BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes
BioDnaSequenceAlignment Class Reference

#include <BioDnaSequenceAlignment.h>

Inheritance diagram for BioDnaSequenceAlignment:
Inheritance graph
[legend]
Collaboration diagram for BioDnaSequenceAlignment:
Collaboration graph
[legend]

List of all members.

Public Member Functions

void setSequence1 (BioDnaSequence)
void setSequence2 (BioDnaSequence)
void setSequence1 (BioGenBank)
void setSequence2 (BioGenBank)
void setSequence1 (BioFasta)
void setSequence2 (BioFasta)
void setSequence1 (BioEmbl)
void setSequence2 (BioEmbl)
void setSequence1 (string)
void setSequence2 (string)
void setSubstitutionMatrix (string)
void setSubstitutionMatrix (string, string)
void setGapPenalty (int GP=-11, int extn=-9999)
void setMatchMisMatchScore (int MS=1, int MMS=0)
void showScoringMatrix (ostream &=cout)
void setSequence1 (BioDnaSequence)
void setSequence2 (BioDnaSequence)
void setSequence1 (BioGenBank)
void setSequence2 (BioGenBank)
void setSequence1 (BioFasta)
void setSequence2 (BioFasta)
void setSequence1 (BioEmbl)
void setSequence2 (BioEmbl)
void setSequence1 (string)
void setSequence2 (string)
void setSubstitutionMatrix (string)
void setSubstitutionMatrix (string, string)
void setGapPenalty (int GP=-11, int extn=-9999)
void setMatchMisMatchScore (int MS=1, int MMS=0)
void showScoringMatrix (ostream &=cout)
void setSequence1 (BioDnaSequence)
void setSequence2 (BioDnaSequence)
void setSequence1 (BioGenBank)
void setSequence2 (BioGenBank)
void setSequence1 (BioFasta)
void setSequence2 (BioFasta)
void setSequence1 (BioEmbl)
void setSequence2 (BioEmbl)
void setSequence1 (string)
void setSequence2 (string)
void setSubstitutionMatrix (string)
void setSubstitutionMatrix (string, string)
void setGapPenalty (int GP=-11, int extn=-9999)
void setMatchMisMatchScore (int MS=1, int MMS=0)
void showScoringMatrix (ostream &=cout)
void setSequence1 (BioDnaSequence)
void setSequence2 (BioDnaSequence)
void setSequence1 (BioGenBank)
void setSequence2 (BioGenBank)
void setSequence1 (BioFasta)
void setSequence2 (BioFasta)
void setSequence1 (BioEmbl)
void setSequence2 (BioEmbl)
void setSequence1 (string)
void setSequence2 (string)
void setSubstitutionMatrix (string)
void setSubstitutionMatrix (string, string)
void setGapPenalty (int GP=-11, int extn=-9999)
void setMatchMisMatchScore (int MS=1, int MMS=0)
void showScoringMatrix (ostream &=cout)
void setSequence1 (BioDnaSequence)
void setSequence2 (BioDnaSequence)
void setSequence1 (BioGenBank)
void setSequence2 (BioGenBank)
void setSequence1 (BioFasta)
void setSequence2 (BioFasta)
void setSequence1 (BioEmbl)
void setSequence2 (BioEmbl)
void setSequence1 (string)
void setSequence2 (string)
void setSubstitutionMatrix (string)
void setSubstitutionMatrix (string, string)
void setGapPenalty (int GP=-11, int extn=-9999)
void setMatchMisMatchScore (int MS=1, int MMS=0)
void showScoringMatrix (ostream &=cout)

Protected Member Functions

void formScoringMatrix ()
int getAccValMov (long, long, int)
 BioDnaSequenceAlignment ()
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string, string, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
void formScoringMatrix ()
int getAccValMov (long, long, int)
 BioDnaSequenceAlignment ()
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string, string, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
void formScoringMatrix ()
int getAccValMov (long, long, int)
 BioDnaSequenceAlignment ()
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string, string, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
void formScoringMatrix ()
int getAccValMov (long, long, int)
 BioDnaSequenceAlignment ()
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string, string, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
void formScoringMatrix ()
int getAccValMov (long, long, int)
 BioDnaSequenceAlignment ()
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string, string, int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
 BioDnaSequenceAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)

Protected Attributes

string seq1_
string seq2_
string outSeq1_
string outSeq2_
string seqName1_
string seqName2_
int gapPenalty
int gapExtn
BioMatrix substitutionMatrix
vector< vector< int > > tempMatrix
int status

Static Protected Attributes

static string nucleicAcidSeq

Constructor & Destructor Documentation

BioDnaSequenceAlignment::BioDnaSequenceAlignment ( ) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  ,
string  ,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( ) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  ,
string  ,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( ) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  ,
string  ,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( ) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  ,
string  ,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( ) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
BioDnaSequence  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioDnaSequence  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
BioGenBank  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioGenBank  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
BioFasta  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioFasta  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  ,
string  MatName,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
BioEmbl  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( BioEmbl  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  ,
string  ,
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
string  mat = "IDENTITY",
int  GP = -11,
int  extn = -9999 
) [protected]
BioDnaSequenceAlignment::BioDnaSequenceAlignment ( string  ,
string  ,
int  MS,
int  MMS,
int  GP = -11,
int  extn = -9999 
) [protected]

Member Function Documentation

void BioDnaSequenceAlignment::formScoringMatrix ( ) [protected]
void BioDnaSequenceAlignment::formScoringMatrix ( ) [protected]
void BioDnaSequenceAlignment::formScoringMatrix ( ) [protected]
void BioDnaSequenceAlignment::formScoringMatrix ( ) [protected]
void BioDnaSequenceAlignment::formScoringMatrix ( ) [protected]
int BioDnaSequenceAlignment::getAccValMov ( long  ,
long  ,
int   
) [protected]
int BioDnaSequenceAlignment::getAccValMov ( long  ,
long  ,
int   
) [protected]
int BioDnaSequenceAlignment::getAccValMov ( long  ,
long  ,
int   
) [protected]
int BioDnaSequenceAlignment::getAccValMov ( long  ,
long  ,
int   
) [protected]
int BioDnaSequenceAlignment::getAccValMov ( long  ,
long  ,
int   
) [protected]
void BioDnaSequenceAlignment::setGapPenalty ( int  GP = -11,
int  extn = -9999 
)
void BioDnaSequenceAlignment::setGapPenalty ( int  GP = -11,
int  extn = -9999 
)
void BioDnaSequenceAlignment::setGapPenalty ( int  GP = -11,
int  extn = -9999 
)
void BioDnaSequenceAlignment::setGapPenalty ( int  GP = -11,
int  extn = -9999 
)
void BioDnaSequenceAlignment::setGapPenalty ( int  GP = -11,
int  extn = -9999 
)
void BioDnaSequenceAlignment::setMatchMisMatchScore ( int  MS = 1,
int  MMS = 0 
)
void BioDnaSequenceAlignment::setMatchMisMatchScore ( int  MS = 1,
int  MMS = 0 
)
void BioDnaSequenceAlignment::setMatchMisMatchScore ( int  MS = 1,
int  MMS = 0 
)
void BioDnaSequenceAlignment::setMatchMisMatchScore ( int  MS = 1,
int  MMS = 0 
)
void BioDnaSequenceAlignment::setMatchMisMatchScore ( int  MS = 1,
int  MMS = 0 
)
void BioDnaSequenceAlignment::setSequence1 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence1 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence1 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence1 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence1 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence1 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence1 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence1 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence1 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence1 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence1 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence1 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence1 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence1 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence1 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence1 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence1 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence1 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence1 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence1 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence1 ( string  )
void BioDnaSequenceAlignment::setSequence1 ( string  )
void BioDnaSequenceAlignment::setSequence1 ( string  )
void BioDnaSequenceAlignment::setSequence1 ( string  )
void BioDnaSequenceAlignment::setSequence1 ( string  )
void BioDnaSequenceAlignment::setSequence2 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence2 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence2 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence2 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence2 ( BioDnaSequence  )
void BioDnaSequenceAlignment::setSequence2 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence2 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence2 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence2 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence2 ( BioGenBank  )
void BioDnaSequenceAlignment::setSequence2 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence2 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence2 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence2 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence2 ( BioFasta  )
void BioDnaSequenceAlignment::setSequence2 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence2 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence2 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence2 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence2 ( BioEmbl  )
void BioDnaSequenceAlignment::setSequence2 ( string  )
void BioDnaSequenceAlignment::setSequence2 ( string  )
void BioDnaSequenceAlignment::setSequence2 ( string  )
void BioDnaSequenceAlignment::setSequence2 ( string  )
void BioDnaSequenceAlignment::setSequence2 ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  )
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  ,
string   
)
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  ,
string   
)
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  ,
string   
)
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  ,
string   
)
void BioDnaSequenceAlignment::setSubstitutionMatrix ( string  ,
string   
)
void BioDnaSequenceAlignment::showScoringMatrix ( ostream &  = cout)
void BioDnaSequenceAlignment::showScoringMatrix ( ostream &  = cout)
void BioDnaSequenceAlignment::showScoringMatrix ( ostream &  = cout)
void BioDnaSequenceAlignment::showScoringMatrix ( ostream &  = cout)
void BioDnaSequenceAlignment::showScoringMatrix ( ostream &  = cout)

Member Data Documentation

int BioDnaSequenceAlignment::gapExtn [protected]
int BioDnaSequenceAlignment::gapPenalty [protected]
static string BioDnaSequenceAlignment::nucleicAcidSeq [static, protected]
string BioDnaSequenceAlignment::outSeq1_ [protected]
string BioDnaSequenceAlignment::outSeq2_ [protected]
string BioDnaSequenceAlignment::seq1_ [protected]
string BioDnaSequenceAlignment::seq2_ [protected]
string BioDnaSequenceAlignment::seqName1_ [protected]
string BioDnaSequenceAlignment::seqName2_ [protected]
int BioDnaSequenceAlignment::status [protected]
BioMatrix BioDnaSequenceAlignment::substitutionMatrix [protected]
vector< vector< int > > BioDnaSequenceAlignment::tempMatrix [protected]
The documentation for this class was generated from the following files:
 All Classes Files Functions Variables Typedefs Enumerations Enumerator Friends Defines