AlignmentStruct Class Reference

Output of threading program. More...

#include <open_prospect.h>

Public Member Functions
	AlignmentStruct ()
	~AlignmentStruct ()
AlignmentStruct &	operator= (const AlignmentStruct &rhs)
	AlignmentStruct (const AlignmentStruct &rhs)
void	Free (void)
void	Copy (const AlignmentStruct &rhs)
void	SetAlign (int in_target_len, int *in_target_align, int in_template_len, int *in_template_align)
int	SetAlign (char *target_align, char *template_align)
int	SetAlign (AlignmentStruct &rhs, int target_start=-1, int target_end=-1)
int	SetAlign (ProspectParam *param, WeightArray weights, TemplateStruct *template_data, TargetStruct *target_data, int *core_pos, char *core_del=NULL)
int	SetAlignFromNumStr (char *target_align, char *template_align)
char *	Write_XML (ProspectParam *param, WeightArray weight, TemplateStruct *template_data, TargetStruct *target_data, ScoreStruct *score)
void	GetEnergies (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, EnergyArray energy, long mask=0xFFFFFFFF)
	Calculates the energy of the alignment from the given weights and energy functions.
int	GetFragCount (void)
int	GetFragStart (int frag_num)
int	GetFragStop (int frag_num)
void	CalcFrag (void)
int	GetTargetAlign (int i)
int	GetTemplateAlign (int i)
int	GetTargetLen (void)
int	GetTemplateLen (void)
char *	GetTargetAlignStr (TemplateStruct *template_data, TargetStruct *target_data)
char *	GetTemplateAlignStr (TemplateStruct *template_data, TargetStruct *target_data)
void	GetAlignmentStrings (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, char **template_str, char **template_ss_str, char **target_str, char **target_ss_str, char **align_str, char **core_str)
Data Fields
char	method [20]
Protected Attributes
int *	target_align
int *	template_align
int	target_len
int	template_len
int *	frag_start
int *	frag_stop
int	frag_count
Friends
class	ProspectOutput
class	ProspectThreadingInfo
class	TargetAlignmentStruct

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Detailed Description

Output of threading program.

Each position in the array describes the number of the alternet sequence that it is aligned to. -1 is means that a position is not aligned with the alternet sequence

Parameters:

target_align

This is an array of target_len, which each element

Definition at line 861 of file open_prospect.h.

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Member Function Documentation

void AlignmentStruct::GetEnergies (  ProspectParam *  param, TemplateStruct *  template_data, TargetStruct *  target_data, EnergyArray  energy, long  mask = 0xFFFFFFFF )

Calculates the energy of the alignment from the given weights and energy functions. Parameters: param  Prospect data template_data  The template data target_data  The target data energy  The energy calculated for the given alignement Definition at line 209 of file seq_io.cc. References e_contact, e_count, e_mask, e_mutation, e_mutationfull, e_mutationlog, e_mutscore, e_sec_struct, e_singleton, e_twobody_frozen, TargetStruct::len, TargetStruct::Setup(), and TargetStruct::twobody. Referenced by ScoreStruct::ScoreRaw(), and Write_XML().

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The documentation for this class was generated from the following files:

• src/common/open_prospect.h
• src/common/seq_io.cc

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