X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=67c8ab3feaf7f7a82d611e2ed4b60c44fb86e86e;hb=f3e0de2c55da5c524abb3b404f77cb84aa1ddd34;hp=32f4778a7c1ee19db25eeb4e1eafaf74fabcd617;hpb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 32f4778..67c8ab3 100644
--- a/mothur.h
+++ b/mothur.h
@@ -120,6 +120,52 @@ struct diffPair {
 		reverseProb = rp;
 	}
 };
+
+/**********************************************************/
+struct CommonHeader {
+	unsigned int magicNumber;
+	string version;
+	unsigned long long indexOffset;
+	unsigned int indexLength;
+	unsigned int numReads;
+	unsigned short headerLength;
+	unsigned short keyLength;
+	unsigned short numFlowsPerRead;
+	int flogramFormatCode;
+	string flowChars; //length depends on number flow reads
+	string keySequence; //length depends on key length
+	
+	CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
+	~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+	unsigned short headerLength;
+	unsigned short nameLength;
+	unsigned int numBases;
+	unsigned short clipQualLeft;
+	unsigned short clipQualRight;
+	unsigned short clipAdapterLeft;
+	unsigned short clipAdapterRight;
+	string name; //length depends on nameLength
+	string timestamp;
+	string region;
+	string xy;
+	
+	Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+	~Header() { }
+};
+/**********************************************************/
+struct seqRead {
+	vector<unsigned short> flowgram;
+	vector<unsigned int> flowIndex;
+	string bases;
+	vector<unsigned int> qualScores;
+	
+	seqRead() { }
+	~seqRead() { }
+};
+
 /***********************************************************************/
 struct PDistCell{
 	ull index;