group_search.h File Reference

#include <lazy.h>
#include <query_expr.h>
#include <arbdb_base.h>
#include <arbtools.h>
#include <arb_error.h>
#include <smartptr.h>
#include <cb.h>
#include <vector>
#include <set>
#include <list>
#include <string>

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Classes
struct	ColumnWidths
class	FoundGroup
class	QueriedGroups
class	GroupSearch

Macros
#define	gs_assert(cond)   arb_assert(cond)

Typedefs
typedef std::set< GBDATA * >	GBDATAset
typedef std::set< std::string >	SpeciesNames
typedef std::vector< FoundGroup >	FoundGroupContainer
typedef FoundGroupContainer::const_iterator	FoundGroupCIter
typedef FoundGroupContainer::iterator	FoundGroupIter
typedef std::list < GroupSortCriterion >	SortCriteria
typedef std::set< std::string >	WordSet
typedef std::set< std::string >	TreeNameSet

Enumerations
enum	GroupFoldingMode {   GFM_EXPAND = 1, GFM_TOGGLE = 2, GFM_RECURSE = 4, GFM_PARENTS_ONLY = 8,   GFM_COLLAPSE_REST = 16, GFM_COLLAPSE = 0, GFM_EXPANDREC = GFM_EXPAND|GFM_RECURSE, GFM_EXPANDPARENTS = GFM_EXPAND|GFM_RECURSE|GFM_PARENTS_ONLY,   GFM_EXPANDREC_COLLREST = GFM_EXPANDREC|GFM_COLLAPSE_REST }
enum	GroupMarkMode { GMM_UNMARK = 0, GMM_MARK = 1, GMM_INVERT = 2 }
enum	CollectMode { INTERSECT, UNITE }
enum	CriterionOperator { CO_AND, CO_OR, CO_IGNORE }
enum	CriterionMatch { CM_MATCH, CM_MISMATCH }
enum	CriterionType {   CT_NAME, CT_PARENT_DIRECT, CT_PARENT_ANY, CT_PARENT_ALL,   CT_NESTING_LEVEL, CT_FOLDED, CT_SIZE, CT_MARKED,   CT_MARKED_PC, CT_ZOMBIES, CT_AID, CT_KEELED }
enum	GroupSortCriterion {   GSC_NONE, GSC_REVERSE, GSC_NAME, GSC_TREENAME,   GSC_TREEORDER, GSC_HIT_REASON, GSC_NESTING, GSC_SIZE,   GSC_MARKED, GSC_MARKED_PC, GSC_CLUSTER, GSC_AID,   GSC_KEELED }
enum	DupNameCriterionType { DNC_WHOLENAME, DNC_WORDWISE }
enum	DupTreeCriterionType { DLC_SAME_TREE, DLC_DIFF_TREE, DLC_ANYWHERE }
enum	GroupSearchMode {   GSM_FORGET_EXISTING = 1, GSM_ADD = 2, GSM_MISMATCH = 4, GSM_FIND = GSM_FORGET_EXISTING|GSM_ADD,   GSM_KEEP = 0, GSM_REMOVE = GSM_KEEP|GSM_MISMATCH, GSM_MATCH = 0 }

Functions
	DECLARE_CBTYPE_FVV_AND_BUILDERS (GroupSearchCallback, void, class GroupSearch *)
char *	GS_calc_resulting_groupname (GBDATA *gb_main, const QueriedGroups &queried, int hit_idx, const char *input_name, const char *acisrt, ARB_ERROR &error)

Macro Definition Documentation

#define gs_assert

(

cond

)

arb_assert(cond)

Definition at line 48 of file group_search.h.

Referenced by QueriedGroups::add_informed_group(), GroupCluster::allow_lookup(), Clusterer::buildInferableClusterStartingWith(), Clusterer::calc_max_used_words(), FoundGroup::change_folding(), FINAL_TYPE< SEQTYPE >::compute_tree(), GroupCluster::contains(), criterion_awar_name(), ParentCache::defineParentOf(), FoundGroup::delete_from_DB(), Clusterer::deliverCluster(), DupCriteria::DupCriteria(), DupNameCriterion::DupNameCriterion(), GroupCluster::erase(), Clusterer::find_and_deliverTo(), Clusterer::findBestClusterBasedOnWords(), FoundGroup::get_aid(), TargetGroup::get_clade(), GroupRename_callenv::get_dupidx(), TargetGroup::get_group(), QueriedGroups::get_group_display(), FoundGroup::get_keeled(), TargetGroup::get_keeledStateInfo(), SearchedTree::get_load_error(), FoundGroup::get_marked(), FoundGroup::get_marked_pc(), FoundGroup::get_nesting(), FoundGroup::get_size(), grl_dupidx(), group_set_folded(), Candidate::inform_group(), GroupCluster::insert(), isCorrectParent(), SymmetricMatrixMapper::linear_index(), DupNameCriterion::name_matches_wordwise(), compare_by_criteria::operator()(), QueriedGroups::operator[](), ParentGroupNameQueryKey::ParentGroupNameQueryKey(), GroupSearch::perform_search(), FoundGroup::rename_by_ACI(), SearchedTree::SearchedTree(), FoundGroup::set_cluster_id(), GroupSearch::setDupCriteria(), string2WordSet(), SymmetricMatrixMapper::SymmetricMatrixMapper(), FoundGroup::track_max_widths(), and GroupSearchCommon::~GroupSearchCommon().

Typedef Documentation

typedef std::set<GBDATA*> GBDATAset

Definition at line 229 of file group_search.h.

typedef std::set<std::string> SpeciesNames

Definition at line 232 of file group_search.h.

typedef std::vector<FoundGroup> FoundGroupContainer

Definition at line 233 of file group_search.h.

typedef FoundGroupContainer::const_iterator FoundGroupCIter

Definition at line 234 of file group_search.h.

typedef FoundGroupContainer::iterator FoundGroupIter

Definition at line 235 of file group_search.h.

typedef std::list<GroupSortCriterion> SortCriteria

Definition at line 253 of file group_search.h.

typedef std::set<std::string> WordSet

Definition at line 309 of file group_search.h.

typedef std::set<std::string> TreeNameSet

Definition at line 318 of file group_search.h.

Enumeration Type Documentation

enum GroupFoldingMode

Enumerator
GFM_EXPAND
GFM_TOGGLE
GFM_RECURSE
GFM_PARENTS_ONLY
GFM_COLLAPSE_REST
GFM_COLLAPSE
GFM_EXPANDREC
GFM_EXPANDPARENTS
GFM_EXPANDREC_COLLREST

Definition at line 52 of file group_search.h.

enum GroupMarkMode

Enumerator
GMM_UNMARK
GMM_MARK
GMM_INVERT

Definition at line 66 of file group_search.h.

enum CollectMode

Enumerator
INTERSECT
UNITE

Definition at line 72 of file group_search.h.

enum CriterionOperator

Enumerator
CO_AND
CO_OR
CO_IGNORE

Definition at line 77 of file group_search.h.

enum CriterionMatch

Enumerator
CM_MATCH
CM_MISMATCH

Definition at line 82 of file group_search.h.

enum CriterionType

Enumerator
CT_NAME
CT_PARENT_DIRECT
CT_PARENT_ANY
CT_PARENT_ALL
CT_NESTING_LEVEL
CT_FOLDED
CT_SIZE
CT_MARKED
CT_MARKED_PC
CT_ZOMBIES
CT_AID
CT_KEELED

Definition at line 86 of file group_search.h.

enum GroupSortCriterion

Enumerator
GSC_NONE
GSC_REVERSE
GSC_NAME
GSC_TREENAME
GSC_TREEORDER
GSC_HIT_REASON
GSC_NESTING
GSC_SIZE
GSC_MARKED
GSC_MARKED_PC
GSC_CLUSTER
GSC_AID
GSC_KEELED

Definition at line 237 of file group_search.h.

enum DupNameCriterionType

Enumerator
DNC_WHOLENAME
DNC_WORDWISE

Definition at line 297 of file group_search.h.

enum DupTreeCriterionType

Enumerator
DLC_SAME_TREE
DLC_DIFF_TREE
DLC_ANYWHERE

Definition at line 303 of file group_search.h.

enum GroupSearchMode

Enumerator
GSM_FORGET_EXISTING
GSM_ADD
GSM_MISMATCH
GSM_FIND
GSM_KEEP
GSM_REMOVE
GSM_MATCH

Definition at line 320 of file group_search.h.

Function Documentation

DECLARE_CBTYPE_FVV_AND_BUILDERS	(	GroupSearchCallback	,
		void	,
		class GroupSearch *
	)

char* GS_calc_resulting_groupname	(	GBDATA *	gb_main,
		const QueriedGroups &	queried,
		int	hit_idx,
		const char *	input_name,
		const char *	acisrt,
		ARB_ERROR &	error
	)

Definition at line 2130 of file group_search.cxx.

References GB_await_error(), GB_command_interpreter_in_env(), GBS_global_string(), GBS_trim(), get_GroupRename_customized_ACI_commands(), FoundGroup::get_tree_name(), NULp, result, QueriedGroups::size(), and ta.

Referenced by FoundGroup::rename_by_ACI().