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isite.cpp
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isite.cpp
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#include<cstdio> //fscanf can be useful if sites are read as strings
#include<cstdlib> //for atoi
#include<time.h> //for random number generation
#include<iostream> //for input and output
#include<fstream> //for file input and output
#include<utility> //for std::pair
#include<vector> //for std::vector
#include<map> //for std::map
#include<cstring> //for std::string
#include<algorithm> //for copying vectors
#include<unistd.h> //for better random seed
#include<cassert> //for debugging
#include<set>
#include<sys/stat.h>
#include<sys/types.h>
#include<errno.h>
#include<iomanip>
#include<boost/graph/connected_components.hpp>
#include<boost/lexical_cast.hpp>
#include "Random.hpp"
#include "graph_properties.hpp"
using namespace std;
using namespace boost;
enum output_type {PRINT, NODE_SUMMARY, STATUS, EVOLUTION};
enum op_type {FISSION, FUSION, DUPLICATION, NONE};
int nSelfLoops=0;
double asymmetry=0.0;
int nDuplications=0;
op_type force_op = NONE;
Graph::vertex_descriptor edgeDest(const Graph::vertex_descriptor vd,
const Graph::edge_descriptor ed,
const Graph& graph);
/*
Outputs formatted edge output to standard out
*/
void printEdge(Graph& graph,
Graph::vertex_descriptor& vd,
Graph::edge_descriptor& ed,
vimap& indexmap)
{
Graph::vertex_descriptor connectedNode = edgeDest(vd, ed, graph);
int site = graph[vd].edgeToSite[ed];
if (site == -1)
{
site = graph[vd].selfLoops[ed].first;
int site2 = graph[vd].selfLoops[ed].second;
cout<<" "<<site<<"->"<<site2<<":"<<indexmap(vd);
}
else
{
int connectedSite = graph[connectedNode].edgeToSite[ed];
cout<<" "<<site<<"->"<<connectedSite<<":"<<indexmap(connectedNode);
}
}
/*
Calculates iSite distribution
*/
void isite_distribution(Graph& graph, vector<int>& vmap)
{
vertex_iterator vi, viend;
for (tie(vi, viend)=vertices(graph); vi!=viend; ++vi)
{
int nsites=0;
vertexsites& node = graph[*vi];
for (int i=0; i<node.sites.size(); ++i)
if (!node.sites[i].edges.empty())
++nsites;
if (nsites+1 > vmap.size())
vmap.resize(nsites+1);
++vmap[nsites];
}
}
/*
Prints iSite distribution
*/
void print_distribution(vector<int>& vmap, ostream& outfile)
{
for (int i=0; i<vmap.size(); ++i)
outfile<<i<<": "<<vmap[i]<<endl;
}
/*
Returns the largest component of a graph
*/
Graph get_large_component(Graph& graph, vimap& indexmap)
{
int count=0;
vertex_iterator vi, viend;
for (tie(vi, viend)=vertices(graph); vi!=viend; ++vi)
{
put(indexmap, *vi, count++);
}
//vector<Graph::vertex_descriptor> component(count);
vimap component;
connected_components(graph, component, vertex_index_map(indexmap));
vector<int> component_counts(count, 0);
/*
for (int i=0; i<count; ++i)
component_counts[component[i]]++;
*/
vertex_iterator viter, viter_end;
for (tie(viter, viter_end) = vertices(graph); viter != viter_end; ++viter)
component_counts[component(*viter)]++;
//Determine largest component
int lsize=0;
int whichcomponent = 0;
for (int i=0; component_counts[i]>0; ++i)
if (component_counts[i]>lsize)
{
whichcomponent = i;
lsize = component_counts[i];
}
//Build largest component subgraph
Graph lgcomponent;
map<Graph::vertex_descriptor, Graph::vertex_descriptor> nodeToIndex;
for (tie(viter, viter_end) = vertices(graph); viter != viter_end; ++viter)
if (component(*viter) == whichcomponent)
{
Graph::vertex_descriptor node = add_vertex(lgcomponent);
nodeToIndex[*viter] = node;
}
//Add edges
edge_iterator eiter, eiter_end;
tie(eiter,eiter_end) = edges(graph);
for (; eiter != eiter_end; ++eiter)
{
Graph::vertex_descriptor src = source(*eiter, graph);
Graph::vertex_descriptor tgt = target(*eiter, graph);
if (nodeToIndex.count(src)==1)
add_edge(nodeToIndex[src], nodeToIndex[tgt], lgcomponent);
}
return lgcomponent;
}
/*
Removes parallel edges and self loops
*/
void simplify(Graph& graph)
{
vertex_iterator vi, viend;
AdjIter adji, adjiend;
for (tie(vi, viend)=vertices(graph); vi!=viend; ++vi)
{
//Remove homomeric interactions
while (edge(*vi, *vi, graph).second)
{
Graph::edge_descriptor ed = edge(*vi, *vi, graph).first;
vertexsites& vs = graph[*vi];
int site = vs.selfLoops[ed].first;
vector<edge_descriptor>::iterator pos;
for (pos=vs.sites[site].edges.begin(); *pos!=ed; ++pos);
vs.sites[site].edges.erase(pos);
remove_edge(ed, graph);
}
//Remove parallel interactions
for (tie(adji, adjiend)=adjacent_vertices(*vi, graph); adji!=adjiend; ++adji)
{
while (edge(*vi, *adji, graph).first != edge(*adji, *vi, graph).first)
{
remove_edge(*vi, *adji, graph);
}
}
}
}
/*
Counts the number of triangles in a graph
*/
int triangles(Graph& graph)
{
vertex_iterator vi, viend;
AdjIter adji, adjiend, adji2;
int numTriangles=0;
//Cycle through all vertices
for (tie(vi, viend)=vertices(graph); vi!=viend; vi++)
{
//Cycle through adjacent vertices
for(tie(adji,adjiend)=adjacent_vertices(*vi,graph);adji!=adjiend;adji++)
{
//Check for edges between vertices adjacent to vi aka triangle
for (adji2=adji; adji2!=adjiend; ++adji2)
{
if (edge(*adji, *adji2, graph).second)
numTriangles++;
}
}
}
return numTriangles/3;
}
/*
Counts the number of triples in a graph
*/
int countTriples(Graph& graph)
{
vertex_iterator vi, viend;
int numTriples=0;
for (tie(vi, viend)=vertices(graph); vi!=viend; ++vi)
numTriples+=out_degree(*vi, graph)*(out_degree(*vi,graph)-1)/2;
return numTriples;
}
/*
Counts the number of components in a graph
*/
int components(Graph& graph, vimap& indexmap)
{
dummy_property_map p;
int count=0;
vertex_iterator vi, viend;
for (tie(vi, viend)=vertices(graph); vi!=viend; vi++)
{
put(indexmap, *vi, count++);
}
return connected_components(graph, p, vertex_index_map(indexmap));
}
/*
Determines if node is isolated (only self loops)
*/
bool isolated(Graph::vertex_descriptor vd, Graph& graph)
{
AdjIter adji, adjiend;
for (tie(adji, adjiend) = adjacent_vertices(vd, graph);
adji != adjiend; ++adji)
{
if (*adji != vd) return false;
}
return true;
}
//Stores input parameters
struct parameters
{
string infile;
double prob_loss;
double prob_asym;
double prob_self;
double prob_fusion;
double prob_fission;
unsigned int end_order;
unsigned int iterations;
bool printResult;
} param;
//For vertex index mapping
unsigned int counter;
static Random* rnd;
/*
Given an edge and a vertex, returns the vertex on the opposite end
*/
Graph::vertex_descriptor edgeDest(const Graph::vertex_descriptor vd,
const Graph::edge_descriptor ed,
const Graph& graph)
{
return (vd==source(ed, graph)) ? target(ed, graph) : source(ed, graph);
}
/*
Safely removes a node from the graph
*/
void remove_node(Graph& graph, Graph::vertex_descriptor& vd)
{
graph_traits<Graph>::out_edge_iterator ei, eiend;
for (tie(ei, eiend) = out_edges(vd, graph); ei != eiend; ++ei)
{
if (source(*ei, graph) != target(*ei, graph))
{
//Update connected vertex
Graph::vertex_descriptor connectedVertex;
connectedVertex = edgeDest(vd, *ei, graph);
vertexsites& cvref = graph[connectedVertex];
int connectedSite = cvref.edgeToSite[*ei];
int connectedSiteSize = cvref.sites[connectedSite].edges.size();
int k;
for (k = 0; k < connectedSiteSize; ++k)
{
if (cvref.sites[connectedSite].edges[k]==*ei)
break;
}
cvref.edgeToSite.erase(*ei);
cvref.sites[connectedSite].edges.erase(
cvref.sites[connectedSite].edges.begin()+k);
}
}
clear_vertex(vd, graph);
remove_vertex(vd, graph);
}
/*
Performs fission
VARIABLE NAMES IN DUPLICATION FUNCTION ARE UNINTUITIVE AT THE MOMENT BECAUSE OF THIS
*/
Graph::vertex_descriptor fission(Graph& graph, vimap& indexmap, vector<Graph::vertex_descriptor>& progenies)
{
Graph::vertex_descriptor progenitor = rnd->random_vertex(graph);
vertexsites& vref = graph[progenitor];
progenies.push_back(add_vertex(graph));
progenies.push_back(add_vertex(graph));
put(indexmap, progenies[0], counter++);
put(indexmap, progenies[1], counter++);
vertexsites* pgyref = &graph[progenies[0]];
Graph::vertex_descriptor progeny = progenies[0];
//copy edges and isites
int numSites = vref.sites.size();
for (int i=0, pgysite=0; i < numSites; ++i, ++pgysite)
{
//Check if time to start on second progeny
if (i == numSites/2)
{
pgyref = &graph[progenies[1]];
progeny = progenies[1];
pgysite = 0;
}
isite newSite;
newSite.age = 0;
newSite.homomeric = false;
int siteEdges = vref.sites[i].edges.size();
for (int j=0; j < siteEdges; j++) //cycle through edges
{
Graph::edge_descriptor original_edge;
original_edge = vref.sites[i].edges[j];
//self loop
if (vref.edgeToSite[original_edge] == -1)
{
newSite.homomeric = true;
++nSelfLoops;
int site1 = vref.selfLoops[original_edge].first;
int site2 = vref.selfLoops[original_edge].second;
//self loop on same node
if (site1 == site2)
{
Graph::edge_descriptor ed, ed_tie;
bool temp_bool;
//copy self loop
tie(ed, temp_bool) = add_edge(progeny, progeny, graph);
//create edge between parent and child
tie(ed_tie, temp_bool) = add_edge(progenitor, progeny, graph);
//update progeny site
newSite.edges.push_back(ed);
newSite.edges.push_back(ed_tie);
pgyref->edgeToSite[ed] = -1;
pgyref->selfLoops[ed] = make_pair(pgysite, pgysite);
pgyref->edgeToSite[ed_tie] = pgysite;
//update progenitor site
vref.sites[i].edges.push_back(ed_tie);
vref.edgeToSite[ed_tie] = i;
}
//self loop on different nods
else
{
assert(0==1);
}
}
else
{
Graph::edge_descriptor ed, ed2;
bool temp_bool;
Graph::vertex_descriptor vd = edgeDest(progenitor, original_edge, graph);
vertexsites& vdref = graph[vd];
tie(ed, temp_bool) = add_edge(progeny, vd, graph);
//update child iSite
newSite.edges.push_back(ed);
pgyref->edgeToSite[ed] = pgysite;
//update other node's iSite
ed2 = vref.sites[i].edges[j];
vdref.sites[vdref.edgeToSite[ed2]].edges.push_back(ed);
vdref.edgeToSite[ed] = vdref.edgeToSite[ed2];
}
}
pgyref->sites.push_back(newSite);
}
return progenitor;
}
/*
Fuses duplications of two nodes
*/
Graph::vertex_descriptor duplicate(Graph& graph, vimap& indexmap, vector<Graph::vertex_descriptor>& progenitors, bool fuse)
{
progenitors.push_back(rnd->random_vertex(graph));
//Make 'while' to do arbitrary number of nodes NOT IMPLEMENTED
if (fuse)
{
Graph::vertex_descriptor progenitor;
while ((progenitor=rnd->random_vertex(graph)) == progenitors[0]);
progenitors.push_back(progenitor);
}
#ifdef DEBUG
cout << "**Duplication**" << endl;
for (unsigned int i=0; i<progenitors.size(); ++i)
cout << "Parent: " << indexmap(progenitors[i]) << endl;
#endif
//get a new vertex
Graph::vertex_descriptor progeny = add_vertex(graph);
put(indexmap, progeny, counter++);
vertexsites& pgyref = graph[progeny];
#ifdef DEBUG
cout << "Child: " << indexmap(progeny) << endl;
#endif
//copy edges and isites
int totalSites=0;
for (vector<Graph::vertex_descriptor>::iterator it = progenitors.begin();
it != progenitors.end(); ++it)
{
vertexsites& vref = graph[*it];
int numSites = vref.sites.size();
for (int i=0; i < numSites; ++totalSites, ++i)
{
isite newSite;
newSite.age = 0;
newSite.homomeric = false;
int siteEdges = vref.sites[i].edges.size();
for (int j=0; j < siteEdges; j++) //cycle through edges
{
Graph::edge_descriptor original_edge;
original_edge = vref.sites[i].edges[j];
if (edgeDest(*it, original_edge, graph) == progeny) continue;
//self loop
if (vref.edgeToSite[original_edge] == -1)
{
newSite.homomeric = true;
++nSelfLoops;
int site1 = vref.selfLoops[original_edge].first;
int site2 = vref.selfLoops[original_edge].second;
//self loop on same node
if (site1 == site2)
{
Graph::edge_descriptor ed, ed_tie;
bool temp_bool;
//copy self loop
tie(ed, temp_bool) = add_edge(progeny, progeny, graph);
//create edge between parent and child
tie(ed_tie, temp_bool) = add_edge(*it, progeny, graph);
//update child site
newSite.edges.push_back(ed);
newSite.edges.push_back(ed_tie);
pgyref.edgeToSite[ed] = -1;
pgyref.selfLoops[ed] = make_pair(totalSites, totalSites);
pgyref.edgeToSite[ed_tie] = totalSites;
//update parent site
vref.sites[i].edges.push_back(ed_tie);
vref.edgeToSite[ed_tie] = i;
}
//self loop on different nodes
else
{
assert(0==1);
}
}
else
{
Graph::edge_descriptor ed, ed2;
bool temp_bool;
Graph::vertex_descriptor vd = edgeDest(*it, original_edge, graph);
vertexsites& vdref = graph[vd];
tie(ed, temp_bool) = add_edge(progeny,vd,graph);
//update child iSite
newSite.edges.push_back(ed);
pgyref.edgeToSite[ed]=totalSites;
//update other node's iSite
ed2 = vref.sites[i].edges[j];
vdref.sites[vdref.edgeToSite[ed2]].edges.push_back(ed);
vdref.edgeToSite[ed]=vdref.edgeToSite[ed2];
}
}
pgyref.sites.push_back(newSite);
}
}
return progeny;
}
/*
Performs iSite algorithm
1)Duplicate random node
2)For each iSite, use prob_asym to choose parent or child
3)For each edge on chosen site, use prob_loss to determine if lost
4)Remove isolated vertices (vertex with degree=0)
*/
void duplication(Graph& graph, vimap& indexmap)
{
++nDuplications;
vector<Graph::vertex_descriptor> progenitors;
Graph::vertex_descriptor progeny;
double res = rnd->rand();
op_type op = res<param.prob_fission ? FISSION : res<param.prob_fission+param.prob_fusion ? FUSION : DUPLICATION;
if ((op == FISSION && force_op == NONE) || force_op == FISSION)
{
progeny = fission(graph, indexmap, progenitors); //actually progenitor in this case!
remove_node(graph, progeny);
return;
}
else if ((op == FUSION && force_op == NONE) || force_op == FUSION)
{
progeny = duplicate(graph, indexmap, progenitors, true);
remove_node(graph, progenitors[0]);
remove_node(graph, progenitors[1]);
return;
}
else
progeny=duplicate(graph, indexmap, progenitors, false);
force_op = NONE;
unsigned int full_subfuncs = 0;
vertexsites& pgyref = graph[progeny];
//prob_asym
pair<int, int> actualAsym(0,0); //progenitor, progeny asymmetry
for (unsigned int pr=0, py=0; pr < progenitors.size(); ++pr)
{
vertexsites& pgrref = graph[progenitors[pr]];
int numSites = pgrref.sites.size();
int site;
#ifdef DEBUG
cout<<indexmap(progenitors[pr])<<": iSites: "<<numSites<<endl;
#endif
for (int i=0; i<numSites; ++i, ++py)
{
Graph::vertex_descriptor vertexLoss, notLost;
#ifdef DEBUG
//cout<<"\niSite: "<<graph[progeny].sites[py].site_name<<endl;
#endif
if (rnd->rand() < param.prob_asym) //Parent loss
{
#ifdef DEBUG
cout<<"Asymmetry: Progenitor"<<endl;
#endif
vertexLoss = progenitors[pr];
notLost = progeny;
site = i;
}
else //Child loss
{
#ifdef DEBUG
cout<<"Asymmetry: Progeny"<<endl;
#endif
vertexLoss = progeny;
notLost = progenitors[pr];
site = py;
}
vertexsites& vlref = graph[vertexLoss];
//prob_loss
int numEdges = vlref.sites[site].edges.size();
#ifdef DEBUG
cout<< "Edges: " << numEdges << endl;
#endif
for (int j=0; j<numEdges; ++j)
{
#ifdef DEBUG
cout<<"\tLoss ";
printEdge(graph, vertexLoss, vlref.sites[site].edges[j], indexmap);
#endif
Graph::edge_descriptor edgeLoss;
edgeLoss = vlref.sites[site].edges[j];
double prob_loss;
/*
if (source(edgeLoss, graph) == target(edgeLoss, graph))
prob_loss = param.prob_self;
else if (edgeDest(vertexLoss, edgeLoss, graph) == notLost)
prob_loss = param.prob_self;
else
prob_loss = param.prob_loss;
*/
if (vlref.sites[site].homomeric)
prob_loss = param.prob_self;
else
prob_loss = param.prob_loss;
if (rnd->rand() < prob_loss) //Edge is lost
{
#ifdef DEBUG
cout<<": Yes"<<endl;
#endif
vertexLoss==progenitors[pr] ? ++actualAsym.first : ++actualAsym.second;
//Remove from vertexLoss
vlref.edgeToSite.erase(edgeLoss);
vlref.sites[site].edges.erase(
vlref.sites[site].edges.begin()+j);
//Check for self loop
if (source(edgeLoss, graph) != target(edgeLoss, graph))
{
//Update connected vertex
Graph::vertex_descriptor connectedVertex;
connectedVertex = edgeDest(vertexLoss, edgeLoss, graph);
vertexsites& cvref = graph[connectedVertex];
int connectedSite = cvref.edgeToSite[edgeLoss];
int connectedSiteSize = cvref.sites[connectedSite].edges.size();
int k;
for (k=0; k<connectedSiteSize; ++k)
{
if (cvref.sites[connectedSite].edges[k]==edgeLoss)
break;
}
cvref.edgeToSite.erase(edgeLoss);
cvref.sites[connectedSite].edges.erase(
cvref.sites[connectedSite].edges.begin()+k);
}
else --nSelfLoops;
remove_edge(edgeLoss, graph);
--j;
--numEdges;
}
#ifdef DEBUG
else cout<<": No"<<endl;
#endif
}//cycle through edges
}//cycle through iSites
/*
//Check progenitor for empty iSites
for (int i=0; i<numSites; ++i)
if (pgrref.sites[i].edges.size()==0)
{
pgrref.sites.erase(
pgrref.sites.begin() + i);
map<edge_descriptor,int>::iterator mit;
for (mit=pgrref.edgeToSite.begin();
mit!=pgrref.edgeToSite.end();
mit++)
{
if (mit->second > i) mit->second--;
}
--i;
--numSites;
}
*/
//If progenitor is isolated, delete it
if (isolated(progenitors[pr], graph))
{
clear_vertex(progenitors[pr], graph);
remove_vertex(progenitors[pr], graph);
++full_subfuncs;
}
}//cycle through progenitors
/*
//Check progeny for empty iSites
for (int i=0, size=pgyref.sites.size(); i<size; ++i)
if (pgyref.sites[i].edges.size()==0)
{
pgyref.sites.erase(
pgyref.sites.begin() + i);
map<edge_descriptor,int>::iterator mit;
for (mit=pgyref.edgeToSite.begin();
mit!=pgyref.edgeToSite.end();
mit++)
{
if (mit->second > i) mit->second--;
}
--i;
--size;
}
*/
//If progeny is isolated, delete it
if (isolated(progeny, graph))
{
clear_vertex(progeny, graph);
remove_vertex(progeny, graph);
//Failure
force_op = DUPLICATION;
--nDuplications;
return;
}
//Failure
else if (full_subfuncs == progenitors.size())
{
force_op = DUPLICATION;
--nDuplications;
return;
}
//Update actual asymmetry
double thisAsym;
if (actualAsym.first+actualAsym.second != 0)
if (actualAsym.first > actualAsym.second)
thisAsym = (double)actualAsym.first / ((double)actualAsym.first+(double)actualAsym.second);
else
thisAsym = (double)actualAsym.second / ((double)actualAsym.first+(double)actualAsym.second);
else
thisAsym = .5;
asymmetry = asymmetry*(((double)nDuplications-1.0)/(double)nDuplications)+thisAsym*(1.0/(double)nDuplications);
}
/*
Determines sites/edges to be duplicated/removed
Returns false if duplication should be ignored (100% asym for progeny and 100% subfunc)
*/
bool determineInteractions(Graph& graph,
vimap& indexmap,
vector<Graph::vertex_descriptor>& progenitors,
vector<bool>& progenitorLoss,
vector<bool>& progenyAdd,
vector<pair<bool, bool> >& selfLoops)
{
pair<int, int> actualAsym(0,0); //progenitor, progeny asymmetry
//Choose random vertices
progenitors.push_back(rnd->random_vertex(graph));
int progenitorDegree = out_degree(progenitors[0], graph);
//Make 'while' to do arbitrary number of progenitors NOT IMPLEMENTED
if (rnd->rand() <= param.prob_fusion)
{
Graph::vertex_descriptor progenitor;
//Needs to be modified to work with arbitrary number
while ((progenitor=rnd->random_vertex(graph)) == progenitors[0]);
progenitors.push_back(progenitor);
progenitorDegree += out_degree(progenitor, graph);
}
#ifdef DEBUG
cout << "**Duplication**" << endl;
for (unsigned int i=0; i<progenitors.size(); ++i)
cout << "Parent: " << indexmap(progenitors[i]) << endl;
#endif
progenitorLoss.resize(progenitorDegree);
progenyAdd.resize(progenitorDegree);
int progenyDegree = 0;
bool onlySelfLoops = true;
//Cycle through progenitors
for (int prog=0, x=0; prog<progenitors.size(); ++prog)
{
//Cycle through iSites
int numSites = graph[progenitors[prog]].sites.size();
#ifdef DEBUG
cout<<indexmap(progenitors[prog])<<": iSites: "<<numSites<<endl;
#endif
for (int site=0; site<numSites; ++site)
{
//prob_asym
bool asym_progenitor = (rnd->rand() <= param.prob_asym);
#ifdef DEBUG
//cout<<"\niSite: "<<graph[progenitors[prog]].sites[site].site_name<<endl;
cout << "Asymmetry: " << (asym_progenitor ? "Progenitor" : "Progeny") << endl;
#endif
//Cycle through edges
int numEdges = graph[progenitors[prog]].sites[site].edges.size();
#ifdef DEBUG
cout<< "Edges: " << numEdges << endl;
#endif
for (int edge=0; edge<numEdges; ++edge, ++x)
{
double prob_loss;
//Check for self loop
if (graph[progenitors[prog]].edgeToSite[graph[progenitors[prog]].sites[site].edges[edge]]==-1)
{
prob_loss = param.prob_self;
//Probability of keeping homomeric interactions
selfLoops.push_back(pair<bool,bool>((rnd->rand()<=prob_loss),(rnd->rand()<=prob_loss)));
//Paralogous interaction is determined like other heteromeric interactions
//but with selfLoopLoss probability
}
else //heteromeric
prob_loss = param.prob_loss;
//Need to check if edge between fused nodes
if (rnd->rand() <= prob_loss)
{
if (asym_progenitor) //loss progenitor
{
progenitorLoss[x] = true;
progenyAdd[x] = true;
++actualAsym.first;
++progenyDegree;
if (prob_loss == param.prob_self)
onlySelfLoops = false;
}
else //loss progeny
{
progenitorLoss[x] = false;
progenyAdd[x] = false;
++actualAsym.second;
}
}
else //no loss
{
progenitorLoss[x] = false;
progenyAdd[x] = true;
++progenyDegree;
onlySelfLoops = false;
} //if (loss)
} //Cycle through edges
} //Cycle through iSites
} //Cycle through progenitors
//Modify this to keep isolated nodes with self loops
if (progenyDegree == 0 || onlySelfLoops)
return false;
//Duplication is happening
++nDuplications;
//Update actual asymmetry
double thisAsym;
if (actualAsym.first+actualAsym.second != 0)
if (actualAsym.first > actualAsym.second)
thisAsym = (double)actualAsym.first / ((double)actualAsym.first+(double)actualAsym.second);
else
thisAsym = (double)actualAsym.second / ((double)actualAsym.first+(double)actualAsym.second);
else
thisAsym = .5;
asymmetry = asymmetry*(((double)nDuplications-1.0)/(double)nDuplications)+thisAsym*(1.0/(double)nDuplications);
return true;
}
/*
Performs iSite algorithm
1) Determine sites/edges to be duplicated/removed
2) Duplicate /remove edges
*/
void preemptiveDuplication(Graph& graph, vimap& indexmap)
{
vector<Graph::vertex_descriptor> progenitors;
vector<bool> progenitorLoss;
vector<bool> progenyAdd;
vector<pair<bool,bool> > selfLoops; //progenitorLoss, progenyAdd
//Determine sites/edges to be duplicated/removed
if (!determineInteractions(graph, indexmap, progenitors, progenitorLoss, progenyAdd, selfLoops))
return;
//Add new vertex
Graph::vertex_descriptor progeny = add_vertex(graph);
put(indexmap, progeny, counter++);
#ifdef DEBUG
cout << "Child: " << indexmap(progeny) << endl;
#endif
/*
*Add edges to progeny
*/
//Cycle through progenitors
for (int prog=0, x=0, progeny_site=0, self_loop_it=0; prog<progenitors.size(); ++prog)
{
Graph::vertex_descriptor pr = progenitors[prog];
//Cycle through iSites
int numSites = graph[pr].sites.size();
for (int site=0; site<numSites; ++site, ++progeny_site)
{
isite newSite;
newSite.age = 0;
/*newSite.site_name = *lexical_cast<string>(indexmap(progenitors[prog]))
+ "."
+ graph[progenitors[prog]].sites[site].site_name;*/
//Cycle through edges
//int numEdges = graph[progenitors[prog]].sites[site].edges.size();
for (int edge=0; edge<graph[pr].sites[site].edges.size(); ++edge, ++x)
{
Graph::edge_descriptor original_edge = graph[pr].sites[site].edges[edge];
//Edge is new
if (edgeDest(pr, original_edge, graph) == progeny)
{
--x;
continue;
}
//Self loop
if (graph[pr].edgeToSite[original_edge] == -1)
{
//Self loop needs to be added to progeny
if (selfLoops[self_loop_it].second)
{
++nSelfLoops;
int site1 = graph[pr].selfLoops[original_edge].first;
int site2 = graph[pr].selfLoops[original_edge].second;
//Self loop on same iSite
if (site1 == site2)
{
//Add self loop
Graph::edge_descriptor ed;
bool temp_bool;
tie(ed, temp_bool) = add_edge(progeny, progeny, graph);
//Add to iSite
newSite.edges.push_back(ed);
graph[progeny].edgeToSite[ed] = -1;
graph[progeny].selfLoops[ed] = make_pair(progeny_site, progeny_site);
}
else //Self loop on different iSites NOT IMPLEMENTED
{
assert(0==1);
}
}
//Self loop needs to be removed from progenitor
if (selfLoops[self_loop_it++].first)
{
--nSelfLoops;
graph[pr].selfLoops.erase(original_edge);
graph[pr].edgeToSite.erase(original_edge);
graph[pr].sites[site].edges.erase(
graph[pr].sites[site].edges.begin()+edge);
remove_edge(original_edge, graph);
}
//Add paralogous interaction
if (progenyAdd[x] && !progenitorLoss[x])
{
Graph::edge_descriptor ed;
bool temp_bool;
tie(ed, temp_bool) = add_edge(pr, progeny, graph);
//Add to iSite
newSite.edges.push_back(ed);
graph[progeny].edgeToSite[ed] = progeny_site;
//Update progenitor iSite
graph[pr].sites[site].edges.push_back(ed);
graph[pr].edgeToSite[ed] = site;
}
continue;
}
//Add edge to progeny