X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancedb.cpp;h=ca6ffe8ba61217ac0b66b353e8f33461f4916e52;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=25c95c7a32a2523080bac92b41722ed1f1b91e6d;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/distancedb.cpp b/distancedb.cpp
index 25c95c7..ca6ffe8 100644
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -11,52 +11,101 @@
 #include "database.hpp"
 #include "sequence.hpp"
 #include "distancedb.hpp"
-
+#include "eachgapdist.h"
 
 /**************************************************************************************************/
-
-DistanceDB::DistanceDB(string fastaFileName, string distanceFileName) : Database(fastaFileName) {
-	
-	ifstream inputData;
-	openInputFile(distanceFileName, inputData);
-	int numCandSeqs=count(istreambuf_iterator<char>(inputData),istreambuf_iterator<char>(), '\n');	//	count the number of
-	inputData.seekg(0);																		//	sequences
-
-	hit closestMatch;
-	string candidateSeqName;
-	string junk;
-	
-	mostSimSequenceVector.resize(numCandSeqs);
-	
-	for(int i=0;i<numCandSeqs;i++){
-		inputData >> candidateSeqName >> closestMatch.seqName >> closestMatch.indexNumber >> closestMatch.simScore;
-//		getline(inputData, junk);	
-		mostSimSequenceVector[i] = closestMatch;
+DistanceDB::DistanceDB() { 
+	try {
+		templateAligned = true;  
+		templateSeqsLength = 0; 
+		distCalculator = new eachGapDist();
 	}
-	cout << numCandSeqs << endl;
-	searchIndex = 0;
-	inputData.close();
+	catch(exception& e) {
+		m->errorOut(e, "DistanceDB", "DistanceDB");
+		exit(1);
+	}	
 }
-
 /**************************************************************************************************/
-
-Sequence DistanceDB::findClosestSequence(Sequence* candidateSeq){
-	
-	hit simAccession = mostSimSequenceVector[searchIndex];
-//	string candidateSeqName, closestMatchSeqName, junk;
-//	int closestMatchIndexNumber;
-//	float closestMatchSimScore;
-//	
-//	inputData >> candidateSeqName >> closestMatchSeqName >> closestMatchIndexNumber >> closestMatchSimScore;
-//	getline(inputData, junk);	
-
-//	searchScore = 100. * closestMatchSimScore;
-
-	searchScore = 100. * simAccession.simScore;
-	searchIndex++;
-//	return templateSequences[closestMatchIndexNumber];
-	return templateSequences[simAccession.indexNumber];
+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 (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
+				
+		data.push_back(seq);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DistanceDB", "addSequence");
+		exit(1);
+	}	
+}
+/**************************************************************************************************/
+//returns indexes to top matches
+vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
+	try {
+		vector<int> topMatches;
+		bool templateSameLength = true;
+		string sequence = query->getAligned();
+		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 (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();
+				
+				//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
+			
+			//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);
+			}
+		
+		}else{
+			m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length."); m->mothurOutEndLine();
+			exit(1);
+		}
+		
+		return topMatches;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DistanceDB", "findClosestSequence");
+		exit(1);
+	}	
+}
+/**************************************************************************************************/
+bool DistanceDB::isAligned(string seq){
+	try {
+		bool aligned;
+		
+		int pos = seq.find_first_of(".-");
+		
+		if (pos != seq.npos) {
+			aligned = true;
+		}else { aligned = false; }
+		
+		
+		return aligned;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DistanceDB", "isAligned");
+		exit(1);
+	}	
 }
 
 /**************************************************************************************************/