X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=6a50cb0b8aa31e4a3a3b6c9c97e77416f53eeeb1;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=5f84d441c20d0fd8a0ed8f9284b7a32dfc9b4214;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 5f84d44..6a50cb0 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -25,6 +28,13 @@ public:
 	Sequence(string, string);
 	Sequence(ifstream&);
 	Sequence(istringstream&);
+	Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
+									alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
+	
+	//these constructors just set the unaligned string to save space
+	Sequence(string, string, string);  
+	Sequence(ifstream&, string);
+	Sequence(istringstream&, string);
 	
 	void setName(string);
 	void setUnaligned(string);
@@ -32,17 +42,22 @@ 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();
 	int getLongHomoPolymer();
 	bool getIsAligned();
 	void printSequence(ostream&);
@@ -50,9 +65,9 @@ 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;