PT_new_design.cxx File Reference

#include "pt_split.h"
#include <PT_server_prototypes.h>
#include <struct_man.h>
#include "probe_tree.h"
#include "PT_prefixIter.h"
#include <arb_str.h>
#include <arb_defs.h>
#include <arb_sort.h>
#include <arb_strbuf.h>
#include <arb_strarray.h>
#include <climits>
#include <algorithm>
#include <map>
#include <arb_progress.h>

Include dependency graph for PT_new_design.cxx:

Go to the source code of this file.

Classes
struct	dt_bondssum
class	Oligo
class	MatchingOligo
class	PD_formatter
struct	ptnd_chain_count_mishits
class	CentigradePos
class	OutgroupMatcher
class	ProbeOccurrence
class	ProbeIterator
class	PO_Less
struct	SCP_Less
class	ProbeCandidates
class	DesignTargets

Macros
#define	MIN_DESIGN_PROBE_LENGTH   DOMAIN_MIN_LENGTH
#define	DUMP_TPROBES(a, b)

Typedefs
typedef std::map< const PT_pdc *const, PD_formatter >	PD_Formatter4design

Enumerations
enum	ProbeSortMode { PSM_QUALITY, PSM_SEQUENCE }

Functions
void	aisc_link (dll_public *dll, PT_tprobes *tprobe)
int	pt_init_bond_matrix (PT_local *THIS)
static int	ptnd_compare_quality (const void *vtp1, const void *vtp2, void *)
static int	ptnd_compare_sequence (const void *vtp1, const void *vtp2, void *)
static void	sort_tprobes_by (PT_pdc *pdc, ProbeSortMode mode)
static void	clip_tprobes (PT_pdc *pdc, int count)
static int	pt_get_gc_content (char *probe)
static double	pt_get_temperature (const char *probe)
static void	tprobes_sumup_perc_and_calc_quality (PT_pdc *pdc)
static char	hitgroup_idx2char (int idx)
int	get_max_probelen (const PT_pdc *pdc)
int	shown_apos (const PT_tprobes *tprobe)
int	shown_ecoli (const PT_tprobes *tprobe)
int	shown_qual (const PT_tprobes *tprobe)
const PD_formatter &	get_formatter (const PT_pdc *pdc)
void	erase_formatter (const PT_pdc *pdc)
char *	get_design_info (const PT_tprobes *tprobe)
char *	get_design_hinfo (const PT_pdc *pdc)
static int	count_mishits_for_all (POS_TREE2 *pt)
static int	count_mishits_for_matched (char *probe, POS_TREE2 *pt, int height)
static void	remove_tprobes_with_too_many_mishits (PT_pdc *pdc)
static void	remove_tprobes_outside_ecoli_range (PT_pdc *pdc)
static size_t	tprobes_calculate_bonds (PT_local *locs)
int	PT_start_design (PT_pdc *pdc, int)

Variables
static PD_Formatter4design	format4design

Macro Definition Documentation

#define MIN_DESIGN_PROBE_LENGTH   DOMAIN_MIN_LENGTH

Definition at line 36 of file PT_new_design.cxx.

Referenced by PT_start_design().

#define DUMP_TPROBES	(		a,
			b
	)

Definition at line 1423 of file PT_new_design.cxx.

Referenced by PT_start_design().

Typedef Documentation

typedef std::map<const PT_pdc*const, PD_formatter> PD_Formatter4design

Definition at line 509 of file PT_new_design.cxx.

Enumeration Type Documentation

enum ProbeSortMode

Enumerator
PSM_QUALITY
PSM_SEQUENCE

Definition at line 299 of file PT_new_design.cxx.

Function Documentation

void aisc_link ( dll_public *  dll, PT_tprobes *  tprobe  )

inline

Definition at line 48 of file PT_new_design.cxx.

Referenced by ProbeCandidates::create_tprobes(), and sort_tprobes_by().

int pt_init_bond_matrix

(

PT_local *

THIS

)

Definition at line 50 of file PT_new_design.cxx.

Referenced by init_bond_matrix().

static int ptnd_compare_quality ( const void *  vtp1, const void *  vtp2, void *    )

static

Definition at line 280 of file PT_new_design.cxx.

References cmp, and double_cmp().

Referenced by sort_tprobes_by().

static int ptnd_compare_sequence ( const void *  vtp1, const void *  vtp2, void *    )

static

Definition at line 292 of file PT_new_design.cxx.

Referenced by sort_tprobes_by().

static void sort_tprobes_by ( PT_pdc *  pdc, ProbeSortMode  mode  )

static

Definition at line 304 of file PT_new_design.cxx.

References aisc_link(), aisc_unlink(), GB_sort(), NULp, PSM_QUALITY, PSM_SEQUENCE, ptnd_compare_quality(), and ptnd_compare_sequence().

Referenced by PT_start_design().

static void clip_tprobes ( PT_pdc *  pdc, int  count  )

static

Definition at line 337 of file PT_new_design.cxx.

Referenced by PT_start_design().

static int pt_get_gc_content ( char *  probe )

static

Definition at line 351 of file PT_new_design.cxx.

References PT_C, and PT_G.

Referenced by get_design_info().

static double pt_get_temperature ( const char *  probe )

static

Definition at line 362 of file PT_new_design.cxx.

References PT_C, and PT_G.

Referenced by ProbeCandidates::create_tprobes(), and get_design_info().

static void tprobes_sumup_perc_and_calc_quality ( PT_pdc *  pdc )

static

Definition at line 371 of file PT_new_design.cxx.

Referenced by PT_start_design().

static char hitgroup_idx2char ( int  idx )

static

Definition at line 408 of file PT_new_design.cxx.

References pt_assert.

Referenced by get_design_info().

int get_max_probelen ( const PT_pdc *  pdc )

inline

Definition at line 421 of file PT_new_design.cxx.

Referenced by get_design_hinfo(), and PT_start_design().

int shown_apos ( const PT_tprobes *  tprobe )

inline

Definition at line 425 of file PT_new_design.cxx.

References info2bio().

Referenced by get_design_info().

int shown_ecoli ( const PT_tprobes *  tprobe )

inline

Definition at line 426 of file PT_new_design.cxx.

References PT_abs_2_ecoli_rel().

Referenced by get_design_info().

int shown_qual ( const PT_tprobes *  tprobe )

inline

Definition at line 427 of file PT_new_design.cxx.

Referenced by get_design_info().

const PD_formatter& get_formatter ( const PT_pdc *  pdc )

inline

Definition at line 512 of file PT_new_design.cxx.

References pt_assert.

Referenced by get_design_hinfo(), and get_design_info().

void erase_formatter ( const PT_pdc *  pdc )

inline

Definition at line 522 of file PT_new_design.cxx.

Referenced by get_design_hinfo(), get_design_info(), and PT_start_design().

char* get_design_info

(

const PT_tprobes *

tprobe

)

Definition at line 524 of file PT_new_design.cxx.

References abs, buffer, BUFFERSIZE, complement_probe(), create_reversed_probe(), erase_formatter(), GB_give_buffer(), GB_give_buffer2(), get_formatter(), hitgroup_idx2char(), probe_2_readable(), pt_assert, pt_get_gc_content(), pt_get_temperature(), shown_apos(), shown_ecoli(), and shown_qual().

char* get_design_hinfo

(

const PT_pdc *

pdc

)

Definition at line 605 of file PT_new_design.cxx.

References ARB_strdup(), buffer, BUFFERSIZE, erase_formatter(), GB_give_buffer(), GBS_global_string_copy(), PD_formatter::get_apos_width(), PD_formatter::get_ecol_width(), get_formatter(), PD_formatter::get_grps_width(), PD_formatter::get_max_designed_len(), get_max_probelen(), PD_formatter::get_qual_width(), NULp, pt_assert, and s.

static int count_mishits_for_all ( POS_TREE2 *  pt )

static

go down the tree to chains and leafs; count the species that are in the non member group

Definition at line 723 of file PT_new_design.cxx.

References probe_struct_global::abs_pos, MostUsedPos::announce(), AbsLoc::get_abs_pos(), AbsLoc::get_pid(), POS_TREE2::is_chain(), POS_TREE2::is_leaf(), ptnd_chain_count_mishits::mishits, probe_input_data::outside_group(), psg, PT_BASES, PT_forwhole_chain(), PT_QU, and PT_read_son().

Referenced by count_mishits_for_matched().

static int count_mishits_for_matched ( char *  probe, POS_TREE2 *  pt, int  height  )

static

search down the tree to find matching species for the given probe

Definition at line 747 of file PT_new_design.cxx.

References count_mishits_for_all(), ReadableDataLoc::get_pid(), DataLoc::get_rel_pos(), probe_input_data::get_size(), POS_TREE2::is_leaf(), POS_TREE2::is_node(), ptnd_chain_count_mishits::mishits, PT_A, PT_BASES, PT_forwhole_chain(), and PT_read_son().

Referenced by remove_tprobes_with_too_many_mishits().

static void remove_tprobes_with_too_many_mishits ( PT_pdc *  pdc )

static

Check for direct mishits

Definition at line 783 of file PT_new_design.cxx.

References probe_struct_global::abs_pos, MostUsedPos::clear(), count_mishits_for_matched(), MostUsedPos::get_most_used(), min, psg, and probe_struct_global::TREE_ROOT2().

Referenced by PT_start_design().

static void remove_tprobes_outside_ecoli_range ( PT_pdc *  pdc )

static

Check the probes position.

Definition at line 805 of file PT_new_design.cxx.

References PT_abs_2_ecoli_rel().

Referenced by PT_start_design().

static size_t tprobes_calculate_bonds ( PT_local *  locs )

static

check the average bond size. returns number of tprobes

checks probe hairpin bonds

Definition at line 819 of file PT_new_design.cxx.

References MaxBond::get_max_bond().

Referenced by PT_start_design().

int PT_start_design	(	PT_pdc *	pdc,
		int
	)

Definition at line 1426 of file PT_new_design.cxx.

References OutgroupMatcher::calculate_outgroup_matches(), clip_tprobes(), ProbeCandidates::create_tprobes(), DUMP_TPROBES, erase_formatter(), error(), fputs(), GBS_global_string(), GBT_splitNdestroy_string(), gene_flag, DesignTargets::generate(), DesignTargets::get_added_count(), DesignTargets::get_count(), DesignTargets::get_error(), get_max_probelen(), locs, MIN_DESIGN_PROBE_LENGTH, names, probe_compress_sequence(), PSM_QUALITY, PSM_SEQUENCE, pt_assert, pt_export_error_if(), ptpd_read_names(), remove_tprobes_outside_ecoli_range(), remove_tprobes_with_too_many_mishits(), seq, CharPtrArray::size(), sort_tprobes_by(), SPLIT_DROPEMPTY, tprobes_calculate_bonds(), and tprobes_sumup_perc_and_calc_quality().

Variable Documentation

PD_Formatter4design format4design

static

Definition at line 510 of file PT_new_design.cxx.