ajphylo.c

Function ajPhyloDistNew

Constructor for AjPPhyloDist

Prototype

AjPPhyloDist ajPhyloDistNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloDist RETURNAjPPhyloDist object

From EMBOSS 2.8.0

Function ajPhyloFreqNew

Constructor for AjPPhyloFreq

Prototype

AjPPhyloFreq ajPhyloFreqNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloFreq RETURNAjPPhyloFreq object

From EMBOSS 2.8.0

Function ajPhyloPropNew

Constructor for AjPPhyloProp

Prototype

AjPPhyloProp ajPhyloPropNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloProp RETURNAjPPhyloProp object

From EMBOSS 2.8.0

Function ajPhyloStateNew

Constructor for AjPPhyloState

Prototype

AjPPhyloState ajPhyloStateNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloState RETURNAjPPhyloState object

From EMBOSS 2.8.0

Function ajPhyloTreeNew

Constructor for AjPPhyloTree

Prototype

AjPPhyloTree ajPhyloTreeNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloTree RETURNAjPPhyloTree object

From EMBOSS 2.8.0

Function ajPhyloDistDel

Destructor for AjPPhyloDist

Prototype

void ajPhyloDistDel (
      AjPPhyloDist* pthis
);

TypeNameRead/WriteDescription
AjPPhyloDist*pthisDeleteDistance object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloFreqDel

Destructor for AjPPhyloFreq

Prototype

void ajPhyloFreqDel (
      AjPPhyloFreq* pthis
);

TypeNameRead/WriteDescription
AjPPhyloFreq*pthisDeletefrequency object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloPropDel

Destructor for AjPPhyloProp

Prototype

void ajPhyloPropDel (
      AjPPhyloProp* pthis
);

TypeNameRead/WriteDescription
AjPPhyloProp*pthisDeleteProperties object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloStateDel

Destructor for AjPPhyloState

Prototype

void ajPhyloStateDel (
      AjPPhyloState* pthis
);

TypeNameRead/WriteDescription
AjPPhyloState*pthisDeleteDiscrete states object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloStateDelarray

Destructor for AjPPhyloState array

Prototype

void ajPhyloStateDelarray (
      AjPPhyloState** pthis
);

TypeNameRead/WriteDescription
AjPPhyloState**pthisDeleteStates object array
void RETURN

From EMBOSS 4.1.0

Function ajPhyloTreeDel

Destructor for AjPPhyloTree

Prototype

void ajPhyloTreeDel (
      AjPPhyloTree* pthis
);

TypeNameRead/WriteDescription
AjPPhyloTree*pthisDeleteTrees object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloTreeDelarray

Destructor for AjPPhyloTree array

Prototype

void ajPhyloTreeDelarray (
      AjPPhyloTree** pthis
);

TypeNameRead/WriteDescription
AjPPhyloTree**pthisDeleteTrees object array
void RETURN

From EMBOSS 4.1.0

Function ajPhyloDistRead

Reads phylogenetic distance matrix from a file

Prototype

AjPPhyloDist* ajPhyloDistRead (
      const AjPStr filename,
      ajint size,
      AjBool missing
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
ajintsizeInputNumber of rows in distance matrix
AjBoolmissingInputMissing values (replicates zero) allowed
AjPPhyloDist* RETURNPhylogenetic distances object on success NULL on failure

From EMBOSS 2.8.0

Function ajPhyloDistTrace

Reports phylogenetic distance data to the debug file

Prototype

void ajPhyloDistTrace (
      const AjPPhyloDist thys
);

TypeNameRead/WriteDescription
const AjPPhyloDistthysInputPhylogenetic frequencies object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloFreqRead

Reads phylogenetic frequencies from a file

Prototype

AjPPhyloFreq ajPhyloFreqRead (
      const AjPStr filename,
      AjBool contchar,
      AjBool genedata,
      AjBool indiv
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
AjBoolcontcharInputContinuous character data expected
AjBoolgenedataInputGene frequency data expected
AjBoolindivInputMultiple individuals for one name only for continuous character data.
AjPPhyloFreq RETURNPhylogenetic frequencies object on success NULL on failure

From EMBOSS 2.8.0

Function ajPhyloFreqTrace

Reports phylogenetic frequencies data to the debug file

Prototype

void ajPhyloFreqTrace (
      const AjPPhyloFreq thys
);

TypeNameRead/WriteDescription
const AjPPhyloFreqthysInputPhylogenetic frequencies object
void RETURN

From EMBOSS 2.8.0

Function ajPhyloPropRead

Reads phylogenetic properties (weights, factors, ancestral states) from a file

Prototype

AjPPhyloProp ajPhyloPropRead (
      const AjPStr filename,
      const AjPStr propchars,
      ajint len,
      ajint size
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
const AjPStrpropcharsInputValid property characters
ajintlenInputLength of properties string
ajintsizeInputNumber of property sets expected If zero, read first only or whatever the file says
AjPPhyloProp RETURNPhylogenetic properties object on success NULL on failure

From EMBOSS 2.8.0

Function ajPhyloPropGetSize

Returns size (number of property strings)

Prototype

ajint ajPhyloPropGetSize (
      const AjPPhyloProp thys
);

TypeNameRead/WriteDescription
const AjPPhyloPropthysInputProperties object
ajint RETURNNumber of property strings

From EMBOSS 2.8.0

Function ajPhyloPropTrace

Reports phylogenetic property data to the debug file

Prototype

void ajPhyloPropTrace (
      const AjPPhyloProp thys
);

TypeNameRead/WriteDescription
const AjPPhyloPropthysInputPhylogenetic frequencies object
void RETURN

From EMBOSS 2.9.0

Function ajPhyloStateRead

Reads phylogenetic discrete states from a file

Prototype

AjPPhyloState* ajPhyloStateRead (
      const AjPStr filename,
      const AjPStr statechars
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
const AjPStrstatecharsInputValid state characters
AjPPhyloState* RETURNPhylogenetic discrete states object on success NULL on failure

From EMBOSS 2.8.0

Function ajPhyloStateTrace

Reports phylogenetic discrete state data to the debug file

Prototype

void ajPhyloStateTrace (
      const AjPPhyloState thys
);

TypeNameRead/WriteDescription
const AjPPhyloStatethysInputPhylogenetic discrete states object
void RETURN

From EMBOSS 2.9.0

Function ajPhyloTreeRead

Reads phylogenetic trees from a file.

Prototype

AjPPhyloTree* ajPhyloTreeRead (
      const AjPStr filename,
      ajint size
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
ajintsizeInputNumber of trees expected If zero, read all trees
AjPPhyloTree* RETURNPhylogenetic tree object array on success NULL on failure

From EMBOSS 2.8.0

Function ajPhyloTreeTrace

Reports phylogenetic discrete state data to the debug file

Prototype

void ajPhyloTreeTrace (
      const AjPPhyloTree thys
);

TypeNameRead/WriteDescription
const AjPPhyloTreethysInputPhylogenetic discrete states object
void RETURN

From EMBOSS 2.9.0

Function ajPhyloExit

Cleans up phylogenetic data internal memory

Prototype

void ajPhyloExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.1.0