Abstract base class for all sorts of alignments. More...

Inheritance diagram for AlignmentBase:

Public Member Functions
	AlignmentBase ()
	Default constructor.

	AlignmentBase (const AlignmentBase &orig)
	Copy constructor.

virtual	~AlignmentBase ()
	Destructor.

virtual void	addAlignment (const AlignmentBase &other)
	Combine two multiple sequence alignments of same target. More...

virtual double	calculateIdentity ()
	Calculate overall identity. More...

virtual double	calculatePairwiseIdentity (const string &seq1, const string &seq2)
	Calculate pairwise identity between seq1 and seq2. More...

virtual void	clearAlignment ()
	Clear alignment data.

virtual void	clearTemplate ()
	Clear template data.

virtual void	copy (const AlignmentBase &orig)
	Copy orig object to this object ("deep copy"). More...

virtual void	cutTemplate (unsigned int index)
	Remove all templates below index. More...

string	deleteChar (const string &s, unsigned int n)
	Delete n-th character. More...

void	deletePos (unsigned int p)
	Delete character (or '-') from target and all templates at position p. More...

unsigned int	getLength ()
	Return length of alignment.

virtual vector< vector< int > >	getMatchSubset ()

unsigned int	getSequenceLength (const string &seq)
	Return length of seq. More...

virtual string	getTarget () const
	Return target sequence.

virtual int	getTargetAminoAcidOffset () const
	Return target aa offset (only needed for alignment, default = 0).

virtual string	getTargetName () const
	Return target name.

virtual char	getTargetPos (unsigned int p) const
	Return target position p.

virtual string	getTemplate (unsigned int index=0) const
	Return template index sequence.

virtual int	getTemplateAminoAcidOffset (unsigned int index=0) const
	Return template index aa offset (counting from zero).

virtual string	getTemplateName (unsigned int index=0) const
	Return template index name.

virtual char	getTemplatePos (unsigned int p, unsigned int index=0) const
	Return template index position p.

vector< string >	getTokens (const string &text)
	Return vector of words of a line of text. More...

void	insertCharacter (unsigned int p, char c)
	Insert character c in target and all templates at position p. More...

void	insertDash (unsigned int p)
	Insert character '-' in target and all templates at position p. More...

virtual bool	isConserved (unsigned int p, unsigned int index=9999) const
	Check for conservation. If index is 9999 check on all templates. More...

virtual bool	isDeletion (unsigned int p) const
	Check for deletion at position p. More...

virtual bool	isGap (unsigned int p, unsigned int index=0) const
	Check for gap at position p. More...

virtual bool	isInsertion (unsigned int p, unsigned int index=0) const
	Check for insertion at position p. More...

virtual double	matchPositionVector (vector< int > CeTarget, vector< int > CeTemplate, vector< int > seqTarget, vector< int > seqTemplate)
	Companion class to the previous. More...

virtual AlignmentBase *	newCopy ()
	Construct a new "deep copy" of this object. More...

AlignmentBase &	operator= (const AlignmentBase &orig)
	Assignment operator. More...

void	purgeTargetInsertions ()
	Delete all gaps from target and all templates.

virtual void	saveClustal (ostream &output) const
	Save as CLUSTAL like output. More...

virtual void	saveFasta (ostream &output) const
	Save as FASTA like output. More...

virtual void	setTarget (string t, string tName="target")
	Set target to t.

virtual void	setTargetAminoAcidOffset (int orig)
	Set target aa offset (only needed for alignment, default = 0).

virtual void	setTargetPos (unsigned int p, char res)
	Set target residue to res.

virtual void	setTemplate (string t, string tName="template")
	Set template to t. More...

virtual void	setTemplateAminoAcidOffset (unsigned int index, int val)
	Set template index aa offset (counting from zero).

virtual void	setTemplatePos (unsigned int p, char res, unsigned int index=0)
	Set template index residue to res.

virtual vector< int >	shiftMatchSubset (vector< int > inputVector, int newStartPos)
	Return a new vector with positions shifted, depending on new position. More...

unsigned int	size () const
	Return size of alignment.

virtual void	swapTemplate (unsigned int index1, unsigned int index2)
	Swap templates index1 and index2. More...

Static Public Member Functions
static unsigned int	getNewPos (const string &s, unsigned int p)
	Return position of original index if '-' are now present. More...

static unsigned int	getOrigPos (const string &s, unsigned int p)
	Return position of index if '-' would not be there (counting from zero). More...

static string	getPureSequence (const string &s)
	Return sequence without '-' characters. More...

static void	saveClustal (string t, string tName, ostream &output, unsigned int from)
	Save single line in CLUSTAL format.

static void	saveFasta (string t, string tName, ostream &output)
	Save single sequence in FASTA format.

Protected Attributes
vector< string >	seqTemplate
	Template sequences.

vector< string >	seqTemplateName
	Template names.

int	startAaTarget
	Start target aa offset.

vector< int >	startAaTemplates
	Start templates aa offsets.

string	target
	Target sequence.

string	targetName
	Target name.

Detailed Description

Abstract base class for all sorts of alignments.

Member Function Documentation

void addAlignment ( const AlignmentBase & orig )

virtual

Combine two multiple sequence alignments of same target.

The algorithm is so long, because 6 cases are distinguished:

leading insertion for target A or target B
normal insertion for target A or target B
trailing insertion for target A or target B If ignoreInsertion is set, insertions of target A are ignored.

Parameters

orig

double calculateIdentity ( )

virtual

Calculate overall identity.

Returns

double calculatePairwiseIdentity	(	const string &	seq1,
		const string &	seq2
	)

virtual

Calculate pairwise identity between seq1 and seq2.

Parameters

seq1
seq2

Returns

void copy ( const AlignmentBase & orig )

virtual

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

Parameters

orig

void cutTemplate ( unsigned int index )

virtual

Remove all templates below index.

Parameters

index

Reimplemented in Alignment.

string deleteChar	(	const string &	s,
		unsigned int	n
	)

Delete n-th character.

Parameters

s
n

Returns

void deletePos ( unsigned int p )

Delete character (or '-') from target and all templates at position p.

Parameters

p

vector< vector< int > > getMatchSubset ( )

virtual

Return a vector of int containing the aligned aa in target and template. Each position of the vector contains the aa position in the target and in the template (-1 means gap).

Returns

unsigned int getNewPos	(	const string &	s,
		unsigned int	p
	)

static

Return position of original index if '-' are now present.

Parameters

s
p

Returns

unsigned int getOrigPos	(	const string &	s,
		unsigned int	p
	)

static

Return position of index if '-' would not be there (counting from zero).

If original index points to a dash, it returns the position of the first non-dash left character, again taking '-' not into account.

Parameters

s
p

Returns

string getPureSequence ( const string & s )

static

Return sequence without '-' characters.

Parameters

s

Returns

unsigned int getSequenceLength ( const string & seq )

Return length of seq.

Parameters

seq

Returns

vector< string > getTokens ( const string & text )

Return vector of words of a line of text.

Parameters

text

Returns

void insertCharacter	(	unsigned int	p,
		char	c
	)

Insert character c in target and all templates at position p.

Parameters

p
c

void insertDash ( unsigned int p )

Insert character '-' in target and all templates at position p.

Parameters

p

bool isConserved	(	unsigned int	p,
		unsigned int	index = `9999`
	)		const

virtual

Check for conservation. If index is 9999 check on all templates.

Parameters

p
index

Returns

bool isDeletion ( unsigned int p ) const

virtual

Check for deletion at position p.

Parameters

p

Returns

bool isGap	(	unsigned int	p,
		unsigned int	index = `0`
	)		const

virtual

Check for gap at position p.

Parameters

p
index

Returns

bool isInsertion	(	unsigned int	p,
		unsigned int	index = `0`
	)		const

virtual

Check for insertion at position p.

Parameters

p
index

Returns

double matchPositionVector	(	vector< int >	CeTarget,
		vector< int >	CeTemplate,
		vector< int >	seqTarget,
		vector< int >	seqTemplate
	)

virtual

Companion class to the previous.

Parameters

CeTarget
CeTemplate
seqTarget
seqTemplate

Returns

AlignmentBase * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

AlignmentBase & operator= ( const AlignmentBase & orig )

Assignment operator.

Parameters

orig

Returns

void saveClustal ( ostream & output ) const

virtual

Save as CLUSTAL like output.

Parameters

output

void saveFasta ( ostream & output ) const

virtual

Save as FASTA like output.

Parameters

output

Reimplemented in Alignment.

void setTemplate	(	string	t,
		string	tName = `"template"`
	)

virtual

Set template to t.

Parameters

t
tName

vector< int > shiftMatchSubset	(	vector< int >	inputVector,
		int	newStartPos
	)

virtual

Return a new vector with positions shifted, depending on new position.

Parameters

inputVector
newStartPos

Returns

void swapTemplate	(	unsigned int	index1,
		unsigned int	index2
	)

virtual

Swap templates index1 and index2.

Parameters

index1
index2

Reimplemented in Alignment.

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

Align2/Sources/AlignmentBase.h
Align2/Sources/AlignmentBase.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation