TreeRead.h File Reference

#include <arbdbt.h>

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Macros
#define	DEFAULT_BRANCH_LENGTH_MARKER   -1000.0

Functions
bool	is_marked_as_default_len (GBT_LEN len)
void	TREE_scale (TreeNode *tree, double length_scale, double bootstrap_scale)
TreeNode *	TREE_load (const char *path, TreeRoot *troot, char **commentPtr, bool allow_length_scaling, char **warningPtr)
GB_ERROR	TREE_load_to_db (GBDATA *gb_main, const char *treefile, const char *tree_name)

Macro Definition Documentation

#define DEFAULT_BRANCH_LENGTH_MARKER   -1000.0

Definition at line 19 of file TreeRead.h.

Referenced by is_marked_as_default_len(), and TreeReader::load().

Function Documentation

bool is_marked_as_default_len ( GBT_LEN  len )

inline

Definition at line 20 of file TreeRead.h.

References DEFAULT_BRANCH_LENGTH_MARKER.

Referenced by TREE_scale().

void TREE_scale	(	TreeNode *	tree,
		double	length_scale,
		double	bootstrap_scale
	)

Definition at line 14 of file TreeTools.cxx.

References DEFAULT_BRANCH_LENGTH, TreeNode::is_leaf(), is_marked_as_default_len(), TreeNode::leftlen, TreeNode::leftson, TreeNode::parse_bootstrap(), REMARK_BOOTSTRAP, REMARK_NONE, REMARK_OTHER, TreeNode::remove_remark(), TreeNode::rightlen, TreeNode::rightson, and TreeNode::set_bootstrap().

Referenced by main(), and TREE_load().

TreeNode* TREE_load	(	const char *	path,
		TreeRoot *	troot,
		char **	commentPtr,
		bool	allow_length_scaling,
		char **	warningPtr
	)

Definition at line 620 of file TreeRead.cxx.

References TreeRoot::delete_by_node(), destroy(), error(), TreeReader::error, GB_export_errorf(), GBS_global_string(), GBS_log_action_to(), TreeReader::get_max_found_bootstrap(), TreeReader::get_max_found_branchlen(), TreeReader::get_warnings(), TreeNode::is_leaf(), TreeReader::load(), name_only(), NULp, TreeReader::takeComment(), tree, tree_assert, and TREE_scale().

Referenced by ARB_main(), build_consensus_tree(), main(), and TREE_load_to_db().

GB_ERROR TREE_load_to_db	(	GBDATA *	gb_main,
		const char *	treefile,
		const char *	tree_name
	)

Definition at line 701 of file TreeRead.cxx.

References GB_transaction::close(), destroy(), error(), GB_await_error(), GBT_message(), GBT_write_tree_with_remark(), NULp, ta, TREE_load(), and warnings.

Referenced by calc_pvp(), and tree_load_cb().