X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filters.h;h=b00cb35afb66aff2fbe2a132ccf4491b17b8cd35;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=4c396070a911000018710a3b652f2f81439e1db7;hpb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;p=mothur.git

diff --git a/filters.h b/filters.h
index 4c39607..b00cb35 100644
--- a/filters.h
+++ b/filters.h
@@ -19,7 +19,7 @@
 class Filters {
 
 public:
-	Filters() {};
+	Filters() { m = MothurOut::getInstance(); };
 	~Filters(){};
 		
 	string getFilter()			{	return filter;		}
@@ -28,6 +28,8 @@ public:
 	void setSoft(float s)		{		soft = s;		}
 	void setTrump(float t)		{		trump = t;		}
 	void setNumSeqs(int num)	{	numSeqs = num;		}
+	vector<int> a, t, g, c, gap;
+	
 	
 	void initialize() {
 		a.assign(alignmentLength, 0);
@@ -44,6 +46,14 @@ public:
 			if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){	filter[i] = 0;	}
 		}
 	}
+
+	void mergeFilter(string newFilter){
+		for(int i=0;i<alignmentLength;i++){
+			if(newFilter[i] == '0'){
+				filter[i] = 0;
+			}
+		}
+	}
 	
 	void doVertical() {
 
@@ -67,11 +77,13 @@ public:
 
 	void doHard(string hard) {
 		ifstream fileHandle;
-		openInputFile(hard, fileHandle);
+		m->openInputFile(hard, fileHandle);
 	
 		fileHandle >> filter;
 	
 		fileHandle.close();
+        
+        if (filter.length() != alignmentLength) {  m->mothurOut("[ERROR]: Sequences are not all the same length as the filter, please correct.\n");  m->control_pressed = true; }
 	}
 
 	void getFreqs(Sequence seq) {
@@ -89,10 +101,10 @@ public:
 		
 protected:
 	string filter;
-	vector<int> a, t, g, c, gap;
 	int alignmentLength, numSeqs;
 	float soft;
 	char trump;
+	MothurOut* m;
 
 };