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inc/indiscern; inc/good
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@vbrover
vbrover committed Apr 10, 2021
1 parent 00e5cb1 commit a7232a4
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Showing 4 changed files with 198 additions and 125 deletions.
202 changes: 153 additions & 49 deletions phylogeny/distTree.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -81,36 +81,46 @@ void dissimTransform (Real &target)

// Neighbor

Neighbor::Neighbor (const Leaf* leaf_arg,
size_t dissimType_arg,
Real target_arg)
: leaf (leaf_arg)
, dissimType (dissimType_arg)
, target (target_arg)
{
ASSERT (leaf);
ASSERT (leaf->graph);
ASSERT (target >= 0.0);
}



Neighbor::Neighbor (const Leaf* leaf_arg,
size_t dissimType_arg)
: leaf (leaf_arg)
, dissimType (dissimType_arg)
struct Neighbor
{
ASSERT (leaf);
ASSERT (leaf->graph);
}


const Leaf* leaf {nullptr};
// !nullptr
size_t dissimType {no_index};
Real target {NaN};
// > 0


Neighbor (const Leaf* leaf_arg,
size_t dissimType_arg,
Real target_arg)
: leaf (leaf_arg)
, dissimType (dissimType_arg)
, target (target_arg)
{
ASSERT (leaf);
ASSERT (leaf->graph);
ASSERT (target >= 0.0);
}
Neighbor (const Leaf* leaf_arg,
size_t dissimType_arg)
: leaf (leaf_arg)
, dissimType (dissimType_arg)
{
ASSERT (leaf);
ASSERT (leaf->graph);
}

bool Neighbor::operator< (const Neighbor &other) const
{
LESS_PART (*this, other, dissimType);
return leaf < other. leaf;
}

bool operator< (const Neighbor &other) const
{
LESS_PART (*this, other, dissimType);
return leaf < other. leaf;
}
bool operator== (const Neighbor &other) const
{ return leaf == other. leaf
&& dissimType == other. dissimType;
}
};



Expand Down Expand Up @@ -148,6 +158,7 @@ void Triangle::qc () const
QC_ASSERT (child);
QC_ASSERT (child->graph);
QC_ASSERT (child->badCriterion >= 0.0);
QC_IMPLY (child->good, ! child_hybrid);
for (const bool i : {false, true})
{
const Parent& p = parents [i];
Expand All @@ -156,6 +167,7 @@ void Triangle::qc () const
QC_ASSERT (p. leaf->badCriterion >= 0.0);
QC_ASSERT (child->getDiscernible () != p. leaf->getDiscernible ());
QC_ASSERT (p. dissim > 0.0);
QC_IMPLY (p. leaf->good, ! p. hybrid);
}
QC_ASSERT (! ( child_hybrid
&& parents [false]. hybrid
Expand Down Expand Up @@ -378,11 +390,18 @@ void TriangleParentPair::finish (const DistTree &tree,
)
{
const Parent& p = parents [i];
if (child_classSize < all * classSizeFrac_max)
if ( ! childrenGood ()
&& child_classSize < all * classSizeFrac_max
)
setChildrenHybrid ();
else if ((Real) p. classSize < all * classSizeFrac_max)
else if ( ! best->parents [i]. leaf->good
&& (Real) p. classSize < all * classSizeFrac_max
)
best->parents [i]. hybrid = true;
else if (child_classSize + (Real) p. classSize < all * classSizeFrac_max)
else if ( ! childrenGood ()
&& ! best->parents [i]. leaf->good
&& child_classSize + (Real) p. classSize < all * classSizeFrac_max
)
{
setChildrenHybrid ();
best->parents [i]. hybrid = true;
Expand All @@ -392,13 +411,18 @@ void TriangleParentPair::finish (const DistTree &tree,

{
const Prob p = child_classSize / all;
if (p <= classSizeFrac_max)
if ( ! childrenGood ()
&& p <= classSizeFrac_max
)
{
// aa bb ab
setChildrenHybrid ();
return;
}
if (p >= 1.0 - classSizeFrac_max)
if ( ! best->parents [0]. leaf->good
&& ! best->parents [1]. leaf->good
&& p >= 1.0 - classSizeFrac_max
)
{
// ab ac aa
// common(ab,ac) = 1/4 aa <= random halves of aa
Expand Down Expand Up @@ -577,6 +601,25 @@ size_t TriangleParentPair::child_parent2parents (const DistTree &tree,



bool TriangleParentPair::childrenGood () const
{
for (const Triangle& tr : triangles)
if (tr. child->good)
return true;
return false;
}



void TriangleParentPair::setChildrenHybrid ()
{
ASSERT (! childrenGood ());
for (Triangle& tr : triangles)
tr. child_hybrid = true;
}




//

Expand Down Expand Up @@ -614,7 +657,12 @@ void DTNode::qc () const
//QC_ASSERT (! DistTree_sp::variance_min);
QC_ASSERT (! inDiscernible ());
for (const DiGraph::Arc* arc : arcs [false])
QC_ASSERT (static_cast <const DTNode*> (arc->node [false]) -> inDiscernible ());
{
const Leaf* leaf = static_cast <const DTNode*> (arc->node [false]) -> asLeaf ();
QC_ASSERT (leaf);
QC_ASSERT (leaf->inDiscernible ());
QC_ASSERT (leaf->good == static_cast <const DTNode*> (arcs [false]. front () -> node [false]) -> asLeaf () -> good);
}
}
}

Expand All @@ -637,12 +685,7 @@ void DTNode::saveContent (ostream& os) const
os << " " << err_densityS << "=" << errorDensity;

if (maxDeformationDissimNum != dissims_max)
{
const Dissim& dissim = getDistTree (). dissims [maxDeformationDissimNum];
os << " " << deformationS << "=" << dissim. leaf1->getName ()
<< ':' << dissim. leaf2->getName ();
os << " " << deformation_criterionS << "=" << dissim. getDeformation ();
}
os << " " << getDeformationS ();
else if (const DistTree::DeformationPair* dp = findPtr (getDistTree (). node2deformationPair, this))
os << " " << deformationS << '=' << dp->leafName1
<< ':' << dp->leafName2
Expand Down Expand Up @@ -710,6 +753,20 @@ Real DTNode::getDeformation () const



string DTNode::getDeformationS () const
{
ASSERT (maxDeformationDissimNum != dissims_max);

ostringstream os;
const Dissim& dissim = getDistTree (). dissims [maxDeformationDissimNum];
os << deformationS << "=" << dissim. leaf1->getName ()
<< ':' << dissim. leaf2->getName ()
<< " " << deformation_criterionS << "=" << dissim. getDeformation ();
return os. str ();
}



void DTNode::saveFeatureTree (ostream &os,
bool withTime,
size_t offset) const
Expand Down Expand Up @@ -5506,6 +5563,32 @@ VectorPtr<DTNode> DistTree::getDiscernibles () const
}



void DistTree::setGoodLeaves (const string &goodFName)
{
LineInput f (goodFName);
while (f. nextLine ())
{
trim (f. line);
if (strBlank (f. line))
continue;
if (const Leaf* leaf = findPtr (name2leaf, f. line))
{
for (const DiGraph::Arc* arc : leaf->getDiscernible () -> arcs [false])
{
const Leaf* child = static_cast <const DTNode*> (arc->node [false]) -> asLeaf ();
ASSERT (child);
if (child->good)
break; // All children are good
var_cast (child) -> good = true;
}
var_cast (leaf) -> good = true;
}
}
}




void DistTree::printInput (ostream &os) const
{
Expand Down Expand Up @@ -8216,9 +8299,11 @@ VectorPtr<Leaf> DistTree::findCriterionOutliers (const Dataset &leafErrorDs,
for (const auto& it : name2leaf)
{
const Leaf* leaf = it. second;
if (leaf->graph)
if (leaf->normCriterion > outlier_min_excl)
res << leaf;
if ( leaf->graph
&& ! leaf->good
&& leaf->normCriterion > outlier_min_excl
)
res << leaf;
}

res. sort (leafRelCriterionStrictlyGreater);
Expand Down Expand Up @@ -8272,9 +8357,11 @@ VectorPtr<Leaf> DistTree::findDeformationOutliers (Real deformation_mean,
for (const auto& it : name2leaf)
{
const Leaf* leaf = it. second;
if (leaf->graph)
if (leaf->getDeformation () / deformation_mean > outlier_min_excl)
res << leaf;
if ( leaf->graph
&& ! leaf->good
&& leaf->getDeformation () / deformation_mean > outlier_min_excl
)
res << leaf;
}
res. sort (leafDeformationStrictlyGreater);

Expand All @@ -8288,7 +8375,7 @@ VectorPtr<Leaf> DistTree::findDeformationOutliers (Real deformation_mean,
namespace
{


struct TriangleType
{
const Leaf* parent1;
Expand All @@ -8313,6 +8400,8 @@ struct TriangleType



#if 0
??
struct RequestCandidate
{
const Leaf* leaf1 {nullptr};
Expand All @@ -8339,8 +8428,6 @@ struct RequestCandidate



#if 0
??
void hybrid2requests (size_t from,
size_t to,
Vector<RequestCandidate> &res,
Expand Down Expand Up @@ -8818,6 +8905,23 @@ Vector<Pair<const Leaf*>> DistTree::getMissingLeafPairs_ancestors (size_t depth_
ASSERT (leaf);
if (! leaf->graph)
continue;
if (! leaf->discernible)
{
bool main = true;
for (const DiGraph::Arc* arc : leaf->getParent () -> arcs [false])
{
const Leaf* sibling = static_cast <const DTNode*> (arc->node [false]) -> asLeaf ();
ASSERT (sibling);
ASSERT (! sibling->discernible);
if (sibling->name < leaf->name)
{
main = false;
break;
}
}
if (! main)
continue;
}
const VectorPtr<Leaf> matches (leaf->getSparseLeafMatches (leaf->name, depth_max, true, refreshDissims));
for (const Leaf* match : matches)
if (leaf->getDiscernible () != match->getDiscernible ())
Expand Down
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