X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filters.h;h=b00cb35afb66aff2fbe2a132ccf4491b17b8cd35;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=13607e78045a35a9a3ac00c675ba6c0b46995f42;hpb=94ba64671398f3c9e591df90536833123de0fd34;p=mothur.git

diff --git a/filters.h b/filters.h
index 13607e7..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;		}
@@ -77,11 +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) {
@@ -102,6 +104,7 @@ protected:
 	int alignmentLength, numSeqs;
 	float soft;
 	char trump;
+	MothurOut* m;
 
 };