ClustalV.cxx File Reference

#include "ClustalV.hxx"
#include "seq_search.hxx"
#include <cctype>
#include <climits>

Include dependency graph for ClustalV.cxx:

Go to the source code of this file.

Macros
#define	MASTER_GAP_OPEN   50
#define	CHEAP_GAP_OPEN   20
#define	DEFAULT_GAP_OPEN   30
#define	MASTER_GAP_EXTEND   18
#define	CHEAP_GAP_EXTEND   5
#define	DEFAULT_GAP_EXTEND   10
#define	DEFAULT_IMPROBABLY_MUTATION   10
#define	DEFAULT_PROBABLY_MUTATION   4
#define	DYNAMIC_PENALTIES
#define	MAX_GAP_OPEN_DISCOUNT   (DEFAULT_GAP_OPEN-CHEAP_GAP_OPEN)
#define	MAX_GAP_EXTEND_DISCOUNT   (DEFAULT_GAP_EXTEND-CHEAP_GAP_EXTEND)
#define	MAXN   2
#define	MAX_BASETYPES   21
#define	IF_MATRIX_DUMP(xxx)
#define	UNKNOWN_ACID   255
#define	NUCLEIDS   16
#define	cheap_if(cond)   ((cond) ? 1 : 2)
#define	COMPARABLE_BASES   5
#define	AF   0
#define	MHO   1
#define	BO   1

Typedefs
typedef int	Boolean

Functions
int	master_gap_open (int beforePosition)
int	master_gap_extend (int beforePosition)
int	master_gapAtWithOpenPenalty (int atPosition, int length, int penalty)
int	master_gapAt (int atPosition, int length)
int	slave_gap_open (int)
int	slave_gap_extend (int)
int	slave_gapAtWithOpenPenalty (int atPosition, int length, int penalty)
int	slave_gapAt (int atPosition, int length)
static int	baseCmp (unsigned char c1, unsigned char c2)
int	baseMatch (char c1, char c2)
static int	getPenalty (char c1, char c2)
ARB_ERROR	MAXLENtooSmall ()
void *	ckalloc (size_t bytes, ARB_ERROR &error)
static ARB_ERROR	init_myers (long max_seq_length)
static void	make_pamo (int nv)
static void	fill_pam ()
static void	exit_myers ()
static ARB_ERROR	init_show_pair (long max_seq_length)
static void	exit_show_pair ()
int	set_displ (int offset, int value)
int	decr_displ (int offset, int value)
void	add (int v)
int	calc_weight (int iat, int jat, int v1, int v2)
static int	diff (int v1, int v2, int v3, int v4, int st, int en)
static void	do_align (int &score, long act_seq_length)
static int	add_ggaps (long)
static int	res_index (const char *t, char c)
static void	p_encode (const unsigned char *seq, unsigned char *naseq, int l)
static void	n_encode (const unsigned char *seq, unsigned char *naseq, int l)
ARB_ERROR	ClustalV_align (int is_dna, int weighted, const char *seq1, int length1, const char *seq2, int length2, const int *gapsBefore1, int max_seq_length, const char *&res1, const char *&res2, int &reslen, int &score)
void	ClustalV_exit ()

Variables
static bool	module_initialized = false
static Boolean	dnaflag
static Boolean	is_weight
static int	xover
static int	little_pam
static int	big_pam
static int	pamo [(MAX_BASETYPES-1)*MAX_BASETYPES/2]
static int	pam [MAX_BASETYPES][MAX_BASETYPES]
static int	pos1
static int	pos2
static int **	naa1
static int **	naa2
static int **	naas
static int	seqlen_array [MAXN+1]
static unsigned char *	seq_array [MAXN+1]
static int	group [MAXN+1]
static int	alist [MAXN+1]
static int	fst_list [MAXN+1]
static int	snd_list [MAXN+1]
static int	nseqs
static int	weights [MAX_BASETYPES][MAX_BASETYPES]
static size_t	displ_size = 0
static int *	displ
static int *	zza
static int *	zzb
static int *	zzc
static int *	zzd
static int	print_ptr
static int	last_print
static const int *	gaps_before_position
static const char *	amino_acid_order = "XCSTPAGNDEQHRKMILVFYW"
static const char *	nucleic_acid_order = "-ACGTUMRWSYKVHDBN"
static const char *	nucleic_maybe_A = "-A----AAA---AAA-A"
static const char *	nucleic_maybe_C = "--C---C--CC-CC-CC"
static const char *	nucleic_maybe_G = "---G---G-G-GG-GGG"
static const char *	nucleic_maybe_T = "----T---T-TT-TTTT"
static const char *	nucleic_maybe_U = "-----U--U-UU-UUUU"
static const char *	nucleic_maybe [6] = { NULp, nucleic_maybe_A, nucleic_maybe_C, nucleic_maybe_G, nucleic_maybe_T, nucleic_maybe_U }
static char *	result [3]
static char	pam250mt []
static char *	matptr = pam250mt

Macro Definition Documentation

#define MASTER_GAP_OPEN   50

Definition at line 21 of file ClustalV.cxx.

Referenced by master_gap_open().

#define CHEAP_GAP_OPEN   20

Definition at line 22 of file ClustalV.cxx.

#define DEFAULT_GAP_OPEN   30

Definition at line 24 of file ClustalV.cxx.

Referenced by master_gap_open(), and slave_gap_open().

#define MASTER_GAP_EXTEND   18

Definition at line 26 of file ClustalV.cxx.

Referenced by master_gap_extend().

#define CHEAP_GAP_EXTEND   5

Definition at line 27 of file ClustalV.cxx.

#define DEFAULT_GAP_EXTEND   10

Definition at line 29 of file ClustalV.cxx.

Referenced by master_gap_extend(), and slave_gap_extend().

#define DEFAULT_IMPROBABLY_MUTATION   10

Definition at line 31 of file ClustalV.cxx.

Referenced by getPenalty().

#define DEFAULT_PROBABLY_MUTATION   4

Definition at line 32 of file ClustalV.cxx.

Referenced by getPenalty().

#define DYNAMIC_PENALTIES

Definition at line 34 of file ClustalV.cxx.

#define MAX_GAP_OPEN_DISCOUNT   (DEFAULT_GAP_OPEN-CHEAP_GAP_OPEN)

Definition at line 38 of file ClustalV.cxx.

Referenced by master_gap_open().

#define MAX_GAP_EXTEND_DISCOUNT   (DEFAULT_GAP_EXTEND-CHEAP_GAP_EXTEND)

Definition at line 39 of file ClustalV.cxx.

Referenced by master_gap_extend().

#define MAXN   2

Definition at line 41 of file ClustalV.cxx.

#define MAX_BASETYPES   21

Definition at line 50 of file ClustalV.cxx.

Referenced by do_align(), exit_myers(), fill_pam(), and init_myers().

#define IF_MATRIX_DUMP

(

xxx

)

Definition at line 103 of file ClustalV.cxx.

Referenced by diff().

#define UNKNOWN_ACID   255

Definition at line 175 of file ClustalV.cxx.

Referenced by res_index().

#define NUCLEIDS   16

Definition at line 178 of file ClustalV.cxx.

Referenced by fill_pam().

#define cheap_if

(

cond

)

((cond) ? 1 : 2)

Definition at line 193 of file ClustalV.cxx.

Referenced by baseCmp().

#define COMPARABLE_BASES   5

Referenced by baseCmp().

#define AF   0

Referenced by diff().

#define MHO   1

Referenced by diff().

#define BO   1

Referenced by diff().

Typedef Documentation

typedef int Boolean

Definition at line 45 of file ClustalV.cxx.

Function Documentation

int master_gap_open ( int  beforePosition )

inline

Definition at line 106 of file ClustalV.cxx.

References DEFAULT_GAP_OPEN, MASTER_GAP_OPEN, and MAX_GAP_OPEN_DISCOUNT.

Referenced by diff(), do_align(), and master_gapAt().

int master_gap_extend ( int  beforePosition )

inline

Definition at line 119 of file ClustalV.cxx.

References DEFAULT_GAP_EXTEND, MASTER_GAP_EXTEND, and MAX_GAP_EXTEND_DISCOUNT.

Referenced by diff(), and master_gapAtWithOpenPenalty().

int master_gapAtWithOpenPenalty ( int  atPosition, int  length, int  penalty  )

inline

Definition at line 132 of file ClustalV.cxx.

References master_gap_extend().

Referenced by master_gapAt().

int master_gapAt ( int  atPosition, int  length  )

inline

Definition at line 155 of file ClustalV.cxx.

References master_gap_open(), and master_gapAtWithOpenPenalty().

Referenced by diff().

int slave_gap_open ( int  )

inline

Definition at line 159 of file ClustalV.cxx.

References DEFAULT_GAP_OPEN.

Referenced by diff(), and slave_gapAt().

int slave_gap_extend ( int  )

inline

Definition at line 163 of file ClustalV.cxx.

References DEFAULT_GAP_EXTEND.

Referenced by diff(), and slave_gapAtWithOpenPenalty().

int slave_gapAtWithOpenPenalty ( int  atPosition, int  length, int  penalty  )

inline

Definition at line 167 of file ClustalV.cxx.

References slave_gap_extend().

Referenced by diff(), and slave_gapAt().

int slave_gapAt ( int  atPosition, int  length  )

inline

Definition at line 171 of file ClustalV.cxx.

References slave_gap_open(), and slave_gapAtWithOpenPenalty().

Referenced by diff().

static int baseCmp ( unsigned char  c1, unsigned char  c2  )

static

Definition at line 194 of file ClustalV.cxx.

References cheap_if, COMPARABLE_BASES, fa_assert(), and FALLTHROUGH.

Referenced by baseMatch(), and getPenalty().

int baseMatch	(	char	c1,
		char	c2
	)

Definition at line 249 of file ClustalV.cxx.

References baseCmp(), and fa_assert().

Referenced by relatedBases().

static int getPenalty ( char  c1, char  c2  )

static

Definition at line 266 of file ClustalV.cxx.

References baseCmp(), DEFAULT_IMPROBABLY_MUTATION, and DEFAULT_PROBABLY_MUTATION.

Referenced by fill_pam().

ARB_ERROR MAXLENtooSmall ( )

inline

Definition at line 324 of file ClustalV.cxx.

void* ckalloc ( size_t  bytes, ARB_ERROR &  error  )

inline

Definition at line 328 of file ClustalV.cxx.

References NULp.

Referenced by ClustalV_align(), init_myers(), and init_show_pair().

static ARB_ERROR init_myers ( long  max_seq_length )

static

Definition at line 337 of file ClustalV.cxx.

References ckalloc(), error(), and MAX_BASETYPES.

Referenced by ClustalV_align().

static void make_pamo ( int  nv )

static

Definition at line 352 of file ClustalV.cxx.

References little_pam, and pamo.

Referenced by ClustalV_align().

static void fill_pam ( )

static

Definition at line 371 of file ClustalV.cxx.

References getPenalty(), MAX_BASETYPES, NUCLEIDS, pamo, and xover.

Referenced by ClustalV_align().

static void exit_myers ( )

static

Definition at line 408 of file ClustalV.cxx.

References MAX_BASETYPES.

Referenced by ClustalV_exit().

static ARB_ERROR init_show_pair ( long  max_seq_length )

static

Definition at line 419 of file ClustalV.cxx.

References ckalloc(), and error().

Referenced by ClustalV_align().

static void exit_show_pair ( )

static

Definition at line 438 of file ClustalV.cxx.

Referenced by ClustalV_exit().

int set_displ ( int  offset, int  value  )

inline

Definition at line 449 of file ClustalV.cxx.

References fa_assert(), and offset.

Referenced by add(), and diff().

int decr_displ ( int  offset, int  value  )

inline

Definition at line 454 of file ClustalV.cxx.

References fa_assert(), and offset.

Referenced by diff().

void add ( int  v )

inline

Definition at line 461 of file ClustalV.cxx.

References set_displ().

Referenced by References::add_dbid(), add_probe_to_collection_event(), GroupSearch::addSortCriterion(), checkAndMergeFields(), create_new_species(), diff(), lowfreqrandval(), mark_species(), nt_build_conf_string_rek(), arb_test::FINAL_TYPE< T >::of(), SpecSetRegistry::registerTree(), and ED4_manager::update_bases().

int calc_weight ( int  iat, int  jat, int  v1, int  v2  )

inline

Definition at line 472 of file ClustalV.cxx.

References fa_assert(), and seq_array.

Referenced by diff().

static int diff ( int  v1, int  v2, int  v3, int  v4, int  st, int  en  )

static

*************if(!v4)*********BUG*******************************

Definition at line 534 of file ClustalV.cxx.

References add(), AF, BO, calc_weight(), decr_displ(), fa_assert(), IF_MATRIX_DUMP, master_gap_extend(), master_gap_open(), master_gapAt(), MHO, seq_array, set_displ(), slave_gap_extend(), slave_gap_open(), slave_gapAt(), and slave_gapAtWithOpenPenalty().

Referenced by ap_calc_bootstrap_remark_sub(), ap_just_tree_rek(), AW::are_parallel(), aw_status_timer_listen_event(), colorDistSquare(), do_align(), arb_test::value_matcher< T >::dump_expectation(), GB_MEMCMP(), gb_read_bin(), BoundTreeAwarCallback::is_less_than(), GBL_IMPL::modify_trace_indent(), PH_display::monitor_horizontal_scroll_cb(), MatrixDisplay::monitor_horizontal_scroll_cb(), PH_display::monitor_vertical_scroll_cb(), MatrixDisplay::monitor_vertical_scroll_cb(), arb_test::epsilon_similar::operator()(), PTD_write_node_to_disk(), PartRegistry::put_part_from_partial_tree(), SEC_oriented::set_abs_angle(), SQ_pass2(), SQ_pass2_no_tree(), Strcasecmp(), and Strncasecmp().

static void do_align ( int &  score, long  act_seq_length  )

static

Definition at line 807 of file ClustalV.cxx.

References diff(), fa_assert(), master_gap_open(), MAX_BASETYPES, nseqs, pos1, pos2, and seq_array.

Referenced by ClustalV_align().

static int add_ggaps ( long  )

static

Definition at line 877 of file ClustalV.cxx.

References print_ptr.

Referenced by ClustalV_align().

static int res_index ( const char *  t, char  c  )

static

Definition at line 915 of file ClustalV.cxx.

References UNKNOWN_ACID.

Referenced by n_encode(), and p_encode().

static void p_encode ( const unsigned char *  seq, unsigned char *  naseq, int  l  )

static

Definition at line 923 of file ClustalV.cxx.

References aw_message(), fa_assert(), and res_index().

Referenced by ClustalV_align().

static void n_encode ( const unsigned char *  seq, unsigned char *  naseq, int  l  )

static

Definition at line 950 of file ClustalV.cxx.

References aw_message(), fa_assert(), and res_index().

Referenced by ClustalV_align().

ARB_ERROR ClustalV_align	(	int	is_dna,
		int	weighted,
		const char *	seq1,
		int	length1,
		const char *	seq2,
		int	length2,
		const int *	gapsBefore1,
		int	max_seq_length,
		const char *&	res1,
		const char *&	res2,
		int &	reslen,
		int &	score
	)

Definition at line 971 of file ClustalV.cxx.

References add_ggaps(), ckalloc(), do_align(), iupac::encode(), error(), fill_pam(), init_myers(), init_show_pair(), make_pamo(), max, module_initialized, n_encode(), p_encode(), and seq_array.

Referenced by cannot_fast_align().

void ClustalV_exit

(

)

Definition at line 1049 of file ClustalV.cxx.

References exit_myers(), exit_show_pair(), module_initialized, and seq_array.

Referenced by Aligner::run().

Variable Documentation

bool module_initialized = false

static

Definition at line 43 of file ClustalV.cxx.

Referenced by ClustalV_align(), and ClustalV_exit().

Boolean dnaflag

static

Definition at line 47 of file ClustalV.cxx.

Boolean is_weight

static

Definition at line 48 of file ClustalV.cxx.

int xover

static

Definition at line 52 of file ClustalV.cxx.

Referenced by fill_pam().

int little_pam

static

Definition at line 53 of file ClustalV.cxx.

Referenced by make_pamo().

int big_pam

static

Definition at line 54 of file ClustalV.cxx.

int pamo[(MAX_BASETYPES-1)*MAX_BASETYPES/2]

static

Definition at line 55 of file ClustalV.cxx.

Referenced by fill_pam(), and make_pamo().

int pam[MAX_BASETYPES][MAX_BASETYPES]

static

Definition at line 56 of file ClustalV.cxx.

int pos1

static

Definition at line 58 of file ClustalV.cxx.

Referenced by LocationEditor::create_GEN_position_from_fields(), do_align(), SEC_root::paint(), SEC_root::paintPosAnnotation(), parseLocation(), and SimpleLocation::save().

int pos2

static

Definition at line 59 of file ClustalV.cxx.

Referenced by LocationEditor::create_GEN_position_from_fields(), do_align(), SEC_root::paint(), SEC_root::paintPosAnnotation(), parseLocation(), and SimpleLocation::save().

int** naa1

static

Definition at line 60 of file ClustalV.cxx.

int** naa2

static

Definition at line 61 of file ClustalV.cxx.

int** naas

static

Definition at line 62 of file ClustalV.cxx.

int seqlen_array[MAXN+1]

static

Definition at line 63 of file ClustalV.cxx.

unsigned char* seq_array[MAXN+1]

static

Definition at line 64 of file ClustalV.cxx.

Referenced by calc_weight(), ClustalV_align(), ClustalV_exit(), diff(), and do_align().

int group[MAXN+1]

static

Definition at line 65 of file ClustalV.cxx.

Referenced by bandv_(), iupac::decode(), GroupSearch::delete_found_groups(), arb_test::FINAL_TYPE< T >::dump_brief_description(), arb_test::FINAL_TYPE< T >::dump_expectation(), ED4_terminal::event_sent_by_parent(), export_tree_node_print(), GroupRename_callenv::get_dupidx(), get_SAI_description(), get_SAI_groups(), GroupFoldedKey::get_target_data(), NestingLevelKey::get_target_data(), ParentGroupNameQueryKey::get_target_data(), Dict::getGroup(), group_selected_by_canvas_cb(), ED4_base::is_in_folded_group(), nds_maintain_viewkeys(), nds_restore_config(), Regroup(), GroupSearch::rename_found_groups(), tinvit_(), toggle_cursor_group_folding(), tree2newick(), and tsturm_().

int alist[MAXN+1]

static

Definition at line 66 of file ClustalV.cxx.

int fst_list[MAXN+1]

static

Definition at line 67 of file ClustalV.cxx.

int snd_list[MAXN+1]

static

Definition at line 68 of file ClustalV.cxx.

int nseqs

static

Definition at line 70 of file ClustalV.cxx.

Referenced by do_align().

int weights[MAX_BASETYPES][MAX_BASETYPES]

static

Definition at line 71 of file ClustalV.cxx.

Referenced by AP_weights::AP_weights(), ST_ML::calc_st_ml(), colstat_2_gnuplot_cb(), WeightedFilter::create_aliview(), WeightedFilter::create_weights(), ColumnStat::get_weights(), AP_weights::get_weights(), AP_weights::is_unweighted(), load_probe_collection(), probe_collection_update_parameters(), AP_weights::weight(), and AP_weights::~AP_weights().

size_t displ_size = 0

static

Definition at line 74 of file ClustalV.cxx.

int* displ

static

Definition at line 77 of file ClustalV.cxx.

int* zza

static

Definition at line 78 of file ClustalV.cxx.

int* zzb

static

Definition at line 79 of file ClustalV.cxx.

int* zzc

static

Definition at line 80 of file ClustalV.cxx.

int* zzd

static

Definition at line 81 of file ClustalV.cxx.

int print_ptr

static

Definition at line 82 of file ClustalV.cxx.

Referenced by add_ggaps().

int last_print

static

Definition at line 83 of file ClustalV.cxx.

const int* gaps_before_position

static

Definition at line 85 of file ClustalV.cxx.

const char* amino_acid_order = "XCSTPAGNDEQHRKMILVFYW"

static

Definition at line 176 of file ClustalV.cxx.

const char* nucleic_acid_order = "-ACGTUMRWSYKVHDBN"

static

Definition at line 179 of file ClustalV.cxx.

const char* nucleic_maybe_A = "-A----AAA---AAA-A"

static

Definition at line 180 of file ClustalV.cxx.

const char* nucleic_maybe_C = "--C---C--CC-CC-CC"

static

Definition at line 181 of file ClustalV.cxx.

const char* nucleic_maybe_G = "---G---G-G-GG-GGG"

static

Definition at line 182 of file ClustalV.cxx.

const char* nucleic_maybe_T = "----T---T-TT-TTTT"

static

Definition at line 183 of file ClustalV.cxx.

const char* nucleic_maybe_U = "-----U--U-UU-UUUU"

static

Definition at line 184 of file ClustalV.cxx.

const char* nucleic_maybe[6] = { NULp, nucleic_maybe_A, nucleic_maybe_C, nucleic_maybe_G, nucleic_maybe_T, nucleic_maybe_U }

static

Definition at line 185 of file ClustalV.cxx.

char* result[3]

static

Definition at line 277 of file ClustalV.cxx.

char pam250mt[]

static

Initial value:

= {
    12,
     0, 2,
    -2, 1, 3,
    -3, 1, 0, 6,
    -2, 1, 1, 1, 2,
    -3, 1, 0, -1, 1, 5,
    -4, 1, 0, -1, 0, 0, 2,
    -5, 0, 0, -1, 0, 1, 2, 4,
    -5, 0, 0, -1, 0, 0, 1, 3, 4,
    -5, -1, -1, 0, 0, -1, 1, 2, 2, 4,
    -3, -1, -1, 0, -1, -2, 2, 1, 1, 3, 6,
    -4, 0, -1, 0, -2, -3, 0, -1, -1, 1, 2, 6,
    -5, 0, 0, -1, -1, -2, 1, 0, 0, 1, 0, 3, 5,
    -5, -2, -1, -2, -1, -3, -2, -3, -2, -1, -2, 0, 0, 6,
    -2, -1, 0, -2, -1, -3, -2, -2, -2, -2, -2, -2, -2, 2, 5,
    -6, -3, -2, -3, -2, -4, -3, -4, -3, -2, -2, -3, -3, 4, 2, 6,
    -2, -1, 0, -1, 0, -1, -2, -2, -2, -2, -2, -2, -2, 2, 4, 2, 4,
    -4, -3, -3, -5, -4, -5, -4, -6, -5, -5, -2, -4, -5, 0, 1, 2, -1, 9,
     0, -3, -3, -5, -3, -5, -2, -4, -4, -4, 0, -4, -4, -2, -1, -1, -2, 7, 10,
    -8, -2, -5, -6, -6, -7, -4, -7, -7, -5, -3, 2, -3, -4, -5, -2, -6, 0, 0, 17
}

Definition at line 279 of file ClustalV.cxx.

char* matptr = pam250mt

static

Definition at line 302 of file ClustalV.cxx.