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SecSequenceData Class Reference

Print alignment of two sequences considering also secondary structure. More...

+ Inheritance diagram for SecSequenceData:
+ Collaboration diagram for SecSequenceData:

Public Member Functions

 SecSequenceData (int n, const string &seq1, const string &seq2, const string &sec1, const string &sec2, const string &name1="Seq1", const string &name2="Seq2")
 Default constructor. More...
 
 SecSequenceData (const SecSequenceData &orig)
 Copy constructor. More...
 
virtual ~SecSequenceData ()
 Destructor.
 
virtual void add (string s, int n)
 Insert a sequence at position n of the vector.
 
virtual void calculateMatch (int i, int tbi, int j, int tbj)
 Calculate single match positions. More...
 
virtual void clear ()
 Insert a void string in all positions of the vector.
 
virtual void copy (const SecSequenceData &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual void copy (const AlignmentData &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual AlignmentgenerateMatch (double score=0.00)
 Generate and return an ensemble of suboptimal alignments. More...
 
virtual void getMatch ()
 Reverse the strings of the vector.
 
virtual string getSequence (int n)
 Return the sequence at position n of the vector. More...
 
virtual SecSequenceDatanewCopy ()
 Construct a new "deep copy" of this object.
 
SecSequenceDataoperator= (const SecSequenceData &orig)
 Assignment operator. More...
 
virtual void outputMatch (ostream &os, bool fasta=false)
 Control if the strings of the vector are similar and print them. More...
 
virtual void setSequence (string s, int n)
 Set the sequence at position n of the vector. More...
 
virtual bool similar (char a, char b)
 Define if two residues are similar. More...
 

Data Fields

vector< string > match
 Matching alignment positions.
 
int n
 Number of strings in the alignment.
 
string name1
 Name of target sequence.
 
string name2
 Name of template sequence.
 

Detailed Description

Print alignment of two sequences considering also secondary structure.

Constructor & Destructor Documentation

SecSequenceData ( int  n,
const string &  seq1,
const string &  seq2,
const string &  sec1,
const string &  sec2,
const string &  _n1 = "Seq1",
const string &  _n2 = "Seq2" 
)

Default constructor.

Parameters
n
seq1
seq2
sec1
sec2
_n1
_n2
SecSequenceData ( const SecSequenceData orig)

Copy constructor.

Parameters
orig

Member Function Documentation

void calculateMatch ( int  i,
int  tbi,
int  j,
int  tbj 
)
virtual

Calculate single match positions.

Parameters
i
tbi
j
tbj

Implements AlignmentData.

void copy ( const SecSequenceData orig)
virtual

Copy orig object to this object ("deep copy").

Parameters
orig
void copy ( const AlignmentData orig)
virtualinherited

Copy orig object to this object ("deep copy").

Parameters
orig
Alignment & generateMatch ( double  score = 0.00)
virtual

Generate and return an ensemble of suboptimal alignments.

Parameters
score
Returns

Implements AlignmentData.

string getSequence ( int  n)
virtual

Return the sequence at position n of the vector.

Parameters
n
Returns

Implements AlignmentData.

SecSequenceData & operator= ( const SecSequenceData orig)

Assignment operator.

Parameters
orig
Returns
void outputMatch ( ostream &  os,
bool  fasta = false 
)
virtual

Control if the strings of the vector are similar and print them.

Parameters
os
fasta

Implements AlignmentData.

void setSequence ( string  s,
int  n 
)
virtual

Set the sequence at position n of the vector.

Parameters
s
n
bool similar ( char  a,
char  b 
)
virtualinherited

Define if two residues are similar.

Parameters
a
b
Returns

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