_String* StringFromConsole (bool)
{
fflush(stdout);
_String * returnme = new _String (32L, true);
#if not defined __HEADLESS__ && not defined _MINGW32_MEGA_
int readAChar;
while ((readAChar = getc(stdin)) != '\n') {
if (readAChar == EOF) {
CheckReceptacleAndStore (&hasEndBeenReached,empty,false,new _Constant (1.), false);
break;
}
*returnme << readAChar;
}
#else
WarnError ("Unhandled standard input interaction in StringFromConsole for headless HyPhy");
return NULL;
#endif
returnme->Finalize ();
return returnme;
}
void _LikelihoodFunction::ReconstructAncestors (_DataSet &target,_SimpleList& doTheseOnes, _String& baseResultID, bool sample, bool doMarginal, bool doLeaves)
/*
Reconstruct ancestors for a likelihood function using
-- target : the _DataSet object that will receive the results
-- doTheseOnes : a _sorted_ array of partition indices to include in this operation; is assumed to contain valid indices (i.e. 0 -- number of partitions - 1)
-- baseResultID: the HBL identifier of the dataset that will receive the result; used as a prefix for .marginal_support_matrix support matrix (when doMarginal = true)
-- sample : if true, an ancestral sample (weighted by likelihood) is drawn, otherwise an ML (or maginal) reconstruction is carried out
-- doMarginal : if sample == false, doMarginal determines how the ancestors are reconstructed; if true, the reconstruction is marginal (maximizes
the likelihood of each node while summing over the rest), otherwise it is joint.
-- doLeaves : if sample == false and doMarginal == false (for now) and doLeaves == true, then the procedure will also
reconstruct (joint ML) the best assignment of leaves
*/
{
_DataSetFilter *dsf = (_DataSetFilter*)dataSetFilterList (theDataFilters(doTheseOnes.lData[0]));
_TheTree *firstTree = (_TheTree*)LocateVar(theTrees(doTheseOnes.lData[0]));
target.SetTranslationTable (dsf->GetData());
target.ConvertRepresentations();
computationalResults.ZeroUsed();
PrepareToCompute();
// check if we need to deal with rate variation
_Matrix *rateAssignments = nil;
if (!doMarginal && indexCat.lLength>0)
rateAssignments = (_Matrix*)checkPointer(ConstructCategoryMatrix(doTheseOnes,_hyphyLFConstructCategoryMatrixClasses,false));
else
Compute(); // need to do this to populate rate matrices
long siteOffset = 0,
patternOffset = 0,
sequenceCount ;
for (long i = 0; i<doTheseOnes.lLength; i++)
{
long partIndex = doTheseOnes.lData[i];
_TheTree *tree = (_TheTree*)LocateVar(theTrees(partIndex));
dsf = (_DataSetFilter*)dataSetFilterList (theDataFilters(partIndex));
long catCounter = 0;
if (rateAssignments)
{
_SimpleList pcats;
PartitionCatVars (pcats,partIndex);
catCounter = pcats.lLength;
}
if (i==0)
{
tree->AddNodeNamesToDS (&target,sample == false && doLeaves,!(doLeaves && doMarginal) ,2*(doMarginal == false && sample == false && doLeaves));
// store internal or leaf node names in the dataset
sequenceCount = target.GetNames().lLength;
}
else
{
if (!tree->Equal(firstTree)) // incompatible likelihood function
{
ReportWarning ((_String("Ancestor reconstruction had to ignore partition ")&_String(partIndex+1)&" of the likelihood function since it has a different tree topology than the first part."));
continue;
}
_TranslationTable * mtt = target.GetTT()->MergeTables(dsf->GetData()->GetTT());
if (mtt)
{
target.SetTranslationTable (mtt);
DeleteObject (mtt);
}
else
{
ReportWarning ((_String("Ancestor reconstruction had to ignore partition ")&_String(partIndex+1)&" of the likelihood function since it has a character alphabet incompatible with the first part."));
continue;
}
}
_List * expandedMap = dsf->ComputePatternToSiteMap(),
* thisSet;
if (sample)
{
_AVLListX * nodeMapper = tree->ConstructNodeToIndexMap(true);
thisSet = new _List;
_SimpleList* tcc = (_SimpleList*)treeTraversalMasks(partIndex);
if (tcc)
{
long shifter = dsf->GetDimension()*dsf->NumberDistinctSites()*tree->GetINodeCount();
for (long cc = 0; cc <= catCounter; cc++)
tree->FillInConditionals(dsf, conditionalInternalNodeLikelihoodCaches[partIndex] + cc*shifter, tcc);
}
tree->SampleAncestorsBySequence (dsf, *(_SimpleList*)optimalOrders.lData[partIndex],
&tree->GetRoot(),
nodeMapper,
conditionalInternalNodeLikelihoodCaches[partIndex],
*thisSet,
nil,
*expandedMap,
catCounter?rateAssignments->theData+siteOffset:nil,
catCounter);
nodeMapper->DeleteAll(false);DeleteObject (nodeMapper);
}
else
{
if (doMarginal)
{
_Matrix *marginals = new _Matrix;
_String supportMxID = baseResultID & '.' & _hyMarginalSupportMatrix;
thisSet = RecoverAncestralSequencesMarginal (partIndex, *marginals, *expandedMap, doLeaves);
CheckReceptacleAndStore(&supportMxID, "ReconstructAncestors", true, marginals, false);
}
else
thisSet = tree->RecoverAncestralSequences (dsf,
*(_SimpleList*)optimalOrders.lData[partIndex],
*expandedMap,
conditionalInternalNodeLikelihoodCaches[partIndex],
catCounter?rateAssignments->theData+siteOffset:nil,
catCounter,
conditionalTerminalNodeStateFlag[partIndex],
(_GrowingVector*)conditionalTerminalNodeLikelihoodCaches(partIndex),
doLeaves
);
}
_String * sampledString = (_String*)(*thisSet)(0);
for (long siteIdx = 0; siteIdx<sampledString->sLength; siteIdx++)
target.AddSite (sampledString->sData[siteIdx]);
for (long seqIdx = 1;seqIdx < sequenceCount; seqIdx++)
{
sampledString = (_String*)(*thisSet)(seqIdx);
for (long siteIdx = 0;siteIdx<sampledString->sLength; siteIdx++)
target.Write2Site (siteOffset + siteIdx, sampledString->sData[siteIdx]);
}
DeleteObject (thisSet);
DeleteObject (expandedMap);
siteOffset += dsf->GetSiteCount();
patternOffset += dsf->GetSiteCount();
}
target.Finalize();
target.SetNoSpecies(target.GetNames().lLength);
if (rateAssignments)
DeleteObject (rateAssignments);
DoneComputing ();
}
//__________________________________________________________________________________
bool CheckReceptacleAndStore (_String name, _String fID, bool checkValid, _PMathObj v, bool dup)
{
return CheckReceptacleAndStore (&name, fID, checkValid, v, dup);
}