X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.cpp;h=7eeca96316511531532232d56519e1900cd7a9c6;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=db153dde6e90b285f7592628789346f3bb696fb6;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/chimera.cpp b/chimera.cpp
index db153dd..7eeca96 100644
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -11,10 +11,10 @@
 
 //***************************************************************************************************************
 //this is a vertical soft filter
-void Chimera::createFilter(vector<Sequence*> seqs) {
+string Chimera::createFilter(vector<Sequence*> seqs, float t) {
 	try {
-		
-		int threshold = int (0.5 * seqs.size());
+		filterString = "";
+		int threshold = int (t * seqs.size());
 //cout << "threshhold = " << threshold << endl;
 		
 		vector<int> gaps;	gaps.resize(seqs[0]->getAligned().length(), 0);
@@ -22,14 +22,16 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 		vector<int> t;		t.resize(seqs[0]->getAligned().length(), 0);
 		vector<int> g;		g.resize(seqs[0]->getAligned().length(), 0);
 		vector<int> c;		c.resize(seqs[0]->getAligned().length(), 0);
-		
+	
 		filterString = (string(seqs[0]->getAligned().length(), '1'));
 		
 		//for each sequence
 		for (int i = 0; i < seqs.size(); i++) {
 		
+			if (m->control_pressed) { return filterString; }
+		
 			string seqAligned = seqs[i]->getAligned();
-			
+		
 			for (int j = 0; j < seqAligned.length(); j++) {
 				//if this spot is a gap
 				if ((seqAligned[j] == '-') || (seqAligned[j] == '.'))	{	gaps[j]++;	}
@@ -44,66 +46,84 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 		//zero out spot where all sequences have blanks
 		int numColRemoved = 0;
 		for(int i = 0;i < seqs[0]->getAligned().length(); i++){
+		
+			if (m->control_pressed) { return filterString; }
+			
 			if(gaps[i] == seqs.size())	{	filterString[i] = '0'; 	numColRemoved++;  }
 			
 			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();
+		m->mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  m->mothurOutEndLine();
+		return filterString;
 	}
 	catch(exception& e) {
-		errorOut(e, "Chimera", "createFilter");
+		m->errorOut(e, "Chimera", "createFilter");
 		exit(1);
 	}
 }
 //***************************************************************************************************************
-void Chimera::runFilter(vector<Sequence*> seqs) {
+map<int, int> Chimera::runFilter(Sequence* seq) {
 	try {
-		
-		//for each sequence
-		for (int i = 0; i < seqs.size(); i++) {
-		
-			string seqAligned = seqs[i]->getAligned();
-			string newAligned = "";
+		map<int, int> maskMap;
+		string seqAligned = seq->getAligned();
+		string newAligned = "";
+		int count = 0;
 			
-			for (int j = 0; j < seqAligned.length(); j++) {
-				//if this spot is a gap
-				if (filterString[j] == '1') { newAligned += seqAligned[j]; }
+		for (int j = 0; j < seqAligned.length(); j++) {
+			//if this spot is a gap
+			if (filterString[j] == '1') { 
+				newAligned += seqAligned[j]; 
+				maskMap[count] = j;
+				count++;
 			}
-			
-			seqs[i]->setAligned(newAligned);
 		}
+			
+		seq->setAligned(newAligned);
 		
+		return maskMap;
 	}
 	catch(exception& e) {
-		errorOut(e, "Chimera", "runFilter");
+		m->errorOut(e, "Chimera", "runFilter");
 		exit(1);
 	}
 }
-
 //***************************************************************************************************************
 vector<Sequence*> Chimera::readSeqs(string file) {
 	try {
+	
+		m->mothurOut("Reading sequences... "); cout.flush();
 		ifstream in;
 		openInputFile(file, in);
+		
 		vector<Sequence*> container;
+		int count = 0;
+		length = 0;
+		unaligned = false;
 		
 		//read in seqs and store in vector
 		while(!in.eof()){
 			
+			if (m->control_pressed) { return container; }
+			
 			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();
+		m->mothurOut("Done."); m->mothurOutEndLine();
+		
 		return container;
 	}
 	catch(exception& e) {
-		errorOut(e, "Chimera", "readSeqs");
+		m->errorOut(e, "Chimera", "readSeqs");
 		exit(1);
 	}
 }
@@ -131,7 +151,7 @@ void Chimera::setMask(string filename) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Chimera", "setMask");
+		m->errorOut(e, "Chimera", "setMask");
 		exit(1);
 	}
 }
@@ -174,7 +194,32 @@ vector< vector<float> > Chimera::readQuantiles() {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Chimera", "readQuantiles");
+		m->errorOut(e, "Chimera", "readQuantiles");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+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) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
+		
+		temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+		
+		return temp;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Chimera", "getSequence");
 		exit(1);
 	}
 }