group_search.cxx File Reference

#include "group_search.h"
#include <arb_strarray.h>
#include <arb_progress.h>
#include <arb_sort.h>
#include <arb_strbuf.h>
#include <arb_defs.h>
#include <gb_aci_impl.h>
#include <ad_cb.h>
#include <TreeNode.h>
#include <map>
#include <stack>
#include <arb_misc.h>
#include <arb_msg_nospam.h>

Include dependency graph for group_search.cxx:

Go to the source code of this file.

Classes
class	FINAL_TYPE< SEQTYPE >
	xml element More...
class	FINAL_TYPE< SEQTYPE >
	xml element More...
class	SearchedTree
class	ParentCache
class	GroupSearchCommon
class	Candidate
class	TargetGroup
struct	GroupInfo
class	DupNameCriterion
class	GroupCluster
class	DupCriteria
class	SymmetricMatrixMapper
class	Clusterer
struct	has_been_deleted
struct	was_modified
struct	compare_by_criteria
struct	GroupRename_callenv
struct	GroupNameQueryKey
struct	GroupFoldedKey
struct	GroupAIDkey
struct	GroupSizeKey
struct	GroupKeeledKey
struct	GroupZombiesKey
class	GroupMarkedKey
class	NestingLevelKey
class	ParentGroupNameQueryKey

Macros
#define	TRIGGER_UPDATE_GROUP_RESULTS   "/tmp/trigger/group_result_update"

Typedefs
typedef SmartPtr< GroupSearchRoot >	GroupSearchRootPtr
typedef vector< SearchedTree >	SearchedTreeContainer
typedef SearchedTreeContainer::iterator	SearchedTreeIter
typedef list< Candidate >	CandidateList
typedef vector< GroupInfo >	GroupInfoVec
typedef set< int >	GroupClusterSet
typedef GroupClusterSet::const_iterator	GroupClusterCIter

Functions
bool	group_is_folded (GBDATA *gb_group)
ARB_ERROR	group_set_folded (GBDATA *gb_group, bool folded)
static void	tree_node_deleted_cb (GBDATA *gb_node, GroupSearchCommon *common, GB_CB_TYPE cbtype)
static void	group_name_changed_cb (GBDATA *gb_group_name, GroupSearchCommon *common)
static void	result_update_cb (GBDATA *, GroupSearchCommon *common)
static void	collect_searched_trees (GBDATA *gb_main, const TreeNameSet &trees_to_search, SearchedTreeContainer &searched_tree)
bool	isCorrectParent (TreeNode *node, GBDATA *gb_group, GBDATA *gb_parent_group)
bool	contains (const WordSet &ws, const string &w)
bool	contains (const WordSet &ws, const char *w)
static void	string2WordSet (const char *name, WordSet &words, const char *wordSeparators, const WordSet &ignored_words)
void	string_to_lower (string &s)
unsigned long	permutations (int elems)
const GroupRename_callenv &	custom_gr_env (GBL_command_arguments *args)
static GB_ERROR	grl_hitidx (GBL_command_arguments *args)
static GB_ERROR	grl_dupidx (GBL_command_arguments *args)
static GB_ERROR	grl_hitcount (GBL_command_arguments *args)
static GB_ERROR	grl_groupsize (GBL_command_arguments *args)
static GB_ERROR	grl_markedingroup (GBL_command_arguments *args)
static GB_ERROR	grl_aid (GBL_command_arguments *args)
static GB_ERROR	grl_nesting (GBL_command_arguments *args)
static const GBL_command_lookup_table &	get_GroupRename_customized_ACI_commands ()
char *	GS_calc_resulting_groupname (GBDATA *gb_main, const QueriedGroups &queried, int hit_idx, const char *input_name, const char *acisrt, ARB_ERROR &error)
static void	set_marks_of (const SpeciesNames &targetSpecies, GBDATA *gb_main, GroupMarkMode mode)

Variables
static GBL_command_definition	groupRename_command_table []

Macro Definition Documentation

#define TRIGGER_UPDATE_GROUP_RESULTS   "/tmp/trigger/group_result_update"

Definition at line 419 of file group_search.cxx.

Typedef Documentation

typedef SmartPtr<GroupSearchRoot> GroupSearchRootPtr

Definition at line 132 of file group_search.cxx.

typedef vector<SearchedTree> SearchedTreeContainer

Definition at line 187 of file group_search.cxx.

typedef SearchedTreeContainer::iterator SearchedTreeIter

Definition at line 188 of file group_search.cxx.

typedef list<Candidate> CandidateList

Definition at line 674 of file group_search.cxx.

typedef vector<GroupInfo> GroupInfoVec

Definition at line 969 of file group_search.cxx.

typedef set<int> GroupClusterSet

Definition at line 1051 of file group_search.cxx.

typedef GroupClusterSet::const_iterator GroupClusterCIter

Definition at line 1052 of file group_search.cxx.

Function Documentation

bool group_is_folded ( GBDATA *  gb_group )

inline

Definition at line 274 of file group_search.cxx.

References GB_entry(), and GB_read_byte().

Referenced by FoundGroup::is_folded(), and FoundGroup::overlap_is_folded().

ARB_ERROR group_set_folded ( GBDATA *  gb_group, bool  folded  )

inline

Definition at line 279 of file group_search.cxx.

References error(), GB_await_error(), GB_BYTE, GB_create(), GB_entry(), GB_write_byte(), and gs_assert.

static void tree_node_deleted_cb ( GBDATA *  gb_node, GroupSearchCommon *  common, GB_CB_TYPE  cbtype  )

static

Definition at line 496 of file group_search.cxx.

References GB_CB_DELETE, GB_entry(), GroupSearchCommon::notify_deleted(), and GroupSearchCommon::notify_modified().

static void group_name_changed_cb ( GBDATA *  gb_group_name, GroupSearchCommon *  common  )

static

Definition at line 512 of file group_search.cxx.

References GB_get_father(), and GroupSearchCommon::notify_modified().

static void result_update_cb ( GBDATA *  , GroupSearchCommon *  common  )

static

Definition at line 518 of file group_search.cxx.

References GroupSearchCommon::refresh_all_results().

static void collect_searched_trees ( GBDATA *  gb_main, const TreeNameSet &  trees_to_search, SearchedTreeContainer &  searched_tree  )

static

Definition at line 571 of file group_search.cxx.

References GBT_get_tree_names().

Referenced by GroupSearch::fold_found_groups(), and GroupSearch::perform_search().

bool isCorrectParent ( TreeNode *  node, GBDATA *  gb_group, GBDATA *  gb_parent_group  )

inline

check correctness of parent (caching)

Parameters

node	the TreeNode where clade is shown in tree
gb_group	the group data related to node (at node for normal groups; at parent-node for keeled groups)
gb_parent_group	the parent group data (may be NULp)

Returns

true if gb_parent_group is the correct parent

Definition at line 677 of file group_search.cxx.

References TreeNode::find_parent_with_groupInfo(), TreeNode::gb_node, gs_assert, TreeNode::is_keeled_group(), TreeNode::is_normal_group(), TreeNode::keelTarget(), and NULp.

Referenced by GroupSearch::perform_search().

bool contains ( const WordSet &  ws, const string &  w  )

inline

Definition at line 927 of file group_search.cxx.

Referenced by contains(), DupNameCriterion::name_matches_wordwise(), and string2WordSet().

bool contains ( const WordSet &  ws, const char *  w  )

inline

Definition at line 928 of file group_search.cxx.

References contains().

static void string2WordSet ( const char *  name, WordSet &  words, const char *  wordSeparators, const WordSet &  ignored_words  )

static

Definition at line 930 of file group_search.cxx.

References contains(), GBT_splitNdestroy_string(), gs_assert, and SPLIT_DROPEMPTY.

Referenced by GroupInfo::GroupInfo(), and GroupSearch::setDupCriteria().

void string_to_lower ( string &  s )

inline

Definition at line 941 of file group_search.cxx.

Referenced by DupNameCriterion::DupNameCriterion(), and GroupInfo::GroupInfo().

unsigned long permutations ( int  elems )

inline

Definition at line 1485 of file group_search.cxx.

const GroupRename_callenv& custom_gr_env ( GBL_command_arguments *  args )

inline

Definition at line 2007 of file group_search.cxx.

References DOWNCAST_REFERENCE, and GBL_command_arguments::get_callEnv().

Referenced by grl_aid(), grl_dupidx(), grl_groupsize(), grl_hitcount(), grl_hitidx(), grl_markedingroup(), and grl_nesting().

static GB_ERROR grl_hitidx ( GBL_command_arguments *  args )

static

Definition at line 2011 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::hit_idx, info2bio(), and GroupRename_callenv::legal_hit_index().

static GB_ERROR grl_dupidx ( GBL_command_arguments *  args )

static

Definition at line 2027 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::get_dupidx(), gs_assert, and info2bio().

static GB_ERROR grl_hitcount ( GBL_command_arguments *  args )

static

Definition at line 2044 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::queried, and QueriedGroups::size().

static GB_ERROR grl_groupsize ( GBL_command_arguments *  args )

static

Definition at line 2053 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::get_hit_group(), and FoundGroup::get_size().

static GB_ERROR grl_markedingroup ( GBL_command_arguments *  args )

static

Definition at line 2067 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::get_hit_group(), and FoundGroup::get_marked().

static GB_ERROR grl_aid ( GBL_command_arguments *  args )

static

Definition at line 2081 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, FoundGroup::get_aid(), and GroupRename_callenv::get_hit_group().

static GB_ERROR grl_nesting ( GBL_command_arguments *  args )

static

Definition at line 2095 of file group_search.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, custom_gr_env(), error(), FORMAT_2_OUT, GroupRename_callenv::get_hit_group(), and FoundGroup::get_nesting().

static const GBL_command_lookup_table& get_GroupRename_customized_ACI_commands ( )

static

Definition at line 2123 of file group_search.cxx.

References ACI_get_standard_commands(), and ARRAY_ELEMS.

Referenced by GS_calc_resulting_groupname().

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().

static void set_marks_of ( const SpeciesNames &  targetSpecies, GBDATA *  gb_main, GroupMarkMode  mode  )

static

Definition at line 2330 of file group_search.cxx.

References GB_read_flag(), GB_write_flag(), GBS_global_string(), GBT_first_species(), GBT_get_name_or_description(), GBT_message(), GBT_next_species(), GMM_INVERT, GMM_MARK, and UNCOVERED.

Referenced by GroupSearch::set_marks_in_found_groups(), and GroupSearch::set_marks_in_group().

Variable Documentation

GBL_command_definition groupRename_command_table[]

static

Initial value:

= {
    { "hitidx",        grl_hitidx },
    { "dupidx",        grl_dupidx },
    { "hitcount",      grl_hitcount },
    { "groupSize",     grl_groupsize },
    { "markedInGroup", grl_markedingroup },
    { "aid",           grl_aid },
    { "nesting",       grl_nesting },

    { NULp, NULp }
}

Definition at line 2111 of file group_search.cxx.