Go to the source code of this file.
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int | NewSymMatrix (symmatrix_t **symmat, const int nrows, const int ncols) |
| Allocates symmat and its members and initialises them. Data will be calloced, i.e. initialised with zeros. More...
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void | SymMatrixSetValue (symmatrix_t *symmat, const int i, const int j, const double value) |
| Sets symmat data of given index to given value. More...
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double | SymMatrixGetValue (symmatrix_t *symmat, const int i, const int j) |
| Returns element of symmat corresponding to given indices. More...
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void | SymMatrixGetValueP (double **value, symmatrix_t *symmat, const int i, const int j) |
| Returns a pointer to an element of symmat corresponding to given indices. More...
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void | FreeSymMatrix (symmatrix_t **symmat) |
| Frees memory allocated by data members of symmat and symmat itself. More...
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void | SymMatrixPrint (symmatrix_t *symmat, char **labels, const char *path, bool bPercID) |
| Print out a symmat in phylip style. Distances are printed on one line per sequence/object. Since we also support matrices with rows<cols, the first line can also be nrows by ncolumns instead of just nrows. More...
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int | SymMatrixRead (char *pcFileIn, symmatrix_t **prSymMat_p, mseq_t *prMSeq) |
| Read a distance matrix in phylip format. More...
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§ FreeSymMatrix()
Frees memory allocated by data members of symmat and symmat itself.
- Parameters
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- Note
- Use in conjunction with NewSymMatrix()
- See also
- NewSymMatrix()
§ NewSymMatrix()
int NewSymMatrix |
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symmatrix_t ** |
symmat, |
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int |
nrows, |
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int |
ncols |
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Allocates symmat and its members and initialises them. Data will be calloced, i.e. initialised with zeros.
- Parameters
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[out] | symmat | newly allocated and initialised symmatrix instance |
[in] | nrows | number of rows |
[in] | ncols | number of columns |
- Returns
- : non-zero on error
- See also
- FreeSymMatrix()
- Note
- : symmat data will be of fake shape nrows x ncols
§ SymMatrixGetValue()
double SymMatrixGetValue |
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symmatrix_t * |
symmat, |
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const int |
i, |
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const int |
j |
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Returns element of symmat corresponding to given indices.
- Parameters
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[in] | symmat | symmatrix_t of question |
[in] | i | index i |
[in] | j | index j |
- Returns
- requested value
- See also
- SymMatrixSetValue()
- Note
- This is a convenience function that checks index order.
§ SymMatrixGetValueP()
void SymMatrixGetValueP |
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double ** |
val, |
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symmatrix_t * |
symmat, |
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const int |
i, |
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const int |
j |
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Returns a pointer to an element of symmat corresponding to given indices.
- Parameters
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[out] | val | Value to be set |
[in] | symmat | symmatrix_t of question |
[in] | i | index i |
[in] | j | index j |
- Returns
- pointer to value
- See also
- SymMatrixGetValue()
- Note
- This is a convenience function that checks index order.
§ SymMatrixPrint()
void SymMatrixPrint |
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symmatrix_t * |
symmat, |
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char ** |
labels, |
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const char * |
path, |
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bool |
bPercID |
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) |
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Print out a symmat in phylip style. Distances are printed on one line per sequence/object. Since we also support matrices with rows<cols, the first line can also be nrows by ncolumns instead of just nrows.
- Parameters
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[in] | symmat | the symmatrix_t to print |
[in] | labels | sequence/objects labels/names. must be at least of length symmat nrows |
[in] | path | filename or NULL. If NULL stdout will be used. |
§ SymMatrixRead()
Read a distance matrix in phylip format.
- Parameters
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[in] | pcFileIn | distance matrix filename |
[in] | prMSeq | optional mseq pointer. only used for consistency checking of names/labels |
[out] | prSymMat_p | the symmatrix_t. will be allocated here. |
- Returns
- : non-zero on error
- Note
- : FIXME untested code
§ SymMatrixSetValue()
void SymMatrixSetValue |
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symmatrix_t * |
symmat, |
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const int |
i, |
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const int |
j, |
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const double |
value |
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Sets symmat data of given index to given value.
- Parameters
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[in] | symmat | symmatrix_t whose data is to be set |
[in] | i | first index |
[in] | j | second index |
[in] | value | value used to set data point |
- See also
- SymMatrixGetValue()
- Note
- This is a convenience function that checks index order.