#include "fast_aligner.hxx"
#include "ClustalV.hxx"
#include "seq_search.hxx"
#include <island_hopping.h>
#include <awtc_next_neighbours.hxx>
#include <awt_sel_boxes.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <arbdbt.h>
#include <ad_cb.h>
#include <arb_defs.h>
#include <arb_progress.h>
#include <RangeList.h>
#include <cctype>
#include <cmath>
#include <climits>
#include <list>
#include <awt_config_manager.hxx>
#include <rootAsWin.h>

Include dependency graph for fast_aligner.cxx:

Classes
struct	AlignParams

struct	SearchRelativeParams

class	AliChange

class	LooseBases

class	AlignmentReference

class	ExplicitReference

class	ConsensusReference

class	SearchRelativesReference

class	Aligner

Macros
#define	GAP_CHAR '-'

#define	QUALITY_NAME "ASC_ALIGNER_CLIENT_SCORE"

#define	INSERTS_NAME "AMI_ALIGNER_MASTER_INSERTS"

#define	FA_AWAR_ROOT "faligner/"

#define	FA_AWAR_TO_ALIGN FA_AWAR_ROOT "what"

#define	FA_AWAR_REFERENCE FA_AWAR_ROOT "against"

#define	FA_AWAR_REFERENCE_NAME FA_AWAR_ROOT "sagainst"

#define	FA_AWAR_RANGE FA_AWAR_ROOT "range"

#define	FA_AWAR_PROTECTION FA_AWAR_ROOT "protection"

#define	FA_AWAR_AROUND FA_AWAR_ROOT "around"

#define	FA_AWAR_MIRROR FA_AWAR_ROOT "mirror"

#define	FA_AWAR_REPORT FA_AWAR_ROOT "report"

#define	FA_AWAR_SHOW_GAPS_MESSAGES FA_AWAR_ROOT "show_gaps"

#define	FA_AWAR_CONTINUE_ON_ERROR FA_AWAR_ROOT "continue_on_error"

#define	FA_AWAR_ACTION_ON_ERROR FA_AWAR_ROOT "action_on_error"

#define	FA_AWAR_USE_SECONDARY FA_AWAR_ROOT "use_secondary"

#define	FA_AWAR_NEXT_RELATIVES FA_AWAR_ROOT "next_relatives"

#define	FA_AWAR_RELATIVE_RANGE FA_AWAR_ROOT "relrange"

#define	FA_AWAR_PT_SERVER_ALIGNMENT "tmp/" FA_AWAR_ROOT "relative_ali"

#define	FA_AWAR_SAI_RANGE_NAME FA_AWAR_ROOT "sai/sainame"

#define	FA_AWAR_SAI_RANGE_CHARS FA_AWAR_ROOT "sai/chars"

#define	FA_AWAR_ISLAND_HOPPING_ROOT "island_hopping/"

#define	FA_AWAR_USE_ISLAND_HOPPING FA_AWAR_ISLAND_HOPPING_ROOT "use"

#define	FA_AWAR_ESTIMATE_BASE_FREQ FA_AWAR_ISLAND_HOPPING_ROOT "estimate_base_freq"

#define	FA_AWAR_BASE_FREQ_A FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_a"

#define	FA_AWAR_BASE_FREQ_C FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_c"

#define	FA_AWAR_BASE_FREQ_G FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_g"

#define	FA_AWAR_BASE_FREQ_T FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_t"

#define	FA_AWAR_SUBST_PARA_AC FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ac"

#define	FA_AWAR_SUBST_PARA_AG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ag"

#define	FA_AWAR_SUBST_PARA_AT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_at"

#define	FA_AWAR_SUBST_PARA_CG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_cg"

#define	FA_AWAR_SUBST_PARA_CT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ct"

#define	FA_AWAR_SUBST_PARA_GT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_gt"

#define	FA_AWAR_EXPECTED_DISTANCE FA_AWAR_ISLAND_HOPPING_ROOT "expected_dist"

#define	FA_AWAR_STRUCTURE_SUPPLEMENT FA_AWAR_ISLAND_HOPPING_ROOT "struct_suppl"

#define	FA_AWAR_THRESHOLD FA_AWAR_ISLAND_HOPPING_ROOT "threshold"

#define	FA_AWAR_GAP_A FA_AWAR_ISLAND_HOPPING_ROOT "gapa"

#define	FA_AWAR_GAP_B FA_AWAR_ISLAND_HOPPING_ROOT "gapb"

#define	FA_AWAR_GAP_C FA_AWAR_ISLAND_HOPPING_ROOT "gapc"

#define	ACID '*'

#define	GAP '-'

#define	TEST_BETTER_SCORE()

#define	CAN_SCORE_LEFT() (masterLeft.leftOf() && slaveLeft.leftOf())

#define	CAN_SCORE_RIGHT() (masterRight.rightOf() && slaveRight.rightOf())

#define	SCORE_LEFT()

#define	SCORE_RIGHT()

#define	MIN_ALIGNMENT_RANGE 4

#define	XOFF -25

#define	YOFF 0

Enumerations
enum	FA_report { FA_NO_REPORT, FA_TEMP_REPORT, FA_REPORT }

enum	FA_range { FA_WHOLE_SEQUENCE, FA_AROUND_CURSOR, FA_SELECTED_RANGE, FA_SAI_MULTI_RANGE }

enum	FA_turn { FA_TURN_NEVER, FA_TURN_INTERACTIVE, FA_TURN_ALWAYS }

enum	FA_reference { FA_REF_EXPLICIT, FA_REF_CONSENSUS, FA_REF_RELATIVES }

enum	FA_alignTarget { FA_CURRENT, FA_MARKED, FA_SELECTED }

enum	FA_errorAction { FA_NO_ACTION, FA_MARK_FAILED, FA_MARK_ALIGNED }

Functions
ARB_ERROR	species_not_found (GB_CSTR species_name)

static ARB_ERROR	reverseComplement (GBDATA *gb_species, GB_CSTR ali, int max_protection)

static void	build_reverse_complement (AW_window aw, const AlignDataAccess data_access)

static const char *	read_name (GBDATA *gbd)

int	relatedBases (char base1, char base2)

char	alignQuality (char slave, char master)

double	log3 (double d)

double	partSignificance (long seq1len, long seq2len, long partlen)

ARB_ERROR	bufferTooSmall ()

long	insertsToNextBase (AlignBuffer *alignBuffer, const SequencePosition &master)

void	insertBase (AlignBuffer alignBuffer, SequencePosition &master, SequencePosition &slave, FastAlignReport report)

void	insertSlaveBases (AlignBuffer alignBuffer, SequencePosition &slave, int length, FastAlignReport report)

void	insertGap (AlignBuffer alignBuffer, SequencePosition &master, FastAlignReport report)

static ARB_ERROR	insertClustalValigned (AlignBuffer alignBuffer, SequencePosition &master, SequencePosition &slave, const char masterAlignment, const char slaveAlignment, long alignmentLength, FastAlignReport report)

static ARB_ERROR	insertAligned (AlignBuffer alignBuffer, SequencePosition &master, SequencePosition &slave, long partLength, FastAlignReport report)

static ARB_ERROR	cannot_fast_align (const CompactedSubSequence &master, long moffset, long mlength, const CompactedSubSequence &slaveSequence, long soffset, long slength, int max_seq_length, AlignBuffer alignBuffer, FastAlignReport report)

long	calcSequenceChecksum (const char *data, long length)

static CompactedSubSequence *	readCompactedSequence (GBDATA gb_species, const char ali, ARB_ERROR errorPtr, char dataPtr, long seqChksum, PosRange range)

static ARB_ERROR	writeStringToAlignment (GBDATA *gb_species, GB_CSTR alignment, GB_CSTR data_name, GB_CSTR str, bool temporary)

static ARB_ERROR	alignCompactedTo (CompactedSubSequence toAlignSequence, const FastSearchSequence alignTo, int max_seq_length, GB_CSTR alignment, long toAlignChksum, GBDATA gb_toAlign, GBDATA gb_alignTo, const AlignParams &ali_params)

ARB_ERROR	FastAligner_delete_temp_entries (GBDATA gb_species, const char alignment)

static ARB_ERROR	align_error (ARB_ERROR olderr, GBDATA gb_toAlign, GBDATA gb_alignTo)

static ARB_ERROR	alignTo (GBDATA gb_toAlign, GB_CSTR alignment, const FastSearchSequence alignTo, GBDATA *gb_alignTo, int max_seq_length, const AlignParams &ali_params)

static ARB_ERROR	alignToGroupConsensus (GBDATA *gb_toAlign, GB_CSTR alignment, Aligner_get_consensus_func get_consensus, int max_seq_length, const AlignParams &ali_params)

static void	appendNameAndUsedBasePositions (char *toString, GBDATA gb_species, int usedBasePositions)

int	min (int i, int j)

static ARB_ERROR	alignToNextRelative (SearchRelativeParams &relSearch, int max_seq_length, FA_turn turnAllowed, GB_CSTR alignment, GBDATA *gb_toAlign, const AlignParams &ali_params)

void	FastAligner_start (AW_window aw, const AlignDataAccess data_access)

static void	nullcb ()

void	FastAligner_create_variables (AW_root *root, AW_default db1)

void	FastAligner_set_align_current (AW_root *root, AW_default db1)

void	FastAligner_set_reference_species (AW_root *root)

static AW_window *	create_island_hopping_window (AW_root *root)

static AW_window *	create_family_settings_window (AW_root *root)

AW_window *	FastAligner_create_window (AW_root root, const AlignDataAccess data_access)

Variables
static IslandHopping *	island_hopper = NULp

static GB_alignment_type	global_alignmentType = GB_AT_UNKNOWN

static int	currentSequenceNumber

static int	overallSequenceNumber

static LooseBases	unaligned_bases

static AWT_config_mapping_def	aligner_config_mapping []

Macro Definition Documentation

#define GAP_CHAR '-'

Definition at line 116 of file fast_aligner.cxx.

Referenced by alignCompactedTo(), alignQuality(), insertAligned(), insertClustalValigned(), insertGap(), and insertSlaveBases().

#define QUALITY_NAME "ASC_ALIGNER_CLIENT_SCORE"

Definition at line 117 of file fast_aligner.cxx.

Referenced by alignCompactedTo(), and FastAligner_delete_temp_entries().

#define INSERTS_NAME "AMI_ALIGNER_MASTER_INSERTS"

Definition at line 118 of file fast_aligner.cxx.

Referenced by alignCompactedTo(), and FastAligner_delete_temp_entries().

#define FA_AWAR_ROOT "faligner/"

Definition at line 120 of file fast_aligner.cxx.

#define FA_AWAR_TO_ALIGN FA_AWAR_ROOT "what"

Definition at line 121 of file fast_aligner.cxx.

Referenced by build_reverse_complement(), FastAligner_create_variables(), FastAligner_create_window(), FastAligner_set_align_current(), and FastAligner_start().

#define FA_AWAR_REFERENCE FA_AWAR_ROOT "against"

Definition at line 122 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_REFERENCE_NAME FA_AWAR_ROOT "sagainst"

Definition at line 123 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), FastAligner_set_reference_species(), and FastAligner_start().

#define FA_AWAR_RANGE FA_AWAR_ROOT "range"

Definition at line 124 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_PROTECTION FA_AWAR_ROOT "protection"

Definition at line 125 of file fast_aligner.cxx.

Referenced by build_reverse_complement(), FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_AROUND FA_AWAR_ROOT "around"

Definition at line 126 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_MIRROR FA_AWAR_ROOT "mirror"

Definition at line 127 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_REPORT FA_AWAR_ROOT "report"

Definition at line 128 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_SHOW_GAPS_MESSAGES FA_AWAR_ROOT "show_gaps"

Definition at line 129 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_CONTINUE_ON_ERROR FA_AWAR_ROOT "continue_on_error"

Definition at line 130 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_ACTION_ON_ERROR FA_AWAR_ROOT "action_on_error"

Definition at line 131 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_USE_SECONDARY FA_AWAR_ROOT "use_secondary"

Definition at line 132 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_NEXT_RELATIVES FA_AWAR_ROOT "next_relatives"

Definition at line 133 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_RELATIVE_RANGE FA_AWAR_ROOT "relrange"

Definition at line 134 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_PT_SERVER_ALIGNMENT "tmp/" FA_AWAR_ROOT "relative_ali"

Definition at line 135 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_SAI_RANGE_NAME FA_AWAR_ROOT "sai/sainame"

Definition at line 136 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_SAI_RANGE_CHARS FA_AWAR_ROOT "sai/chars"

Definition at line 137 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_ISLAND_HOPPING_ROOT "island_hopping/"

Definition at line 139 of file fast_aligner.cxx.

#define FA_AWAR_USE_ISLAND_HOPPING FA_AWAR_ISLAND_HOPPING_ROOT "use"

Definition at line 140 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables(), FastAligner_create_window(), and FastAligner_start().

#define FA_AWAR_ESTIMATE_BASE_FREQ FA_AWAR_ISLAND_HOPPING_ROOT "estimate_base_freq"

Definition at line 141 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_BASE_FREQ_A FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_a"

Definition at line 142 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_BASE_FREQ_C FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_c"

Definition at line 143 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_BASE_FREQ_G FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_g"

Definition at line 144 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), and FastAligner_create_variables().

#define FA_AWAR_BASE_FREQ_T FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_t"

Definition at line 145 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_AC FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ac"

Definition at line 146 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_AG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ag"

Definition at line 147 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_AT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_at"

Definition at line 148 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_CG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_cg"

Definition at line 149 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_CT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ct"

Definition at line 150 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_SUBST_PARA_GT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_gt"

Definition at line 151 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_EXPECTED_DISTANCE FA_AWAR_ISLAND_HOPPING_ROOT "expected_dist"

Definition at line 152 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_STRUCTURE_SUPPLEMENT FA_AWAR_ISLAND_HOPPING_ROOT "struct_suppl"

Definition at line 153 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_THRESHOLD FA_AWAR_ISLAND_HOPPING_ROOT "threshold"

Definition at line 154 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_GAP_A FA_AWAR_ISLAND_HOPPING_ROOT "gapa"

Definition at line 155 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_GAP_B FA_AWAR_ISLAND_HOPPING_ROOT "gapb"

Definition at line 156 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define FA_AWAR_GAP_C FA_AWAR_ISLAND_HOPPING_ROOT "gapc"

Definition at line 157 of file fast_aligner.cxx.

Referenced by create_island_hopping_window(), FastAligner_create_variables(), and FastAligner_start().

#define ACID '*'

Referenced by insertClustalValigned().

#define GAP '-'

Referenced by insertClustalValigned().

#define TEST_BETTER_SCORE ( )

Value:

do {                                                                \
        if (score>bestScore) {                                          \
            bestScore = score;                                          \
            bestLength = masterRight.text() - masterLeft.text();        \
            bestMasterLeft = masterLeft;                                \
            bestSlaveLeft = slaveLeft;                                  \
        }                                                               \
    } while (0)

Definition at line 781 of file fast_aligner.cxx.

#define CAN_SCORE_LEFT ( ) (masterLeft.leftOf() && slaveLeft.leftOf())

Definition at line 791 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

#define CAN_SCORE_RIGHT ( ) (masterRight.rightOf() && slaveRight.rightOf())

Definition at line 792 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

#define SCORE_LEFT ( )

Value:

do {                                                                \
        score += *(--masterLeft).text()==*(--slaveLeft).text() ? match : mismatch; \
        TEST_BETTER_SCORE();                                            \
    } while (0)

Definition at line 794 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

#define SCORE_RIGHT ( )

Value:

do {                                                                \
        score += *(++masterRight).text()==*(++slaveRight).text() ? match : mismatch; \
        TEST_BETTER_SCORE();                                            \
    } while (0)

Definition at line 800 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

#define MIN_ALIGNMENT_RANGE 4

Referenced by FastSearchSequence::fast_align().

#define XOFF -25

Referenced by create_island_hopping_window().

#define YOFF 0

Referenced by create_island_hopping_window().

Enumeration Type Documentation

enum FA_report

Enumerator
FA_NO_REPORT
FA_TEMP_REPORT
FA_REPORT

Definition at line 52 of file fast_aligner.cxx.

enum FA_range

Enumerator
FA_WHOLE_SEQUENCE
FA_AROUND_CURSOR
FA_SELECTED_RANGE
FA_SAI_MULTI_RANGE

Definition at line 58 of file fast_aligner.cxx.

enum FA_turn

Enumerator
FA_TURN_NEVER
FA_TURN_INTERACTIVE
FA_TURN_ALWAYS

Definition at line 65 of file fast_aligner.cxx.

enum FA_reference

Enumerator
FA_REF_EXPLICIT
FA_REF_CONSENSUS
FA_REF_RELATIVES

Definition at line 71 of file fast_aligner.cxx.

enum FA_alignTarget

Enumerator
FA_CURRENT
FA_MARKED
FA_SELECTED

Definition at line 77 of file fast_aligner.cxx.

enum FA_errorAction

Enumerator
FA_NO_ACTION
FA_MARK_FAILED
FA_MARK_ALIGNED

Definition at line 83 of file fast_aligner.cxx.

Function Documentation

ARB_ERROR species_not_found ( GB_CSTR species_name )

inline

Definition at line 170 of file fast_aligner.cxx.

References GBS_global_string().

Referenced by alignToNextRelative(), and build_reverse_complement().

static ARB_ERROR reverseComplement	(	GBDATA *	gb_species,
		GB_CSTR	ali,
		int	max_protection
	)

static

Definition at line 174 of file fast_aligner.cxx.

References error(), fa_assert(), GB_AT_UNKNOWN, GB_get_root(), gb_main, GB_read_security_write(), GB_read_string(), GB_read_string_count(), GB_write_string(), GBS_global_string(), GBT_determine_T_or_U(), GBT_find_sequence(), GBT_get_alignment_type(), GBT_get_name_or_description(), GBT_reverseComplementNucSequence(), length, NULp, and seq.

Referenced by build_reverse_complement().

static void build_reverse_complement	(	AW_window *	aw,
		const AlignDataAccess *	data_access
	)

static

static const char* read_name ( GBDATA * gbd )

static

Definition at line 340 of file fast_aligner.cxx.

References GBT_get_name().

Referenced by align_error(), alignCompactedTo(), and alignToGroupConsensus().

int relatedBases	(	char	base1,
		char	base2
	)

inline

Definition at line 346 of file fast_aligner.cxx.

References baseMatch().

Referenced by alignQuality().

char alignQuality	(	char	slave,
		char	master
	)

inline

Definition at line 350 of file fast_aligner.cxx.

References fa_assert(), GAP_CHAR, relatedBases(), and result.

Referenced by alignCompactedTo(), insertAligned(), insertBase(), insertClustalValigned(), insertGap(), and insertSlaveBases().

double log3 ( double d )

inline

Definition at line 477 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align(), and partSignificance().

double partSignificance	(	long	seq1len,
		long	seq2len,
		long	partlen
	)

inline

Definition at line 480 of file fast_aligner.cxx.

References log3().

Referenced by FastSearchSequence::fast_align().

ARB_ERROR bufferTooSmall ( )

inline

Definition at line 486 of file fast_aligner.cxx.

Referenced by cannot_fast_align(), insertAligned(), and insertClustalValigned().

long insertsToNextBase	(	AlignBuffer *	alignBuffer,
		const SequencePosition &	master
	)

inline

Definition at line 490 of file fast_aligner.cxx.

References CompactedSubSequence::expdPosition(), SequencePosition::expdPosition(), CompactedSubSequence::length(), AlignBuffer::offset(), SequencePosition::rightOf(), and SequencePosition::sequence().

Referenced by insertAligned(), and insertClustalValigned().

void insertBase	(	AlignBuffer *	alignBuffer,
		SequencePosition &	master,
		SequencePosition &	slave,
		FastAlignReport *	report
	)

inline

Definition at line 505 of file fast_aligner.cxx.

References alignQuality(), FastAlignReport::count_aligned_base(), AlignBuffer::set(), and SequencePosition::text().

Referenced by insertAligned(), and insertClustalValigned().

void insertSlaveBases	(	AlignBuffer *	alignBuffer,
		SequencePosition &	slave,
		int	length,
		FastAlignReport *	report
	)

inline

Definition at line 518 of file fast_aligner.cxx.

References alignQuality(), AlignBuffer::copy(), FastAlignReport::count_unaligned_base(), GAP_CHAR, length, and SequencePosition::text().

Referenced by insertClustalValigned().

void insertGap	(	AlignBuffer *	alignBuffer,
		SequencePosition &	master,
		FastAlignReport *	report
	)

inline

Definition at line 528 of file fast_aligner.cxx.

References alignQuality(), FastAlignReport::count_aligned_base(), GAP_CHAR, AlignBuffer::set(), and SequencePosition::text().

Referenced by insertClustalValigned().

static ARB_ERROR insertClustalValigned	(	AlignBuffer *	alignBuffer,
		SequencePosition &	master,
		SequencePosition &	slave,
		const char *	masterAlignment,
		const char *	slaveAlignment,
		long	alignmentLength,
		FastAlignReport *	report
	)

static

Definition at line 539 of file fast_aligner.cxx.

References ACID, alignQuality(), bufferTooSmall(), SequencePosition::expdPosition(), fa_assert(), AlignBuffer::free(), GAP, GAP_CHAR, insertBase(), insertGap(), insertSlaveBases(), insertsToNextBase(), LooseBases::memorize(), FastAlignReport::memorize_insertion(), NULp, and AlignBuffer::set().

Referenced by alignCompactedTo(), and cannot_fast_align().

static ARB_ERROR insertAligned	(	AlignBuffer *	alignBuffer,
		SequencePosition &	master,
		SequencePosition &	slave,
		long	partLength,
		FastAlignReport *	report
	)

static

Definition at line 611 of file fast_aligner.cxx.

References alignQuality(), bufferTooSmall(), SequencePosition::expdPosition(), fa_assert(), AlignBuffer::free(), GAP_CHAR, insertBase(), insertsToNextBase(), FastAlignReport::memorize_insertion(), NULp, and AlignBuffer::set().

Referenced by FastSearchSequence::fast_align().

static ARB_ERROR cannot_fast_align	(	const CompactedSubSequence &	master,
		long	moffset,
		long	mlength,
		const CompactedSubSequence &	slaveSequence,
		long	soffset,
		long	slength,
		int	max_seq_length,
		AlignBuffer *	alignBuffer,
		FastAlignReport *	report
	)

static

Definition at line 673 of file fast_aligner.cxx.

References bufferTooSmall(), ClustalV_align(), cmp, AlignBuffer::copy(), FastAlignReport::count_unaligned_base(), error(), CompactedSubSequence::expdPosition(), CompactedSubSequence::gapsBefore(), GB_AT_AA, GB_AT_DNA, GB_AT_RNA, global_alignmentType, insertClustalValigned(), LooseBases::memorize(), NULp, and CompactedSubSequence::text().

Referenced by FastSearchSequence::fast_align().

long calcSequenceChecksum	(	const char *	data,
		long	length
	)

inline

Definition at line 968 of file fast_aligner.cxx.

References GAP_CHARS, and GB_checksum().

Referenced by alignCompactedTo(), and readCompactedSequence().

static CompactedSubSequence* readCompactedSequence	(	GBDATA *	gb_species,
		const char *	ali,
		ARB_ERROR *	errorPtr,
		char **	dataPtr,
		long *	seqChksum,
		PosRange	range
	)

static

Definition at line 972 of file fast_aligner.cxx.

References calcSequenceChecksum(), PosRange::end(), error(), fa_assert(), GB_read_string(), GB_read_string_count(), GBS_global_string(), GBT_find_sequence(), GBT_get_name_or_description(), is_ali_gap(), PosRange::is_part(), length, NULp, seq, and PosRange::start().

Referenced by alignTo(), and alignToNextRelative().

static ARB_ERROR writeStringToAlignment	(	GBDATA *	gb_species,
		GB_CSTR	alignment,
		GB_CSTR	data_name,
		GB_CSTR	str,
		bool	temporary
	)

static

Definition at line 1053 of file fast_aligner.cxx.

References error(), fa_assert(), GB_DB, GB_is_ancestor_of(), GB_search(), GB_set_temporary(), GB_STRING, GB_write_string(), GBS_global_string(), GBT_get_name_or_description(), and NULp.

Referenced by alignCompactedTo().

static ARB_ERROR alignCompactedTo	(	CompactedSubSequence *	toAlignSequence,
		const FastSearchSequence *	alignTo,
		int	max_seq_length,
		GB_CSTR	alignment,
		long	toAlignChksum,
		GBDATA *	gb_toAlign,
		GBDATA *	gb_alignTo,
		const AlignParams &	ali_params
	)

static

Definition at line 1072 of file fast_aligner.cxx.

References alignQuality(), buffer, calcSequenceChecksum(), AlignBuffer::correctUnalignedPositions(), error(), fa_assert(), FA_NO_REPORT, FA_TEMP_REPORT, FastSearchSequence::fast_align(), AlignBuffer::free(), GAP_CHAR, FastAlignInsertion::gaps(), GB_await_error(), GB_pop_transaction(), GB_push_transaction(), GB_read_string(), GB_read_string_count(), GB_STRING, GB_write_string(), GBT_add_data(), insertClustalValigned(), FastAlignReport::insertion(), INSERTS_NAME, PosRange::is_part(), island_hopper, AlignBuffer::length(), CompactedSubSequence::name(), FastAlignInsertion::next(), NULp, FastAlignInsertion::offset(), AlignBuffer::quality(), QUALITY_NAME, AlignParams::range, read_name(), AlignParams::report, AlignBuffer::restoreDots(), FastSearchSequence::sequence(), AlignBuffer::set(), AlignBuffer::setDotsAtEOSequence(), AlignParams::showGapsMessages, PosRange::size(), PosRange::start(), AlignBuffer::text(), and writeStringToAlignment().

Referenced by alignTo(), and alignToNextRelative().

ARB_ERROR FastAligner_delete_temp_entries	(	GBDATA *	gb_species,
		const char *	alignment
	)

Definition at line 1238 of file fast_aligner.cxx.

References error(), fa_assert(), GB_delete(), GB_FIND, GB_search(), GBT_get_name_or_description(), INSERTS_NAME, NULp, and QUALITY_NAME.

Referenced by ED4_delete_temp_entries().

static ARB_ERROR align_error	(	ARB_ERROR	olderr,
		GBDATA *	gb_toAlign,
		GBDATA *	gb_alignTo
	)

static

Definition at line 1268 of file fast_aligner.cxx.

References ARB_ERROR::deliver(), fa_assert(), GBS_global_string(), and read_name().

Referenced by alignTo(), and alignToNextRelative().

static ARB_ERROR alignTo	(	GBDATA *	gb_toAlign,
		GB_CSTR	alignment,
		const FastSearchSequence *	alignTo,
		GBDATA *	gb_alignTo,
		int	max_seq_length,
		const AlignParams &	ali_params
	)

static

Definition at line 1281 of file fast_aligner.cxx.

References align_error(), alignCompactedTo(), error(), GB_read_char_pntr(), GB_read_string_count(), GBT_find_sequence(), island_hopper, length, NULp, AlignParams::range, and readCompactedSequence().

Referenced by ExplicitReference::align_to(), and alignToGroupConsensus().

static ARB_ERROR alignToGroupConsensus	(	GBDATA *	gb_toAlign,
		GB_CSTR	alignment,
		Aligner_get_consensus_func	get_consensus,
		int	max_seq_length,
		const AlignParams &	ali_params
	)

static

Definition at line 1315 of file fast_aligner.cxx.

References alignTo(), error(), fa_assert(), NULp, AlignParams::range, read_name(), and PosRange::start().

Referenced by ConsensusReference::align_to().

static void appendNameAndUsedBasePositions	(	char **	toString,
		GBDATA *	gb_species,
		int	usedBasePositions
	)

static

Definition at line 1346 of file fast_aligner.cxx.

References fa_assert(), GBS_global_string_copy(), GBT_get_name_or_description(), and NULp.

Referenced by alignToNextRelative().

int min	(	int	i,
		int	j
	)

inline

Definition at line 1371 of file fast_aligner.cxx.

static ARB_ERROR alignToNextRelative	(	SearchRelativeParams &	relSearch,
		int	max_seq_length,
		FA_turn	turnAllowed,
		GB_CSTR	alignment,
		GBDATA *	gb_toAlign,
		const AlignParams &	ali_params
	)