X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=4e72a960a7bb07d4e94df795bea462519f6d777a;hb=3cd964b03f04bc569c4a7d0b99be9908c54c1d44;hp=7cf357e07499ad5797dec8bbc1e647c163993aa8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 7cf357e..4e72a96 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -17,7 +17,7 @@
 struct CommonHeader {
 	unsigned int magicNumber;
 	string version;
-	unsigned long int indexOffset;
+	unsigned long long indexOffset;
 	unsigned int indexLength;
 	unsigned int numReads;
 	unsigned short headerLength;
@@ -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() { } 
@@ -61,25 +64,32 @@ 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();
+	~SffInfoCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "sffinfo";					}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+	string getDescription()		{ return "extract sequences reads from a .sff file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 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&);
@@ -88,7 +98,14 @@ private:
 	int printFastaSeqData(ofstream&, seqRead&, Header&);
 	int printQualSeqData(ofstream&, seqRead&, Header&);
 	int readAccnosFile(string);
-		
+	int parseSffTxt();
+	bool sanityCheck(Header&, seqRead&);
+    
+	//parsesfftxt file functions
+	int parseHeaderLineToInt(ifstream&);
+	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+	vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+	string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/