X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=312e49dcce47e7373b782a110030b46a9617be0a;hb=14cddf859d97118481161bf3e85a647976020758;hp=6a50cb0b8aa31e4a3a3b6c9c97e77416f53eeeb1;hpb=3094cb29c613d9687e861e1d0cf9104b7141d24e;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 6a50cb0..312e49d 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -27,10 +27,8 @@ public:
 	Sequence();
 	Sequence(string, string);
 	Sequence(ifstream&);
+    Sequence(ifstream&, string&, bool);
 	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);
@@ -55,6 +53,8 @@ public:
 	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();
@@ -69,6 +69,8 @@ private:
 	string getCommentString(ifstream&);
 	string getSequenceString(istringstream&, int&);
 	string getCommentString(istringstream&);
+    string getSequenceName(ifstream&);
+    string getSequenceName(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;