34 #ifndef CAV_ALIGNMENT_DISPLAY__HPP
35 #define CAV_ALIGNMENT_DISPLAY__HPP
68 bool IsSqueezable(
int alnLoc,
int *nGaps,
int *startPos,
int maxGaps)
const;
122 const string GetColumnColor(
int alnLoc,
double conservationThreshhold)
const;
126 int firstCol,
int lastCol,
int nColumns,
double conservationThreshhold = 2.0,
131 int firstCol,
int lastCol,
int nColumns,
double conservationThreshhold = 2.0,
135 int DumpFASTA(
int firstCol,
int lastCol,
int nColumns,
bool doLowercase,
CNcbiOstream& outStream)
const;
142 inline bool IsUnaligned(
char ch) {
return (ch >=
'a' && ch <=
'z'); }
143 inline bool IsAligned(
char ch) {
return (ch >=
'A' && ch <=
'Z'); }
144 inline bool IsGap(
char ch) {
return (ch ==
'-'); }
bool IsUnaligned(char ch)
C interface header for cddalignview as function call.
int DumpCondensed(CNcbiOstream &os, unsigned int options, int firstCol, int lastCol, int nColumns, double conservationThreshhold=2.0, const char *titleHTML=NULL, int nFeatures=0, const AlignmentFeature *alnFeatures=NULL) const
int GetFirstAlignedLoc(void) const
vector< TextRow * > TextRows
IndexAlnLocToSeqLocRows indexAlnLocToSeqLocRows
vector< IndexAlnLocToSeqLocRow * > IndexAlnLocToSeqLocRows
void SplitUnaligned(void)
unsigned int GetWidth(void) const
void ShiftUnalignedLeft(void)
const string GetColumnColor(int alnLoc, double conservationThreshhold) const
int DumpText(CNcbiOstream &os, unsigned int options, int firstCol, int lastCol, int nColumns, double conservationThreshhold=2.0, const char *titleHTML=NULL, int nFeatures=0, const AlignmentFeature *alnFeatures=NULL) const
unsigned int GetNRows(void) const
int GetLastAlignedLoc(void) const
AlignmentDisplay(const SequenceSet *sequenceSet, const AlignmentSet *alignmentSet)
static const double SHOW_IDENTITY
int DumpFASTA(int firstCol, int lastCol, int nColumns, bool doLowercase, CNcbiOstream &outStream) const
char GetCharAt(int alnLoc, int row) const
void InsertGaps(int nGaps, int beforePos)
unsigned int Length(void) const
void ReIndex(const TextRow &textRow)
IndexAlnLocToSeqLocRow(const Sequence *seq, int length=0)
const Sequence * sequence
int GetSeqLocAt(int alnLoc) const
void InsertGaps(int nGaps, int beforePos)
void SetSeqLocAt(int alnLoc, int seqLoc)
TextRow(const string &str)
char GetCharAt(int alnLoc) const
void DeleteGaps(int nGaps, int startPos)
unsigned int Length(void) const
void SetCharAt(int alnLoc, char ch)
bool IsSqueezable(int alnLoc, int *nGaps, int *startPos, int maxGaps) const
void InsertGaps(int nGaps, int beforePos)
static const char * str(char *buf, int n)
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
const struct ncbi::grid::netcache::search::fields::SIZE size
The NCBI C++/STL use hints.
NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.
#define row(bind, expected)