X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=kmerdb.cpp;h=9a5d23500be955b459413beee989601f6c0ec78f;hp=bf8679e57a932af0567df8a456f038b76fbf0fae;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347

diff --git a/kmerdb.cpp b/kmerdb.cpp
index bf8679e..9a5d235 100644
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -42,12 +42,14 @@ KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "KmerDB", "KmerDB");
+		m->errorOut(e, "KmerDB", "KmerDB");
 		exit(1);
 	}	
 
 }
 /**************************************************************************************************/
+KmerDB::KmerDB() : Database() {}
+/**************************************************************************************************/
 
 KmerDB::~KmerDB(){}
 
@@ -55,9 +57,12 @@ KmerDB::~KmerDB(){}
 
 vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
 	try {
+		if (num > numSeqs) { m->mothurOut("[WARNING]: you requested " + toString(num) + " closest sequences, but the template only contains " + toString(numSeqs) + ", adjusting."); m->mothurOutEndLine(); num = numSeqs; }
+		
 		vector<int> topMatches;
 		Kmer kmer(kmerSize);
 		searchScore = 0;
+		Scores.clear();
 		
 		vector<int> matches(numSeqs, 0);						//	a record of the sequences with shared kmers
 		vector<int> timesKmerFound(kmerLocations.size()+1, 0);	//	a record of the kmers that we have already found
@@ -73,28 +78,46 @@ vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
 			}
 			timesKmerFound[kmerNumber] = 1;						//	ok, we've seen the kmer now
 		}
-	
-		vector<seqMatch> seqMatches;
-		for(int i=0;i<numSeqs;i++){		
-			seqMatch temp(i, matches[i]);
-			seqMatches.push_back(temp);
-		}
 		
-		//sorts putting largest matches first
-		sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
+		if (num != 1) {
+			vector<seqMatch> seqMatches; seqMatches.resize(numSeqs);
+			for(int i=0;i<numSeqs;i++){		
+				seqMatches[i].seq = i;
+				seqMatches[i].match = matches[i];
+			}
+			
+			//sorts putting largest matches first
+			sort(seqMatches.begin(), seqMatches.end(), compareSeqMatches);
+			
+			searchScore = seqMatches[0].match;
+			searchScore = 100 * searchScore / (float) numKmers;		//	return the Sequence object corresponding to the db
 		
-		searchScore = seqMatches[0].match;
-		searchScore = 100 * searchScore / (float) numKmers;		//	return the Sequence object corresponding to the db
-	
-		//save top matches
-		for (int i = 0; i < num; i++) {
-			topMatches.push_back(seqMatches[i].seq);
+			//save top matches
+			for (int i = 0; i < num; i++) {
+				topMatches.push_back(seqMatches[i].seq);
+				float thisScore = 100 * seqMatches[i].match / (float) numKmers;
+				Scores.push_back(thisScore);
+			}
+		}else{
+			int bestIndex = 0;
+			int bestMatch = -1;
+			for(int i=0;i<numSeqs;i++){	
+				
+				if (matches[i] > bestMatch) {
+					bestIndex = i;
+					bestMatch = matches[i];
+				}
+			}
+			
+			searchScore = bestMatch;
+			searchScore = 100 * searchScore / (float) numKmers;		//	return the Sequence object corresponding to the db
+			topMatches.push_back(bestIndex);
+			Scores.push_back(searchScore);
 		}
-		
 		return topMatches;		
 	}
 	catch(exception& e) {
-		errorOut(e, "KmerDB", "findClosestSequences");
+		m->errorOut(e, "KmerDB", "findClosestSequences");
 		exit(1);
 	}	
 }
@@ -105,7 +128,10 @@ void KmerDB::generateDB(){
 	try {
 		
 		ofstream kmerFile;										//	once we have the kmerLocations folder print it out
-		openOutputFile(kmerDBName, kmerFile);					//	to a file
+		m->openOutputFile(kmerDBName, kmerFile);					//	to a file
+		
+		//output version
+		kmerFile << "#" << m->getVersion() << endl;
 		
 		for(int i=0;i<maxKmer;i++){								//	step through all of the possible kmer numbers
 			kmerFile << i << ' ' << kmerLocations[i].size();	//	print the kmer number and the number of sequences with
@@ -118,7 +144,7 @@ void KmerDB::generateDB(){
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "KmerDB", "generateDB");
+		m->errorOut(e, "KmerDB", "generateDB");
 		exit(1);
 	}	
 	
@@ -143,7 +169,7 @@ void KmerDB::addSequence(Sequence seq) {
 		count++;
 	}
 	catch(exception& e) {
-		errorOut(e, "KmerDB", "addSequence");
+		m->errorOut(e, "KmerDB", "addSequence");
 		exit(1);
 	}	
 }
@@ -154,6 +180,9 @@ void KmerDB::readKmerDB(ifstream& kmerDBFile){
 					
 		kmerDBFile.seekg(0);									//	start at the beginning of the file
 		
+		//read version
+		string line = m->getline(kmerDBFile); m->gobble(kmerDBFile);
+		
 		string seqName;
 		int seqNumber;
 
@@ -170,9 +199,57 @@ void KmerDB::readKmerDB(ifstream& kmerDBFile){
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "KmerDB", "readKmerDB");
+		m->errorOut(e, "KmerDB", "readKmerDB");
+		exit(1);
+	}	
+}
+
+/**************************************************************************************************/
+int KmerDB::getCount(int kmer) {
+	try {
+		if (kmer < 0) { return 0; }  //if user gives negative number
+		else if (kmer > maxKmer) {	return 0;	}  //or a kmer that is bigger than maxkmer
+		else {	return kmerLocations[kmer].size();	}  // kmer is in vector range
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KmerDB", "getCount");
+		exit(1);
+	}	
+}
+/**************************************************************************************************/
+int KmerDB::getReversed(int kmerNumber) {
+	try {
+		Kmer kmer(kmerSize);
+		
+		if (kmerNumber < 0) { return 0; }  //if user gives negative number
+		else if (kmerNumber > maxKmer) {	return 0;	}  //or a kmer that is bigger than maxkmer
+		else {	return kmer.getReverseKmerNumber(kmerNumber);	}  // kmer is in vector range
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KmerDB", "getReversed");
 		exit(1);
 	}	
 }
+/**************************************************************************************************/
+vector<int> KmerDB::getSequencesWithKmer(int kmer) {
+	try {
+		
+		vector<int> seqs;
+	
+		if (kmer < 0) { }  //if user gives negative number
+		else if (kmer > maxKmer) {	}  //or a kmer that is bigger than maxkmer
+		else {	seqs = kmerLocations[kmer];	}
+		
+		return seqs;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KmerDB", "getSequencesWithKmer");
+		exit(1);
+	}	
+}
+/**************************************************************************************************/
+
 
 /**************************************************************************************************/
+
+