X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filters.h;h=b00cb35afb66aff2fbe2a132ccf4491b17b8cd35;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=94f8d33c0329793f3e1c39c0ea0c467f53493357;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/filters.h b/filters.h
index 94f8d33..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;		}
@@ -46,6 +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() {
 
@@ -69,11 +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) {
@@ -94,6 +104,7 @@ protected:
 	int alignmentLength, numSeqs;
 	float soft;
 	char trump;
+	MothurOut* m;
 
 };