#include "NT_local_proto.h"
#include <arbdbt.h>
#include <arb_progress.h>
#include <arb_defs.h>
#include <arb_strbuf.h>
#include <pos_range.h>
#include <aw_root.hxx>
#include <aw_window.hxx>
#include <limits>
#include <vector>
#include <insdel.h>
#include "NT_local.h"
#include <arb_strarray.h>
#include <aw_awar.hxx>
#include <aw_awar_defs.hxx>
#include <aw_msg.hxx>

Include dependency graph for NT_split_ali.cxx:

Macros
#define	AWAR_SPLIT_ALI_BASE "split_ali/"

#define	AWAR_SPLIT_ALI_BTMP "tmp/" AWAR_SPLIT_ALI_BASE

#define	AWAR_SPLIT_ALI_TARGET AWAR_SPLIT_ALI_BTMP "target"

#define	AWAR_SPLIT_ALI_POSITIONS AWAR_SPLIT_ALI_BASE "pos"

#define	AWAR_SPLIT_ALI_MARKED AWAR_SPLIT_ALI_BASE "marked"

#define	AWAR_SPLIT_ALI_OVERWRITE AWAR_SPLIT_ALI_BASE "overwrite"

Typedefs
typedef vector< ExplicitRange >	RangeVec

Functions
static GB_ERROR	calculate_and_check_ranges (int ali_source_len, const int *splitBefore, RangeVec &ranges)

CONSTEXPR_INLINE int	digits (int parts)

const char *	target_ali_name (const char *ali_target_prefix, int p, int digits)

char *	build_split_id (const RangeVec &ranges)

static GB_ERROR	split_data_into_parts (GBDATA gb_data, const RangeVec &ranges, const char ali_target_prefix)

static GB_ERROR	copy_field_into_partial_alignments (GBDATA gb_data, const int parts, const char ali_target_prefix)

static GB_ERROR	split_alignment (GBDATA gb_main, const char ali_source, const char ali_target_prefix, const int splitBefore, bool markedOnly, bool overwriteAlignments)

static void	create_splitAlignment_awars (AW_root root, AW_default properties, GBDATA gb_main)

static void	split_ali_cb (AW_window *aww)

static void	use_editor_range_cb (AW_window *aww)

AW_window *	NT_create_splitAlignment_window (AW_root *awr)

Variables
static const int	END__ = numeric_limits<int>::max()

Macro Definition Documentation

#define AWAR_SPLIT_ALI_BASE "split_ali/"

Definition at line 456 of file NT_split_ali.cxx.

#define AWAR_SPLIT_ALI_BTMP "tmp/" AWAR_SPLIT_ALI_BASE

Definition at line 457 of file NT_split_ali.cxx.

#define AWAR_SPLIT_ALI_TARGET AWAR_SPLIT_ALI_BTMP "target"

Definition at line 459 of file NT_split_ali.cxx.

Referenced by create_splitAlignment_awars(), NT_create_splitAlignment_window(), and split_ali_cb().

#define AWAR_SPLIT_ALI_POSITIONS AWAR_SPLIT_ALI_BASE "pos"

Definition at line 460 of file NT_split_ali.cxx.

Referenced by create_splitAlignment_awars(), NT_create_splitAlignment_window(), split_ali_cb(), and use_editor_range_cb().

#define AWAR_SPLIT_ALI_MARKED AWAR_SPLIT_ALI_BASE "marked"

Definition at line 461 of file NT_split_ali.cxx.

Referenced by create_splitAlignment_awars(), NT_create_splitAlignment_window(), and split_ali_cb().

#define AWAR_SPLIT_ALI_OVERWRITE AWAR_SPLIT_ALI_BASE "overwrite"

Definition at line 462 of file NT_split_ali.cxx.

Referenced by create_splitAlignment_awars(), NT_create_splitAlignment_window(), and split_ali_cb().

Typedef Documentation

typedef vector<ExplicitRange> RangeVec

Definition at line 28 of file NT_split_ali.cxx.

Function Documentation

static GB_ERROR calculate_and_check_ranges	(	int	ali_source_len,
		const int *	splitBefore,
		RangeVec &	ranges
	)

static

Definition at line 32 of file NT_split_ali.cxx.

References PosRange::after(), error(), GBS_global_string(), info2bio(), intersection(), PosRange::is_empty(), NULp, PosRange::prior(), and PosRange::start().

Referenced by split_alignment().

CONSTEXPR_INLINE int digits ( int parts )

Definition at line 56 of file NT_split_ali.cxx.

Referenced by copy_field_into_partial_alignments(), AWT_configuration_selection::fill(), float_shift_factor(), gbl_round(), get_short(), DBwriter::renumberDuplicateGenes(), split_alignment(), and split_data_into_parts().

const char* target_ali_name	(	const char *	ali_target_prefix,
		int	p,
		int	digits
	)

inline

Definition at line 60 of file NT_split_ali.cxx.

References GBS_global_string_copy().

Referenced by copy_field_into_partial_alignments(), split_alignment(), and split_data_into_parts().

char* build_split_id ( const RangeVec & ranges )

inline

Definition at line 66 of file NT_split_ali.cxx.

References GBS_strstruct::get_copy(), GBS_strstruct::put(), and GBS_strstruct::putlong().

Referenced by split_alignment().

static GB_ERROR split_data_into_parts	(	GBDATA *	gb_data,
		const RangeVec &	ranges,
		const char *	ali_target_prefix
	)

static

Definition at line 75 of file NT_split_ali.cxx.

References digits(), error(), GB_await_error(), GB_get_grandfather(), GB_read_as_string(), GB_read_key_pntr(), GB_read_security_write(), GB_read_type(), GB_write_autoconv_string(), GBT_create_sequence_data(), NULp, seq, target_ali_name(), type, and UNCOVERED.

Referenced by split_alignment().

static GB_ERROR copy_field_into_partial_alignments	(	GBDATA *	gb_data,
		const int	parts,
		const char *	ali_target_prefix
	)

static

Definition at line 108 of file NT_split_ali.cxx.

References digits(), error(), GB_get_grandfather(), GB_read_char_pntr(), GB_read_key_pntr(), GB_read_security_write(), GB_read_type(), GB_STRING, GB_write_string(), GBS_global_string_copy(), GBT_create_sequence_data(), NULp, target_ali_name(), and type.

Referenced by split_alignment().

static GB_ERROR split_alignment	(	GBDATA *	gb_main,
		const char *	ali_source,
		const char *	ali_target_prefix,
		const int *	splitBefore,
		bool	markedOnly,
		bool	overwriteAlignments
	)

static

splits one alignment into multiple alignments.

Parameters

ali_source	name of source alignment
ali_target_prefix	prefix of target alignment. will be extended by '_1', '_2', ...
splitBefore	list of positions [0..N-1] where 2nd, 3rd, ... part shall begin. Terminate with 'END__'.
markedOnly	true->operate only on marked species, false->operate on all species
overwriteAlignments	true->delete+recreate existing alignments, false->bail-out with error