some alterations to chimera.slayer

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index f0b1ecc4fb1d31cbb79837579604cffaf84863e9..1442bd8ec8865f0574d338675d5899332814d8a8 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -12,7 +12,7 @@
 #include "dist.h"
 #include "eachgapdist.h"
 #include "ignoregaps.h"
-
+#include "eachgapdistignorens.h"
 
 //***************************************************************************************************************
 void DeCalculator::setMask(string ms) { 
@@ -692,7 +692,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                vector<SeqDist> distsLeft;
                vector<SeqDist> distsRight;
                
-               Dist* distcalculator = new eachGapDist();
+               Dist* distcalculator = new eachGapDistIgnoreNs();
                
                string queryUnAligned = querySeq->getUnaligned();
                int numBases = int(queryUnAligned.length() * 0.33);
@@ -780,7 +780,15 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                //sort by smallest distance
                sort(distsRight.begin(), distsRight.end(), compareSeqDist);
                sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
-                               
+//             cout << distsLeft.size() << '\t' << distsRight.size() << endl;
+//             for(int i=0;i<15;i++){
+//                     cout << "left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
+//             }
+//             for(int i=0;i<15;i++){
+//                     cout << "right\t" << db[distsLeft[i].index]->getName() << '\t' << distsRight[i].dist << endl;
+//             }
+               
+               
                //merge results         
                map<string, string> seen;
                map<string, string>::iterator it;
@@ -796,6 +804,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                                dists.push_back(distsLeft[i]);
                                seen[db[distsLeft[i].index]->getName()] = db[distsLeft[i].index]->getName();
                                lastLeft =  distsLeft[i].dist;
+//                             cout << "loop-left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
                        }
 
                        //add right if you havent already
@@ -804,27 +813,52 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                                dists.push_back(distsRight[i]);
                                seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
                                lastRight =  distsRight[i].dist;
+//                             cout << "loop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
                        }
                        
                        if (dists.size() > numWanted) { lasti = i; break; } //you have enough results
                }
                
+//             cout << "lastLeft\t" << lastLeft << endl;
+               
                //add in dups
                lasti++;
                int i = lasti;
                while (i < distsLeft.size()) {  
-                       if (distsLeft[i].dist == lastLeft) {  dists.push_back(distsLeft[i]);  numWanted++; }
+                       if (distsLeft[i].dist == lastLeft) {
+                               it = seen.find(db[distsLeft[i].index]->getName());
+
+                               if (it == seen.end()) {  
+//                                     cout << "newLoop-left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist <<  endl;
+                                       dists.push_back(distsLeft[i]);
+                                       seen[db[distsRight[i].index]->getName()] = db[distsLeft[i].index]->getName();
+//                                     numWanted++; 
+                               }
+                       }
                        else { break; }
                        i++;
                }
                
+//             cout << "lastRight\t" << lastRight << endl;
+
                i = lasti;
                while (i < distsRight.size()) {  
-                       if (distsRight[i].dist == lastRight) {  dists.push_back(distsRight[i]);  numWanted++; }
+                       if (distsRight[i].dist == lastRight) {
+                               it = seen.find(db[distsRight[i].index]->getName());
+                               
+                               if (it == seen.end()) {  
+//                                     cout << "newLoop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
+                                       dists.push_back(distsRight[i]);
+                                       seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
+//                                     numWanted++; 
+                               }
+                       }
                        else { break; }
                        i++;
                }
 
+               numWanted = seen.size();
+               
                if (numWanted > dists.size()) { 
                        //m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine(); 
                        numWanted = dists.size();
@@ -832,7 +866,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 
 //cout << numWanted << endl;
                for (int i = 0; i < numWanted; i++) {
-//cout << dists[i].seq->getName() << '\t' << dists[i].dist << endl;
+//                     cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
 
                        Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
                        
@@ -853,7 +887,7 @@ Sequence* DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*> db) {
                
                Sequence* seqsMatch;  
                
-               Dist* distcalculator = new eachGapDist();
+               Dist* distcalculator = new eachGapDistIgnoreNs();
                int index = 0;
                int smallest = 1000000;