working on pam

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
index 5c49a936e9293c629e05ea5565f334a43e5cc37c..27e278574493c89d0197d99cbe71c0c3dd03d0d9 100644 (file)
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -11,14 +11,15 @@
 #include "database.hpp"
 #include "sequence.hpp"
 #include "distancedb.hpp"
-#include "eachgapdist.h"
+#include "onegapignore.h"
+
 
 /**************************************************************************************************/
-DistanceDB::DistanceDB() { 
+DistanceDB::DistanceDB() : Database() { 
        try {
                templateAligned = true;  
                templateSeqsLength = 0; 
-               distCalculator = new eachGapDist();
+               distCalculator = new oneGapIgnoreTermGapDist();
        }
        catch(exception& e) {
                m->errorOut(e, "DistanceDB", "DistanceDB");
@@ -29,7 +30,11 @@ DistanceDB::DistanceDB() {
 void DistanceDB::addSequence(Sequence seq) {
        try {
                //are the template sequences aligned
-               if (!isAligned(seq.getAligned())) { templateAligned = false; m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method."); m->mothurOutEndLine(); }
+               if (!isAligned(seq.getAligned())) {
+                       templateAligned = false;
+                       m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method.");
+                       m->mothurOutEndLine(); 
+               }
                
                if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
                                
@@ -45,34 +50,68 @@ void DistanceDB::addSequence(Sequence seq) {
 vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
        try {
                vector<int> topMatches;
+               Scores.clear();
                bool templateSameLength = true;
                string sequence = query->getAligned();
-               vector<seqDist> dists;
+               vector<seqDist> dists; 
+               
+               searchScore = -1.0;
        
-               if (numWanted > data.size()) { m->mothurOut("numwanted is larger than the number of template sequences, using "+ toString(data.size()) + "."); m->mothurOutEndLine(); numWanted = data.size(); }
+               if (numWanted > data.size()){
+                       m->mothurOut("numwanted is larger than the number of template sequences, using "+ toString(data.size()) + ".");
+                       m->mothurOutEndLine();
+                       numWanted = data.size();
+               }
                
                if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
                
                if (templateSameLength && templateAligned) {
-                       //calc distance from this sequence to every sequence in the template
-                       for (int i = 0; i < data.size(); i++) {
-                               distCalculator->calcDist(*query, data[i]);
-                               float dist = distCalculator->getDist();
+                       if (numWanted != 1) {
                                
-                               //save distance to each template sequence
-                               seqDist temp(-1, i, dist);
-                               dists.push_back(temp);
-                       }
-                       
-                       sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
-                       
-                       //fill topmatches with numwanted closest sequences indexes
-                       for (int i = 0; i < numWanted; i++) {
-                               topMatches.push_back(dists[i].seq2);
+                               dists.resize(data.size());
+                               
+                               //calc distance from this sequence to every sequence in the template
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //save distance to each template sequence
+                                       dists[i].seq1 = -1;
+                                       dists[i].seq2 = i;
+                                       dists[i].dist = dist;
+                               }
+                               
+                               sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
+                               
+                               //save distance of best match
+                               searchScore = dists[0].dist;
+                               
+                               //fill topmatches with numwanted closest sequences indexes
+                               for (int i = 0; i < numWanted; i++) {
+                                       topMatches.push_back(dists[i].seq2);
+                                       Scores.push_back(dists[i].dist);
+                               }
+                       }else {
+                               int bestIndex = 0;
+                               float smallDist = 100000;
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //are you smaller?
+                                       if (dist < smallDist) {
+                                               bestIndex = i;
+                                               smallDist = dist;
+                                       }
+                               }
+                               searchScore = smallDist;
+                               topMatches.push_back(bestIndex);
+                               Scores.push_back(smallDist);
                        }
                
                }else{
-                       m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length."); m->mothurOutEndLine();
+                       m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
+                       m->mothurOutEndLine();
                        exit(1);
                }