NT_tree_cmp.cxx File Reference

#include "NT_species_set.h"
#include <aw_msg.hxx>
#include <gb_aci.h>
#include <gb_aci_impl.h>
#include <arb_progress.h>
#include <arb_defs.h>
#include <arb_msg_nospam.h>
#include <string>
#include <climits>

Include dependency graph for NT_tree_cmp.cxx:

Go to the source code of this file.

Classes
class	GroupXfer_callenv

Macros
#define	IMPL_FORMATVALUE_CMD(args, fmt, value)

Functions
const GroupXfer_callenv &	custom_env (GBL_command_arguments *args)
const GroupPenalty &	custom_match (GBL_command_arguments *args)
static GB_ERROR	gxl_groupname (GBL_command_arguments *args)
static GB_ERROR	gxl_penalty (GBL_command_arguments *args)
static GB_ERROR	gxl_ingroup (GBL_command_arguments *args)
static GB_ERROR	gxl_outgroup (GBL_command_arguments *args)
static GB_ERROR	gxl_oldsize (GBL_command_arguments *args)
static GB_ERROR	gxl_newsize (GBL_command_arguments *args)
static GB_ERROR	gxl_unknown (GBL_command_arguments *args)
static GB_ERROR	gxl_keeled (GBL_command_arguments *args)
static const GBL_command_lookup_table &	get_GroupXfer_customized_ACI_commands ()
GB_ERROR	NTREE_move_tree_info (GBDATA *gb_main, const char *tree_source, const char *tree_dest, const char *log_file, GroupTransferMode mode, GroupsToTransfer what, const GroupMatchScorer &scorer, const char *aci)

Variables
static GBL_command_definition	groupXfer_command_table []

Macro Definition Documentation

#define IMPL_FORMATVALUE_CMD	(		args,
			fmt,
			value
	)

Value:

COMMAND_DROPS_INPUT_STREAMS(args);          \
    GB_ERROR error = check_no_parameter(args);  \
    if (!error) FORMAT_2_OUT(args, fmt, value); \
    return error

Definition at line 428 of file NT_tree_cmp.cxx.

Referenced by gxl_groupname(), gxl_ingroup(), gxl_keeled(), gxl_newsize(), gxl_oldsize(), gxl_outgroup(), gxl_penalty(), and gxl_unknown().

Function Documentation

const GroupXfer_callenv& custom_env ( GBL_command_arguments *  args )

inline

Definition at line 423 of file NT_tree_cmp.cxx.

References DOWNCAST_REFERENCE, and GBL_command_arguments::get_callEnv().

Referenced by custom_match(), gxl_groupname(), gxl_newsize(), and gxl_oldsize().

const GroupPenalty& custom_match ( GBL_command_arguments *  args )

inline

Definition at line 424 of file NT_tree_cmp.cxx.

References custom_env(), and GroupXfer_callenv::get_match().

Referenced by gxl_ingroup(), gxl_keeled(), gxl_outgroup(), gxl_penalty(), and gxl_unknown().

static GB_ERROR gxl_groupname ( GBL_command_arguments *  args )

static

Definition at line 434 of file NT_tree_cmp.cxx.

References custom_env(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_penalty ( GBL_command_arguments *  args )

static

Definition at line 435 of file NT_tree_cmp.cxx.

References custom_match(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_ingroup ( GBL_command_arguments *  args )

static

Definition at line 436 of file NT_tree_cmp.cxx.

References custom_match(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_outgroup ( GBL_command_arguments *  args )

static

Definition at line 437 of file NT_tree_cmp.cxx.

References custom_match(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_oldsize ( GBL_command_arguments *  args )

static

Definition at line 438 of file NT_tree_cmp.cxx.

References custom_env(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_newsize ( GBL_command_arguments *  args )

static

Definition at line 439 of file NT_tree_cmp.cxx.

References custom_env(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_unknown ( GBL_command_arguments *  args )

static

Definition at line 440 of file NT_tree_cmp.cxx.

References custom_match(), and IMPL_FORMATVALUE_CMD.

static GB_ERROR gxl_keeled ( GBL_command_arguments *  args )

static

Definition at line 441 of file NT_tree_cmp.cxx.

References custom_match(), and IMPL_FORMATVALUE_CMD.

static const GBL_command_lookup_table& get_GroupXfer_customized_ACI_commands ( )

static

Definition at line 455 of file NT_tree_cmp.cxx.

References ACI_get_standard_commands(), and ARRAY_ELEMS.

Referenced by SpecSetRegistry::write_node_information().

GB_ERROR NTREE_move_tree_info	(	GBDATA *	gb_main,
		const char *	tree_source,
		const char *	tree_dest,
		const char *	log_file,
		GroupTransferMode	mode,
		GroupsToTransfer	what,
		const GroupMatchScorer &	scorer,
		const char *	aci
	)

Definition at line 603 of file NT_tree_cmp.cxx.

References GroupMatchScorer::check_validity(), COMPARE_TOPOLOGY, TreeNode::count_clades(), AP_tree::count_leafs(), arb_progress::done(), error(), SpecSetRegistry::find_best_matches_info(), SpecSetRegistry::finish(), fputs(), GB_begin_transaction(), GB_end_transaction(), GB_export_errorf(), GB_IO_error(), GBK_terminatef(), GBS_global_string_copy(), GBT_log_to_tree_remark(), GBT_overwrite_tree(), ARB_seqtree_root::get_gb_tree(), TreeNode::get_root_node(), KEEP_OLD_NAMES, leafs_2_nodes(), ARB_seqtree_root::linkToDB(), AP_tree_root::loadFromDB(), nt_assert, NULp, SpecSetRegistry::registerTree(), REMOVE_EXISTING_GROUPS, ROOTED, SpecSetRegistry::search_best_match(), SpecSet::set_node, TreeNode::set_root(), SpecSetRegistry::setScorer(), arb_progress::subtitle(), swap(), SpecSetRegistry::write_node_information(), and XFER_GROUPS_WITH_MARKED.

Referenced by ad_move_tree_info().

Variable Documentation

GBL_command_definition groupXfer_command_table[]

static

Initial value:

= {
    { "groupname", gxl_groupname },
    { "penalty",   gxl_penalty },
    { "ingroup",   gxl_ingroup },
    { "outgroup",  gxl_outgroup },
    { "oldsize",   gxl_oldsize },
    { "newsize",   gxl_newsize },
    { "unknown",   gxl_unknown },
    { "keeled",    gxl_keeled },
    { NULp, NULp }
}

Definition at line 443 of file NT_tree_cmp.cxx.