X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=d98edbd3e04f0213a24ed51471d09aab1b74d46a;hb=3b137af694d322b7162e97275c070c41b42597a3;hp=6e9d87c30d0898e0b6027bb5d3e4a22bfaa388bd;hpb=df1ea5f2151b9334c471bf4310f78f51bba098be;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 6e9d87c..d98edbd 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -12,22 +12,23 @@
 
 #include "command.hpp"
 
-#define SFF_MAGIC   0x2e736666 /* ".sff" */
-#define SFF_VERSION "\0\0\0\1"
 
 /**********************************************************/
 struct CommonHeader {
 	unsigned int magicNumber;
-	char* version;
+	string version;
 	unsigned long int indexOffset;
 	unsigned int indexLength;
 	unsigned int numReads;
 	unsigned short headerLength;
 	unsigned short keyLength;
 	unsigned short numFlowsPerRead;
-	char flogramFormatCode;
-	char* flowChars; //length depends on number flow reads
-	char* keySequence; //length depends on key length
+	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 {
@@ -38,14 +39,23 @@ struct Header {
 	unsigned short clipQualRight;
 	unsigned short clipAdapterLeft;
 	unsigned short clipAdapterRight;
-	char* name; //length depends on nameLength
+	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;
-	char* bases;
+	string bases;
 	vector<unsigned int> qualScores;
+	
+	seqRead() { } 
+	~seqRead() { } 
 };
 /**********************************************************/
 
@@ -53,24 +63,43 @@ 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;
-	vector<string> filenames, outputNames;
-	bool abort;
+	string sffFilename, sfftxtFilename, outputDir, accnosName;
+	vector<string> filenames, outputNames, accnosFileNames;
+	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+	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 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&, Header&);
+	int printFlowSeqData(ofstream&, seqRead&, Header&);
+	int printFastaSeqData(ofstream&, seqRead&, Header&);
+	int printQualSeqData(ofstream&, seqRead&, Header&);
+	int readAccnosFile(string);
+	int parseSffTxt();
 	
-	int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
-	int printHeader(ofstream&, Header*, bool);
-	int printSeqData(ofstream&, seqRead*, bool);
-		
+	//parsesfftxt file functions
+	int parseHeaderLineToInt(ifstream&);
+	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+	vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+	string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/