X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pintail.cpp;h=6adfdf91ebeaf30847bee05d90f2c9b22d3c5946;hb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;hp=04dfb0a76467ab6b030cfa60b8462dd7d30afd73;hpb=f7fbd74ffedcf62217109c22e828453eaefa1458;p=mothur.git

diff --git a/pintail.cpp b/pintail.cpp
index 04dfb0a..6adfdf9 100644
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -18,7 +18,7 @@ inline bool compareQuanMembers(quanMember left, quanMember right){
 } 
 //***************************************************************************************************************
 
-Pintail::Pintail(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
+Pintail::Pintail(string filename, string temp, string o) {  fastafile = filename;  templateFile = temp; outputDir = o; }
 //***************************************************************************************************************
 
 Pintail::~Pintail() {
@@ -41,13 +41,15 @@ void Pintail::print(ostream& out) {
 		for (int i = 0; i < querySeqs.size(); i++) {
 			
 			int index = ceil(deviation[i]);
-			
-			if (index == 0) { index=1;  }
 						
 			//is your DE value higher than the 95%
 			string chimera;
-			if (DE[i] > quantiles[index-1][4])		{	chimera = "Yes";	}
-			else									{	chimera = "No";		}
+			if (quantiles[index][4] == 0.0) {
+				chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
+			}else {
+				if (DE[i] > quantiles[index][4])		{	chimera = "Yes";	}
+				else									{	chimera = "No";		}
+			}
 			
 			out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
 			if (chimera == "Yes") {
@@ -72,7 +74,7 @@ void Pintail::print(ostream& out) {
 }
 
 //***************************************************************************************************************
-void Pintail::getChimeras() {
+int Pintail::getChimeras() {
 	try {
 		
 		//read in query sequences and subject sequences
@@ -83,6 +85,8 @@ void Pintail::getChimeras() {
 		
 		int numSeqs = querySeqs.size();
 		
+		if (unaligned) { mothurOut("Your sequences need to be aligned when you use the pintail method."); mothurOutEndLine(); return 1;  }
+		
 		obsDistance.resize(numSeqs);
 		expectedDistance.resize(numSeqs);
 		seqCoef.resize(numSeqs);
@@ -144,23 +148,20 @@ void Pintail::getChimeras() {
 			mothurOut("Done."); mothurOutEndLine();
 		}else {		createProcessesPairs();		}
 		
-/*string o = "foronlinepintailpairs-eachgap";
-ofstream out7;
-openOutputFile(o, out7);
+//string o = "closestmatch.eachgap.fasta";
+//ofstream out7;
+//openOutputFile(o, out7);
 
-for (int i = 0; i < bestfit.size(); i++) {
-	out7 << querySeqs[i]->getName() << endl;
-	out7 << querySeqs[i]->getUnaligned() << endl << endl;
-	
-	out7 << bestfit[i]->getName() << endl;
-	out7 << bestfit[i]->getUnaligned() << endl << endl << endl;
-}		
-out7.close();/*/	
+//for (int i = 0; i < bestfit.size(); i++) {
+	//out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+	//out7 << bestfit[i]->getAligned() << endl;
+//}		
+//out7.close();	
 		//find P
 		mothurOut("Getting conservation... "); cout.flush();
 		if (consfile == "") { 
 			mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
-			probabilityProfile = decalc->calcFreq(templateSeqs, templateFile); 
+			probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFile)); 
 			mothurOut("Done."); mothurOutEndLine();
 		}else				{   probabilityProfile = readFreq();			  }
 
@@ -279,10 +280,19 @@ out7.close();/*/
 			ofstream out4, out5;
 			string noOutliers, outliers;
 			
-			noOutliers = getRootName(templateFile) + "pintail.quanNOOUTLIERS";
-			outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";
+			if ((!filter) && (seqMask == "")) {
+				noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.quan";
+			}else if ((filter) && (seqMask == "")) { 
+				noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.quan";
+			}else if ((!filter) && (seqMask != "")) { 
+				noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.masked.quan";
+			}else if ((filter) && (seqMask != "")) { 
+				noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.masked.quan";
+			}
+
+			//outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";
 			
-			openOutputFile(outliers, out4);
+			/*openOutputFile(outliers, out4);
 			
 			//adjust quantiles
 			for (int i = 0; i < quantilesMembers.size(); i++) {
@@ -321,7 +331,7 @@ out7.close();/*/
 				
 			}
 			
-			out4.close();
+			out4.close();*/
 			
 			decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
 			
@@ -374,6 +384,8 @@ out7.close();/*/
 			
 		delete distcalculator;
 		delete decalc;
+		
+		return 0;
 	}
 	catch(exception& e) {
 		errorOut(e, "Pintail", "getChimeras");
@@ -431,28 +443,9 @@ vector<Sequence*> Pintail::findPairs(int start, int end) {
 		vector<Sequence*> seqsMatches;  
 		
 		for(int i = start; i < end; i++){
-		
-			float smallest = 10000.0;
-			Sequence query = *(querySeqs[i]);
-			Sequence* match;
-			
-			for(int j = 0; j < templateSeqs.size(); j++){
-				
-				Sequence temp = *(templateSeqs[j]);
-				
-				distcalculator->calcDist(query, temp);
-				float dist = distcalculator->getDist();
-				
-				if (dist < smallest) { 
-					match = templateSeqs[j];
-					smallest = dist;
-				}
-			}
-			
-			//make copy so trimSeqs doesn't overtrim
-			Sequence* copy = new Sequence(match->getName(), match->getAligned());
 			
-			seqsMatches.push_back(copy);
+			vector<Sequence*> copy = decalc->findClosest(querySeqs[i], templateSeqs, 1);
+			seqsMatches.push_back(copy[0]);
 		}
 		
 		return seqsMatches;