X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=ad3a4b40c238c4260d36f7afea027b903539c8a0;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=48287af367092715ab999b9ffabf02229c68cacc;hpb=fe5bbb79f9434df947347881c47b430112f4253e;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 48287af..ad3a4b4 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -24,8 +27,8 @@ public:
 	Sequence();
 	Sequence(string, string);
 	Sequence(ifstream&);
+    Sequence(ifstream&, string&, bool);
 	Sequence(istringstream&);
-	
 	//these constructors just set the unaligned string to save space
 	Sequence(string, string, string);  
 	Sequence(ifstream&, string);
@@ -44,9 +47,15 @@ public:
 	string getAligned();
 	string getPairwise();
 	string getUnaligned();
+	string getInlineSeq();
+    int getNumNs();
 	int getNumBases();
 	int getStartPos();
 	int getEndPos();
+	void padToPos(int);
+	void padFromPos(int);
+    int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
+    int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
 	int getAlignLength();
 	int getAmbigBases();
 	void removeAmbigBases();
@@ -57,10 +66,12 @@ 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 getSequenceName(ifstream&);
+    string getSequenceName(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;