ARB
Classes | Macros | Enumerations | Functions | Variables
fast_aligner.cxx File Reference
#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:

Go to the source code of this file.

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 charread_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 CompactedSubSequencereadCompactedSequence (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_windowcreate_island_hopping_window (AW_root *root)
 
static AW_windowcreate_family_settings_window (AW_root *root)
 
AW_windowFastAligner_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   '-'
#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"
#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/"

Definition at line 139 of file fast_aligner.cxx.

#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"

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"
#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   '*'

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: align.cxx:35
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")
Definition: AW_awar.cxx:166

Definition at line 780 of file fast_aligner.cxx.

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

Definition at line 790 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

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

Definition at line 791 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

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

Definition at line 793 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

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

Definition at line 799 of file fast_aligner.cxx.

Referenced by FastSearchSequence::fast_align().

#define MIN_ALIGNMENT_RANGE   4
#define XOFF   -25
#define YOFF   0

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.

Enumerator
FA_REF_EXPLICIT 
FA_REF_CONSENSUS 
FA_REF_RELATIVES 

Definition at line 71 of file fast_aligner.cxx.

Enumerator
FA_CURRENT 
FA_MARKED 
FA_SELECTED 

Definition at line 77 of file fast_aligner.cxx.

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
static void build_reverse_complement ( AW_window aw,
const AlignDataAccess data_access 
)
static
static const char* read_name ( GBDATA gbd)
static

Definition at line 339 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 345 of file fast_aligner.cxx.

References baseMatch().

Referenced by alignQuality().

char alignQuality ( char  slave,
char  master 
)
inline
double log3 ( double  d)
inline

Definition at line 476 of file fast_aligner.cxx.

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

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

Definition at line 479 of file fast_aligner.cxx.

References log3().

Referenced by FastSearchSequence::fast_align().

ARB_ERROR bufferTooSmall ( )
inline

Definition at line 485 of file fast_aligner.cxx.

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

long insertsToNextBase ( AlignBuffer alignBuffer,
const SequencePosition master 
)
inline
void insertBase ( AlignBuffer alignBuffer,
SequencePosition master,
SequencePosition slave,
FastAlignReport report 
)
inline
void insertSlaveBases ( AlignBuffer alignBuffer,
SequencePosition slave,
int  length,
FastAlignReport report 
)
inline
void insertGap ( AlignBuffer alignBuffer,
SequencePosition master,
FastAlignReport report 
)
inline
static ARB_ERROR insertClustalValigned ( AlignBuffer alignBuffer,
SequencePosition master,
SequencePosition slave,
const char masterAlignment,
const char slaveAlignment,
long  alignmentLength,
FastAlignReport report 
)
static
static ARB_ERROR insertAligned ( AlignBuffer alignBuffer,
SequencePosition master,
SequencePosition slave,
long  partLength,
FastAlignReport report 
)
static
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
long calcSequenceChecksum ( const char data,
long  length 
)
inline

Definition at line 967 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
static ARB_ERROR writeStringToAlignment ( GBDATA gb_species,
GB_CSTR  alignment,
GB_CSTR  data_name,
GB_CSTR  str,
bool  temporary 
)
static
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
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

Definition at line 1271 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
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
static void appendNameAndUsedBasePositions ( char **  toString,
GBDATA gb_species,
int  usedBasePositions 
)
static
int min ( int  i,
int  j 
)
inline

Definition at line 1374 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 
)
static
void FastAligner_start ( AW_window aw,
const AlignDataAccess data_access 
)

Definition at line 2168 of file fast_aligner.cxx.

References RangeList::add(), arb_progress::allow_title_reuse(), aw_message_if(), AW_root::awar(), AWAR_CURSOR_POSITION_LOCAL, AWAR_EDITOR_ALIGNMENT, AWAR_NN_FAST_MODE, AWAR_NN_MISMATCHES, AWAR_NN_OLIGO_LEN, AWAR_NN_REL_MATCHES, AWAR_PT_SERVER, AWAR_SPECIES_NAME, AW_root::awar_string(), RangeList::begin(), build_RangeList_from_string(), AlignDataAccess::do_refresh, RangeList::end(), PosRange::end(), error(), FA_AROUND_CURSOR, fa_assert(), FA_AWAR_ACTION_ON_ERROR, FA_AWAR_AROUND, FA_AWAR_BASE_FREQ_A, FA_AWAR_BASE_FREQ_C, FA_AWAR_BASE_FREQ_T, FA_AWAR_CONTINUE_ON_ERROR, FA_AWAR_ESTIMATE_BASE_FREQ, FA_AWAR_EXPECTED_DISTANCE, FA_AWAR_GAP_A, FA_AWAR_GAP_B, FA_AWAR_GAP_C, FA_AWAR_MIRROR, FA_AWAR_NEXT_RELATIVES, FA_AWAR_PROTECTION, FA_AWAR_PT_SERVER_ALIGNMENT, FA_AWAR_RANGE, FA_AWAR_REFERENCE, FA_AWAR_REFERENCE_NAME, FA_AWAR_RELATIVE_RANGE, FA_AWAR_REPORT, FA_AWAR_SAI_RANGE_CHARS, FA_AWAR_SAI_RANGE_NAME, FA_AWAR_SHOW_GAPS_MESSAGES, FA_AWAR_STRUCTURE_SUPPLEMENT, FA_AWAR_SUBST_PARA_AC, FA_AWAR_SUBST_PARA_AG, FA_AWAR_SUBST_PARA_AT, FA_AWAR_SUBST_PARA_CG, FA_AWAR_SUBST_PARA_CT, FA_AWAR_SUBST_PARA_GT, FA_AWAR_THRESHOLD, FA_AWAR_TO_ALIGN, FA_AWAR_USE_ISLAND_HOPPING, FA_AWAR_USE_SECONDARY, FA_CURRENT, FA_MARKED, FA_REF_CONSENSUS, FA_REF_EXPLICIT, FA_REF_RELATIVES, FA_SAI_MULTI_RANGE, FA_SELECTED, FA_SELECTED_RANGE, FA_WHOLE_SEQUENCE, GB_await_error(), GB_have_error(), gb_main, AlignDataAccess::gb_main, GB_read_string(), GBS_global_string(), GBT_expect_SAI(), GBT_find_sequence(), GBT_get_alignment_len(), GBT_get_default_alignment(), AlignDataAccess::get_first_selected_species, get_first_selected_species(), AlignDataAccess::get_group_consensus, AlignDataAccess::get_next_selected_species, get_next_selected_species(), AW_window::get_root(), AlignDataAccess::get_selected_range, SearchRelativeParams::getFamilyFinder(), AlignDataAccess::getHelixString(), PosRange::is_part(), island_hopper, NULp, AW_awar::read_char_pntr(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), AlignDataAccess::refresh_display, FamilyFinder::restrict_2_region(), RSS_BOTH_MIN, PosRange::start(), ta, PosRange::whole(), and AW_awar::write_as_string().

Referenced by FastAligner_create_window().

static void nullcb ( )
static

Definition at line 2424 of file fast_aligner.cxx.

Referenced by FastAligner_create_variables().

void FastAligner_create_variables ( AW_root root,
AW_default  db1 
)
void FastAligner_set_align_current ( AW_root root,
AW_default  db1 
)

Definition at line 2483 of file fast_aligner.cxx.

References AW_root::awar_int(), FA_AWAR_TO_ALIGN, and FA_CURRENT.

void FastAligner_set_reference_species ( AW_root root)
static AW_window* create_island_hopping_window ( AW_root root)
static
static AW_window* create_family_settings_window ( AW_root root)
static
AW_window* FastAligner_create_window ( AW_root root,
const AlignDataAccess data_access 
)

Variable Documentation

IslandHopping* island_hopper = NULp
static
GB_alignment_type global_alignmentType = GB_AT_UNKNOWN
static

Definition at line 163 of file fast_aligner.cxx.

Referenced by alignToNextRelative(), cannot_fast_align(), and Aligner::run().

int currentSequenceNumber
static

Definition at line 165 of file fast_aligner.cxx.

int overallSequenceNumber
static

Definition at line 166 of file fast_aligner.cxx.

LooseBases unaligned_bases
static

Definition at line 336 of file fast_aligner.cxx.

AWT_config_mapping_def aligner_config_mapping[]
static

Definition at line 2609 of file fast_aligner.cxx.