruct::put(), GBS_strstruct::release(), and tree_assert.

Referenced by TREE_write_Newick().

GB_ERROR TREE_write_Newick	(	GBDATA *	gb_main,
		const char *	tree_name,
		const TreeLabeler &	labeler,
		bool	save_branchlengths,
		bool	save_bootstraps,
		bool	save_groupnames,
		bool	pretty,
		LabelQuoting	quoteMode,
		const char *	path
	)