working on search=dist in chimera.slayer

diff --git a/blastdb.cpp b/blastdb.cpp
index 438d90c30961dfbabe5436483f3d33a23fc537ae..2d171391ca24ff1bfa43146de6ac5385de6ed46f 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -123,7 +123,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
-                               
+               cout << seq->getUnaligned() << endl;
                //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
@@ -142,7 +142,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-                       //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
+                       cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
                        
                        //get rest of junk in line
                        //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
@@ -157,7 +157,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                m8FileHandle.close();
                remove((queryFileName+seq->getName()).c_str());
                remove((blastFileName+seq->getName()).c_str());
-//cout << "\n" ;               
+cout << "\n" ;         
                return topMatches;
        }
        catch(exception& e) {

diff --git a/decalc.cpp b/decalc.cpp
index f6203827baec8e2575532ef43b0b2e3703745ca7..3a8c9d5711fa56631a4cac6cac70658fc2ad27f9 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -726,7 +726,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        //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
@@ -738,18 +738,19 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                                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);
 
@@ -758,7 +759,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        
                        distcalculator->calcDist(queryRight, dbRight);
                        float distRight = distcalculator->getDist();
-                       
+
                        SeqDist subjectLeft;
                        subjectLeft.seq = NULL;
                        subjectLeft.dist = distLeft;
@@ -780,6 +781,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                //sort by smallest distance
                sort(distsRight.begin(), distsRight.end(), compareSeqDist);
                sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
+
                
                //merge results         
                map<string, string> seen;
@@ -788,14 +790,15 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                vector<SeqDist> dists;
                float lastRight = distsRight[0].dist;
                float lastLeft = distsLeft[0].dist;
-               //int lasti = 0;
-               for (int i = 0; i < distsLeft.size(); i++) {
-                       
+
+               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;
@@ -804,7 +807,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 
                        //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;
@@ -834,8 +837,6 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        }
                }
                
-
-
                //cout << numWanted << endl;
                for (int i = 0; i < dists.size(); i++) {
 //                     cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;