X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=af0cba814baece3ae9ce4abae02b3fa7370769cf;hb=d9c3ceb4147b827719046c7d742df14288a07722;hp=c634f78b6522e43742800b0a4541d910eb7d6be3;hpb=c27e902ede71ea4d20af65752ef04459c101611b;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index c634f78..af0cba8 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -25,7 +28,6 @@ public:
 	Sequence(string, string);
 	Sequence(ifstream&);
 	Sequence(istringstream&);
-	
 	//these constructors just set the unaligned string to save space
 	Sequence(string, string, string);  
 	Sequence(ifstream&, string);
@@ -37,15 +39,19 @@ public:
 	void setAligned(string);
 	void setLength();
 	void reverseComplement();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
 	string getAligned();
 	string getPairwise();
 	string getUnaligned();
+	string getInlineSeq();
 	int getNumBases();
 	int getStartPos();
 	int getEndPos();
+	void padToPos(int);
+	void padFromPos(int);
 	int getAlignLength();
 	int getAmbigBases();
 	void removeAmbigBases();
@@ -56,9 +62,9 @@ public:
 private:
 	MothurOut* m;
 	void initialize();
-	string getSequenceString(ifstream&);
+	string getSequenceString(ifstream&, int&);
 	string getCommentString(ifstream&);
-	string getSequenceString(istringstream&);
+	string getSequenceString(istringstream&, int&);
 	string getCommentString(istringstream&);
 	string name;
 	string unaligned;