X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.cpp;h=bf16de4e34b795694d1a894ea1005f32353be110;hb=5a1e62397b91f57d0d3aff635891df04b8999a88;hp=7e997b9824439e4e42f495f95a2d101b58a89600;hpb=ec92647e652017e0cd4ba0488a815094f88373b3;p=mothur.git

diff --git a/chimera.cpp b/chimera.cpp
index 7e997b9..bf16de4 100644
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -10,10 +10,10 @@
 #include "chimera.h"
 
 //***************************************************************************************************************
-//this is a vertical filter
+//this is a vertical soft filter
 void Chimera::createFilter(vector<Sequence*> seqs) {
 	try {
-		
+		filterString = "";
 		int threshold = int (0.5 * seqs.size());
 //cout << "threshhold = " << threshold << endl;
 		
@@ -40,6 +40,7 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 			}
 		}
 		
+		//zero out spot where all sequences have blanks
 		//zero out spot where all sequences have blanks
 		int numColRemoved = 0;
 		for(int i = 0;i < seqs[0]->getAligned().length(); i++){
@@ -48,6 +49,7 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 			else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) {	filterString[i] = '0';	numColRemoved++;  }
 			//cout << "a = " << a[i] <<  " t = " << t[i] <<  " g = " << g[i] <<  " c = " << c[i] << endl;
 		}
+	
 //cout << "filter = " << filterString << endl;	
 
 		mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  mothurOutEndLine();
@@ -58,46 +60,52 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 	}
 }
 //***************************************************************************************************************
-void Chimera::runFilter(vector<Sequence*> seqs) {
+void Chimera::runFilter(Sequence* seq) {
 	try {
 		
-		//for each sequence
-		for (int i = 0; i < seqs.size(); i++) {
-		
-			string seqAligned = seqs[i]->getAligned();
-			string newAligned = "";
-			
-			for (int j = 0; j < seqAligned.length(); j++) {
-				//if this spot is a gap
-				if (filterString[j] == '1') { newAligned += seqAligned[j]; }
-			}
+		string seqAligned = seq->getAligned();
+		string newAligned = "";
 			
-			seqs[i]->setAligned(newAligned);
+		for (int j = 0; j < seqAligned.length(); j++) {
+			//if this spot is a gap
+			if (filterString[j] == '1') { newAligned += seqAligned[j]; }
 		}
-		
+			
+		seq->setAligned(newAligned);
 	}
 	catch(exception& e) {
 		errorOut(e, "Chimera", "runFilter");
 		exit(1);
 	}
 }
-
 //***************************************************************************************************************
 vector<Sequence*> Chimera::readSeqs(string file) {
 	try {
+	
+		mothurOut("Reading sequences... "); cout.flush();
 		ifstream in;
 		openInputFile(file, in);
 		vector<Sequence*> container;
+		int count = 0;
+		int length = 0;
+		unaligned = false;
 		
 		//read in seqs and store in vector
 		while(!in.eof()){
 			
-			Sequence* current = new Sequence(in);
-			container.push_back(current);
-			gobble(in);
+			Sequence* current = new Sequence(in);  gobble(in);
+			
+			if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+			else if (length != current->getAligned().length()) { //seqs are unaligned
+				unaligned = true;
+			}
+			
+			if (current->getName() != "") {  container.push_back(current);  }
 		}
 		
 		in.close();
+		mothurOut("Done."); mothurOutEndLine();
+		
 		return container;
 	}
 	catch(exception& e) {
@@ -142,7 +150,7 @@ vector< vector<float> > Chimera::readQuantiles() {
 		openInputFile(quanfile, in);
 		
 		vector< vector<float> > quan;
-		vector <float> temp;
+		vector <float> temp; temp.resize(6, 0);
 		
 		//to fill 0
 		quan.push_back(temp); 
@@ -177,6 +185,31 @@ vector< vector<float> > Chimera::readQuantiles() {
 	}
 }
 //***************************************************************************************************************
+Sequence* Chimera::getSequence(string name) {
+	try{
+		Sequence* temp;
+		
+		//look through templateSeqs til you find it
+		int spot = -1;
+		for (int i = 0; i < templateSeqs.size(); i++) {
+			if (name == templateSeqs[i]->getName()) {  
+				spot = i;
+				break;
+			}
+		}
+		
+		if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+		
+		temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+		
+		return temp;
+	}
+	catch(exception& e) {
+		errorOut(e, "Chimera", "getSequence");
+		exit(1);
+	}
+}
+//***************************************************************************************************************