trim.seqs linker and spacer mods

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index c634f78b6522e43742800b0a4541d910eb7d6be3..af0cba814baece3ae9ce4abae02b3fa7370769cf 100644 (file)
--- 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;