#include "dist.h"
#include "eachgapdist.h"
#include "ignoregaps.h"
-#include "eachgapdistignorens.h"
+#include "eachgapdist.h"
//***************************************************************************************************************
void DeCalculator::setMask(string ms) {
}
//***************************************************************************************************************
//gets closest matches to each end, since chimeras will most likely have different parents on each end
-vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int numWanted) {
+vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int numWanted, int minSim) {
try {
//indexes.clear();
vector<SeqDist> distsLeft;
vector<SeqDist> distsRight;
- Dist* distcalculator = new eachGapDistIgnoreNs();
+ Dist* distcalculator = new eachGapDist();
string queryUnAligned = querySeq->getUnaligned();
int numBases = int(queryUnAligned.length() * 0.33);
//if you are a base
if (isalpha(queryAligned[i])) { baseCount++; }
//if you have 1/3
- if (baseCount >= numBases) { rightSpot = i; break; } //last 1/3
+ if (baseCount > numBases + 1) { rightSpot = i; break; } //last 1/3
}
//trim end
break;
}
}
- rightQuery = queryAligned.substr(rightSpot, (lastBaseSpot-rightSpot)); //sequence from pos spot to end
+ rightQuery = queryAligned.substr(rightSpot, (lastBaseSpot-rightSpot+1)); //sequence from pos spot to end
Sequence queryLeft(querySeq->getName(), leftQuery);
Sequence queryRight(querySeq->getName(), rightQuery);
+
//cout << querySeq->getName() << '\t' << leftSpot << '\t' << rightSpot << '\t' << firstBaseSpot << '\t' << lastBaseSpot << endl;
//cout << queryUnAligned.length() << '\t' << queryLeft.getUnaligned().length() << '\t' << queryRight.getUnaligned().length() << endl;
for(int j = 0; j < thisFilteredTemplate.size(); j++){
string dbAligned = thisFilteredTemplate[j]->getAligned();
string leftDB = dbAligned.substr(firstBaseSpot, (leftSpot-firstBaseSpot+1)); //first 1/3 of the sequence
- string rightDB = dbAligned.substr(rightSpot, (lastBaseSpot-rightSpot)); //last 1/3 of the sequence
-
+ string rightDB = dbAligned.substr(rightSpot, (lastBaseSpot-rightSpot+1)); //last 1/3 of the sequence
+
Sequence dbLeft(thisFilteredTemplate[j]->getName(), leftDB);
Sequence dbRight(thisFilteredTemplate[j]->getName(), rightDB);
distcalculator->calcDist(queryRight, dbRight);
float distRight = distcalculator->getDist();
-
+
SeqDist subjectLeft;
subjectLeft.seq = NULL;
subjectLeft.dist = distLeft;
//sort by smallest distance
sort(distsRight.begin(), distsRight.end(), compareSeqDist);
sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
+
//merge results
map<string, string> seen;
vector<SeqDist> dists;
float lastRight = distsRight[0].dist;
float lastLeft = distsLeft[0].dist;
- //int lasti = 0;
+
+ float maxDist = 1.0 - (minSim / 100.0);
+
for (int i = 0; i < numWanted+1; i++) {
-
if (m->control_pressed) { return seqsMatches; }
//add left if you havent already
it = seen.find(thisTemplate[distsLeft[i].index]->getName());
- if (it == seen.end()) {
+ if (it == seen.end() && distsLeft[i].dist <= maxDist) {
dists.push_back(distsLeft[i]);
seen[thisTemplate[distsLeft[i].index]->getName()] = thisTemplate[distsLeft[i].index]->getName();
lastLeft = distsLeft[i].dist;
//add right if you havent already
it = seen.find(thisTemplate[distsRight[i].index]->getName());
- if (it == seen.end()) {
+ if (it == seen.end() && distsRight[i].dist <= maxDist) {
dists.push_back(distsRight[i]);
seen[thisTemplate[distsRight[i].index]->getName()] = thisTemplate[distsRight[i].index]->getName();
lastRight = distsRight[i].dist;
// cout << "loop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
}
+ if (i == numWanted) { break; }
+
+ }
+
+ //are we still above the minimum similarity cutoff
+ if ((lastLeft >= minSim) || (lastRight >= minSim)) {
+ //add in ties from left
+ int i = numWanted;
+ while (i < distsLeft.size()) {
+ if (distsLeft[i].dist == lastLeft) { dists.push_back(distsLeft[i]); }
+ else { break; }
+ i++;
+ }
+
+ //add in ties from right
+ i = numWanted;
+ while (i < distsRight.size()) {
+ if (distsRight[i].dist == lastRight) { dists.push_back(distsRight[i]); }
+ else { break; }
+ i++;
+ }
}
-
- //numWanted = dists.size();
-
//cout << numWanted << endl;
for (int i = 0; i < dists.size(); i++) {
// cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
- if (thisTemplate[dists[i].index]->getName() != querySeq->getName()) {
+ if ((thisTemplate[dists[i].index]->getName() != querySeq->getName()) && (((1.0-dists[i].dist)*100) >= minSim)) {
Sequence* temp = new Sequence(thisTemplate[dists[i].index]->getName(), thisTemplate[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
-
+ //cout << querySeq->getName() << '\t' << thisTemplate[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
seqsMatches.push_back(temp);
}
Sequence* seqsMatch;
- Dist* distcalculator = new eachGapDistIgnoreNs();
+ Dist* distcalculator = new eachGapDist();
int index = 0;
int smallest = 1000000;