#include "insdel.h"
#include <RangeList.h>
#include <arbdbt.h>
#include <adGene.h>
#include <arb_progress.h>
#include <arb_defs.h>
#include <arb_diff.h>
#include <algorithm>

Include dependency graph for insdel.cxx:

Go to the source code of this file.

Classes
class	UnitPtr

struct	UnitPair

class	AliData

class	AliDataSlice

class	FINAL_TYPE< SEQTYPE >
	xml element More...

class	Deletable

class	TypedAliData< T >

struct	SpecificGap< T >

class	SizeAwarable

class	SpecificAliData< T >

class	SequenceAliData

class	Alignment

class	AliApplicable

class	AliEntryCounter

struct	AliEditCommand

class	AliInsertCommand

class	AliDeleteCommand

class	FINAL_TYPE< SEQTYPE >
	xml element More...

class	AliAutoFormatCommand

class	AliCompositeCommand

class	AliEditor

class	LazyAliData

class	EditedTerminal

Macros
#define	id_assert(cond) arb_assert(cond)

Typedefs
typedef SmartPtr< AliData >	AliDataPtr

Enumerations
enum	TerminalType { IDT_SPECIES = 0, IDT_SAI, IDT_SECSTRUCT }

Functions
template<typename T >
int	compare_type (const T &t1, const T &t2)

SizeAwarable	dontAllowOversize (size_t ali_size)

template<typename T >
GB_ERROR	check_delete_allowed (const T *, size_t, size_t, const Deletable &)

template<>
GB_ERROR	check_delete_allowed (const char *data, size_t start, size_t count, const Deletable &deletable)

AliDataPtr	concat (AliDataPtr left, AliDataPtr right)

AliDataPtr	concat (AliDataPtr left, AliDataPtr mid, AliDataPtr right)

AliDataPtr	partof (AliDataPtr data, size_t pos, size_t amount)

AliDataPtr	before (AliDataPtr data, size_t pos)

AliDataPtr	after (AliDataPtr data, size_t pos)

AliDataPtr	delete_from (AliDataPtr from, size_t pos, size_t amount, GB_ERROR &error)

AliDataPtr	insert_at (AliDataPtr dest, size_t pos, AliDataPtr src)

AliDataPtr	insert_gap (AliDataPtr data, size_t pos, size_t count)

AliDataPtr	format (AliDataPtr data, const size_t wanted_len, GB_ERROR &error)

template<typename T >
AliDataPtr	makeAliData (T *&allocated_data, size_t elems, const T &gap)

AliDataPtr	makeAliSeqData (char *&allocated_data, size_t elems, char gap, char dot)

void	free_insDelBuffer ()

char *	provide_insDelBuffer (size_t neededSpace)

GB_CSTR	alidata2buffer (const AliData &data)

static size_t	countAffectedEntries (GBDATA *Main, const Alignment &ali)

static GB_ERROR	apply_command_to_alignment (const AliEditCommand &cmd, const char cmd_description, GBDATA Main, const char alignment_name, const char deletable_chars)

static GB_ERROR	format_to_alilen (GBDATA Main, const char alignment_name)

GB_ERROR	ARB_format_alignment (GBDATA Main, const char alignment_name)

GB_ERROR	ARB_insdel_columns (GBDATA Main, const char alignment_name, long pos, long count, const char *deletable_chars)

GB_ERROR	ARB_delete_columns_using_SAI (GBDATA Main, const char alignment_name, const RangeList &ranges, const char *deletable_chars)

GB_ERROR	ARB_insert_columns_using_SAI (GBDATA Main, const char alignment_name, const RangeList &ranges, UseRange units, InsertWhere where, size_t amount)

bool	ARB_is_alignment_relative_data (GBDATA *gb_data)

Variables
static GB_CSTR	targetTypeName []

static char *	insDelBuffer = NULp

static size_t	insDelBuffer_size

Macro Definition Documentation

#define id_assert ( cond ) arb_assert(cond)

Definition at line 27 of file insdel.cxx.

Referenced by FINAL_TYPE< SEQTYPE >::apply(), EditedTerminal::apply(), FINAL_TYPE< SEQTYPE >::check_applicable_to(), AliData::check_delete_allowed(), AliDataSlice::cmp_data(), FINAL_TYPE< SEQTYPE >::cmp_data(), SpecificAliData< char >::cmp_data(), AliData::cmpPartWith(), UnitPtr::expect_pointer(), format(), Deletable::get_delete_error(), LazyAliData::has_slice(), insert_gap(), AliDataSlice::operate_on_mem(), FINAL_TYPE< SEQTYPE >::operate_on_mem(), SpecificGap< T >::operate_on_mem(), SpecificAliData< char >::operate_on_mem(), AliData::set_error(), UnitPtr::set_pointer(), AliDataSlice::unit_left_of(), FINAL_TYPE< SEQTYPE >::unit_left_of(), TypedAliData< char >::unit_left_of(), AliDataSlice::unit_right_of(), FINAL_TYPE< SEQTYPE >::unit_right_of(), TypedAliData< char >::unit_right_of(), and UnitPtr::UnitPtr().

Typedef Documentation

typedef SmartPtr<AliData> AliDataPtr

Definition at line 60 of file insdel.cxx.

Enumeration Type Documentation

enum TerminalType

Enumerator
IDT_SPECIES
IDT_SAI
IDT_SECSTRUCT

Definition at line 901 of file insdel.cxx.

Function Documentation

template<typename T >

int compare_type	(	const T &	t1,
		const T &	t2
	)

inline

Definition at line 54 of file insdel.cxx.

Referenced by SpecificGap< T >::cmp_data(), AliData::cmp_whole_data(), SpecificGap< T >::operate_on_mem(), and SpecificAliData< char >::operate_on_mem().

SizeAwarable dontAllowOversize ( size_t ali_size )

inline

Definition at line 471 of file insdel.cxx.

Referenced by makeAliData(), and makeAliSeqData().

template<typename T >

GB_ERROR check_delete_allowed	(	const T *	,
		size_t	,
		size_t	,
		const Deletable &
	)

inline

Definition at line 474 of file insdel.cxx.

References NULp.

template<>

GB_ERROR check_delete_allowed	(	const char *	data,
		size_t	start,
		size_t	count,
		const Deletable &	deletable
	)

inline

Definition at line 478 of file insdel.cxx.

References Deletable::get_delete_error().

AliDataPtr concat	(	AliDataPtr	left,
		AliDataPtr	right
	)

inline

Definition at line 584 of file insdel.cxx.

Referenced by concat(), concatenate_name_parts(), delete_from(), insert_at(), and FieldTransfer::ReadRule::readFrom().

AliDataPtr concat	(	AliDataPtr	left,
		AliDataPtr	mid,
		AliDataPtr	right
	)

inline

Definition at line 587 of file insdel.cxx.

References concat().

AliDataPtr partof	(	AliDataPtr	data,
		size_t	pos,
		size_t	amount
	)

inline

Definition at line 591 of file insdel.cxx.

References AliDataSlice::make().

Referenced by after(), and before().

AliDataPtr before	(	AliDataPtr	data,
		size_t	pos
	)

inline

Definition at line 592 of file insdel.cxx.

References partof().

Referenced by AlignBuffer::correctUnalignedPositions(), delete_from(), insert_at(), AW_cb::set_AW_cb_guards(), and SEC_root::unsplit_loop().

AliDataPtr after	(	AliDataPtr	data,
		size_t	pos
	)

inline

Definition at line 593 of file insdel.cxx.

References partof().

Referenced by AWT_trigger_remote_action(), AlignBuffer::correctUnalignedPositions(), delete_from(), gb_find_internal(), GB_find_sub_by_quark(), GB_find_subcontent_by_quark(), insert_at(), AW_cb::set_AW_cb_guards(), and SEC_root::unsplit_loop().

AliDataPtr delete_from	(	AliDataPtr	from,
		size_t	pos,
		size_t	amount,
		GB_ERROR &	error
	)

inline

Definition at line 595 of file insdel.cxx.

References after(), before(), and concat().

Referenced by AliDeleteCommand::apply(), and format().

AliDataPtr insert_at	(	AliDataPtr	dest,
		size_t	pos,
		AliDataPtr	src
	)

inline

Definition at line 599 of file insdel.cxx.

References after(), before(), and concat().

Referenced by insert_gap().

AliDataPtr insert_gap	(	AliDataPtr	data,
		size_t	pos,
		size_t	count
	)

inline

Definition at line 603 of file insdel.cxx.

References id_assert, insert_at(), UnitPair::left, and UnitPair::right.

Referenced by AliInsertCommand::apply(), and format().

AliDataPtr format	(	AliDataPtr	data,
		const size_t	wanted_len,
		GB_ERROR &	error
	)

inline

Definition at line 615 of file insdel.cxx.

References delete_from(), id_assert, and insert_gap().

Referenced by FINAL_TYPE< SEQTYPE >::apply(), AWT_popup_print_window(), canvas_to_printer(), RegFieldSelection::create_window(), detect_format_props(), main(), match_string(), paper_changed_cb(), seqFileFormat(), seqFileFormatFp(), tree2newick(), ClustersData::update_cluster_selection_list(), and NodeTextBuilder::work().

template<typename T >

AliDataPtr makeAliData	(	T *&	allocated_data,
		size_t	elems,
		const T &	gap
	)

inline

Definition at line 628 of file insdel.cxx.

References Deletable::ANYTHING, and dontAllowOversize().

AliDataPtr makeAliSeqData	(	char *&	allocated_data,
		size_t	elems,
		char	gap,
		char	dot
	)

inline

Definition at line 631 of file insdel.cxx.

References Deletable::ANYTHING, and dontAllowOversize().

void free_insDelBuffer ( )

inline

Definition at line 1162 of file insdel.cxx.

Referenced by apply_command_to_alignment(), and provide_insDelBuffer().

char* provide_insDelBuffer ( size_t neededSpace )

inline

Definition at line 1165 of file insdel.cxx.

References free_insDelBuffer(), insDelBuffer, and insDelBuffer_size.

Referenced by alidata2buffer().

GB_CSTR alidata2buffer ( const AliData & data )

inline

Definition at line 1174 of file insdel.cxx.

References buffer, AliData::copyTo(), AliData::memsize(), and provide_insDelBuffer().

Referenced by EditedTerminal::apply().

static size_t countAffectedEntries	(	GBDATA *	Main,
		const Alignment &	ali
	)

static

Definition at line 1384 of file insdel.cxx.

References AliApplicable::apply_to_alignment(), and AliEntryCounter::get_entry_count().

Referenced by apply_command_to_alignment().

static GB_ERROR apply_command_to_alignment	(	const AliEditCommand &	cmd,
		const char *	cmd_description,
		GBDATA *	Main,
		const char *	alignment_name,
		const char *	deletable_chars
	)

static

Definition at line 1390 of file insdel.cxx.

References Deletable::ANYTHING, AliApplicable::apply_to_alignment(), AliEditCommand::check_applicable_to(), countAffectedEntries(), error(), free_insDelBuffer(), GB_disable_quicksave(), GB_entry(), GB_find_string(), GB_IGNORE_CASE, GB_nextEntry(), GB_read_char_pntr(), GB_read_int(), GB_write_int(), GBT_get_presets(), Deletable::NOTHING, NULp, and SEARCH_CHILD.

Referenced by ARB_delete_columns_using_SAI(), ARB_insdel_columns(), ARB_insert_columns_using_SAI(), and format_to_alilen().

static GB_ERROR format_to_alilen	(	GBDATA *	Main,
		const char *	alignment_name
	)

static

Definition at line 1434 of file insdel.cxx.

References apply_command_to_alignment().

Referenced by ARB_format_alignment().

GB_ERROR ARB_format_alignment	(	GBDATA *	Main,
		const char *	alignment_name
	)

Definition at line 1439 of file insdel.cxx.

References format_to_alilen(), GBT_check_data(), GENOM_ALIGNMENT, and NULp.

Referenced by ali_format_cb(), FINAL_TYPE< SEQTYPE >::finish(), nt_create_all_awars(), and NT_format_all_alignments().

GB_ERROR ARB_insdel_columns	(	GBDATA *	Main,
		const char *	alignment_name,
		long	pos,
		long	count,
		const char *	deletable_chars
	)

Definition at line 1453 of file insdel.cxx.

References apply_command_to_alignment(), error(), GBS_global_string(), and NULp.

Referenced by insdel_event().

GB_ERROR ARB_delete_columns_using_SAI	(	GBDATA *	Main,
		const char *	alignment_name,
		const RangeList &	ranges,
		const char *	deletable_chars
	)

Definition at line 1493 of file insdel.cxx.

References apply_command_to_alignment(), RangeList::empty(), error(), RangeList::rbegin(), and RangeList::rend().

Referenced by insdel_sai_event().

GB_ERROR ARB_insert_columns_using_SAI	(	GBDATA *	Main,
		const char *	alignment_name,
		const RangeList &	ranges,
		UseRange	units,
		InsertWhere	where,
		size_t	amount
	)

Definition at line 1512 of file insdel.cxx.

References apply_command_to_alignment(), BEHIND, RangeList::empty(), error(), INFRONTOF, NULp, RANGES, RangeList::rbegin(), RangeList::rend(), and SINGLE_COLUMNS.

Referenced by insdel_sai_event().

bool ARB_is_alignment_relative_data ( GBDATA * gb_data )

Definition at line 1555 of file insdel.cxx.

References GB_DB, GB_get_father(), GB_read_key_pntr(), GB_read_type(), IDT_SAI, IDT_SPECIES, and AliEditor::shall_edit().

Referenced by split_alignment().

Variable Documentation

GB_CSTR targetTypeName[]

static

Initial value:

= {
    "Species",
    "SAI",
    "SeceditStruct",
}

Definition at line 907 of file insdel.cxx.

char* insDelBuffer = NULp

static

Definition at line 1159 of file insdel.cxx.

Referenced by provide_insDelBuffer().

size_t insDelBuffer_size

static

Definition at line 1160 of file insdel.cxx.

Referenced by provide_insDelBuffer().

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation