X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=af0cba814baece3ae9ce4abae02b3fa7370769cf;hb=36cea83f926066127bf856e7eae1a70ce7e796d0;hp=48287af367092715ab999b9ffabf02229c68cacc;hpb=fe5bbb79f9434df947347881c47b430112f4253e;p=mothur.git diff --git a/sequence.hpp b/sequence.hpp index 48287af..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); @@ -44,9 +46,12 @@ public: 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(); @@ -57,9 +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;