X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=0fdf6fce6647269d476945031255bb585e78ba83;hb=01b7dae5525a480d31a1de5bc273692726da8570;hp=b533f2864eb44e9091f1eacaaeab35fabbf00e01;hpb=dfae916a398508554d35c6b3c8002b69becb53be;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index b533f28..0fdf6fc 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -40,6 +40,9 @@ struct Header {
 	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() { } 
@@ -60,29 +63,44 @@ class SffInfoCommand : public Command {
 	
 public:
 	SffInfoCommand(string);
+	SffInfoCommand();
 	~SffInfoCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
 private:
-	string sffFilename, outputDir, accnosName;
+	string sffFilename, sfftxtFilename, outputDir, accnosName;
 	vector<string> filenames, outputNames, accnosFileNames;
 	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+	int mycount;
 	set<string> seqNames;
+	map<string, vector<string> > outputTypes;
 	
+	//extract sff file functions
 	int extractSffInfo(string, string);
 	int readCommonHeader(ifstream&, CommonHeader&);
 	int readHeader(ifstream&, Header&);
 	int readSeqData(ifstream&, seqRead&, int, int);
+	int decodeName(string&, string&, string&, string);
 	
 	int printCommonHeader(ofstream&, CommonHeader&); 
 	int printHeader(ofstream&, Header&);
-	int printSffTxtSeqData(ofstream&, seqRead&);
+	int printSffTxtSeqData(ofstream&, seqRead&, Header&);
 	int printFlowSeqData(ofstream&, seqRead&, Header&);
 	int printFastaSeqData(ofstream&, seqRead&, Header&);
 	int printQualSeqData(ofstream&, seqRead&, Header&);
 	int readAccnosFile(string);
-		
+	int parseSffTxt();
+	
+	//parsesfftxt file functions
+	int parseHeaderLineToInt(ifstream&);
+	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+	vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+	string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/