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#include "SequenceTree.h"
#include <algorithm>
#include <functional>
#include <map>
#include <memory>
#include <queue>
#include <unordered_map>
#include <vector>
class SequenceTreeNode : public ContigNode
{
public:
SequenceTreeNode(
const ContigNode& contigNode,
const int overlap,
const int maxLength,
const bool forward);
std::vector<SequenceTreeNode> getChildren(
const int maxChildren = std::numeric_limits<int>::max()) const;
const Sequence treeSequence() const;
int treeSequenceStart;
int treeSequenceLength;
int maxLength;
bool forward;
};
const int EXPECTED_BASES_PER_NODE = 4;
SequenceTreeNode::SequenceTreeNode(
const ContigNode& contigNode,
const int overlap,
const int maxLength,
const bool forward)
: ContigNode(contigNode)
, maxLength(maxLength)
, forward(forward)
{
assert(overlap >= 0);
assert(maxLength > 0);
treeSequenceStart = overlap;
const auto& sequence = getContigSequence(*this);
const int size = sequence.size();
int treeSequenceEnd = std::min(overlap + maxLength, size);
assert(treeSequenceStart >= 0);
assert(treeSequenceEnd > 0);
assert(treeSequenceEnd > treeSequenceStart);
treeSequenceLength = treeSequenceEnd - treeSequenceStart;
if (!forward) {
treeSequenceStart = size - treeSequenceEnd;
assert(treeSequenceStart >= 0);
}
assert(treeSequenceStart + treeSequenceLength <= size);
}
std::vector<SequenceTreeNode>
SequenceTreeNode::getChildren(const int maxChildren) const
{
std::vector<SequenceTreeNode> children;
if (maxLength > treeSequenceLength) {
if (forward) {
int step = out_degree(*this, g_contigGraph) / maxChildren;
if (step <= 0) {
step = 1;
}
out_edge_iterator it, itLast;
for (std::tie(it, itLast) = out_edges(*this, g_contigGraph); it != itLast;
std::advance(it, step)) {
ContigNode outig = target(*it, g_contigGraph);
children.push_back(SequenceTreeNode(
outig,
-distanceBetween(*this, outig),
maxLength - treeSequenceLength,
forward));
if (int(children.size()) >= maxChildren) {
break;
}
}
} else {
int step = in_degree(*this, g_contigGraph) / maxChildren;
if (step <= 0) {
step = 1;
}
in_edge_iterator it, itLast;
for (std::tie(it, itLast) = in_edges(*this, g_contigGraph); it != itLast;
std::advance(it, step)) {
ContigNode intig = source(*it, g_contigGraph);
children.push_back(SequenceTreeNode(
intig,
-distanceBetween(intig, *this),
maxLength - treeSequenceLength,
forward));
if (int(children.size()) >= maxChildren) {
break;
}
}
}
}
return children;
}
const Sequence
SequenceTreeNode::treeSequence() const
{
assert(treeSequenceStart >= 0);
assert(treeSequenceLength > 0);
return Sequence(getContigSequence(*this).c_str(), treeSequenceStart, treeSequenceLength);
}
typedef std::list<SequenceTreeNode> Trace;
typedef std::list<Trace> Traces;
static Traces
getTreeTraces(
const ContigNode& start,
const int overlap,
const int maxLength,
const bool forward,
const int maxPaths)
{
assert(maxLength > 0);
Traces traces;
std::queue<std::reference_wrapper<Trace>> queue;
SequenceTreeNode root(start, overlap, maxLength, forward);
int level = 1;
(void)level;
int leaves = 1;
traces.push_back({ root });
queue.push(traces.back());
while (!queue.empty()) {
Trace& trace = queue.front();
queue.pop();
const SequenceTreeNode& node = trace.back();
assert(node.maxLength > 0 && node.maxLength <= maxLength);
assert(int(trace.size()) >= level);
level = trace.size();
auto children = node.getChildren();
if ((children.size() > 0) && (leaves + int(children.size()) - 1 <= maxPaths)) {
for (size_t i = 0; i < children.size(); i++) {
const auto& child = children[i];
assert(child.maxLength > 0);
assert(child.maxLength < node.maxLength);
if (i < children.size() - 1) {
Trace childTrace = trace;
childTrace.push_back(child);
assert(childTrace.size() == trace.size() + 1);
traces.push_back(childTrace);
queue.push(traces.back());
} else {
trace.push_back(child);
queue.push(trace);
}
}
leaves += children.size() - 1;
}
}
return traces;
}
std::vector<Sequence>
getTreeSequences(
const ContigNode& start,
const int overlap,
const int maxLength,
const bool forward,
const int maxPaths)
{
assert(overlap >= 0);
assert(maxLength > 0);
assert(maxPaths >= 1);
auto traces = getTreeTraces(start, overlap, maxLength, forward, maxPaths);
std::vector<Sequence> sequences;
sequences.reserve(traces.size());
for (const auto& trace : traces) {
Sequence sequence;
sequence.reserve(trace.size() * EXPECTED_BASES_PER_NODE);
if (forward) {
for (Trace::const_iterator it = trace.begin(); !(it == trace.end()); it++) {
sequence += it->treeSequence();
}
} else {
for (Trace::const_reverse_iterator it = trace.rbegin(); !(it == trace.rend()); it++) {
sequence += it->treeSequence();
}
}
sequences.push_back(sequence);
}
return sequences;
}
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