X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=sffinfocommand.h;h=b304e485c1270aba1b4b761dc9e7b66af54dcfcf;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=1909e2d43e6d83b3d48ef06922b2d369a0e104d5;hpb=3e8b80da722e11c72bce957e2f42a6e884dd02b6;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 1909e2d..b304e48 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -12,51 +12,9 @@
 
 #include "command.hpp"
 #include "groupmap.h"
+#include "oligos.h"
+#include "trimoligos.h"
 
-/**********************************************************/
-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() { } 
-};
 /**********************************************************/
 
 class SffInfoCommand : public Command {
@@ -81,22 +39,20 @@ public:
 private:
 	string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile, groupfile;
 	vector<string> filenames, outputNames, accnosFileNames, oligosFileNames, groupFileNames;
-	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos, hasGroup;
-	int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
+	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos, hasGroup, reorient, pairedOligos;
+	int mycount, split, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
 	set<string> seqNames;
-    map<string, int> barcodes;
-    map<string, int> primers;
     GroupMap* groupMap;
-    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
     vector<vector<int> > numSplitReads;
     vector<vector<string> > filehandles;
     vector<vector<string> > filehandlesHeaders;
+    Oligos* oligosObject;
     
 	//extract sff file functions
 	int extractSffInfo(string, string, string);
 	int readCommonHeader(ifstream&, CommonHeader&);
 	int readHeader(ifstream&, Header&);
-	bool readSeqData(ifstream&, seqRead&, int, Header&);
+	bool readSeqData(ifstream&, seqRead&, int, Header&, TrimOligos*&, TrimOligos*&);
 	int decodeName(string&, string&, string&, string);
     bool readOligos(string oligosFile);
     bool readGroup(string oligosFile);
@@ -111,7 +67,7 @@ private:
 	int parseSffTxt();
 	bool sanityCheck(Header&, seqRead&);
     int adjustCommonHeader(CommonHeader);
-    int findGroup(Header header, seqRead read, int& barcode, int& primer);
+    int findGroup(Header header, seqRead read, int& barcode, int& primer, TrimOligos*&, TrimOligos*&);
     int findGroup(Header header, seqRead read, int& barcode, int& primer, string);
     string reverseOligo(string oligo);