added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 5ec6e72239d0772548ce10f584ebccb435230d25..b304e485c1270aba1b4b761dc9e7b66af54dcfcf 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -11,52 +11,10 @@
  */
 
 #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 {
@@ -79,24 +37,25 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
-       vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
-       bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
-       int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
+       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, 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;
-    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+    GroupMap* groupMap;
     vector<vector<int> > numSplitReads;
-    vector<vector<string> > filehandles, filehandlesHeaders;
+    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&);
-       int readSeqData(ifstream&, seqRead&, int, Header&);
+       int readHeader(ifstream&, Header&);
+       bool readSeqData(ifstream&, seqRead&, int, Header&, TrimOligos*&, TrimOligos*&);
        int decodeName(string&, string&, string&, string);
     bool readOligos(string oligosFile);
+    bool readGroup(string oligosFile);
        
        int printCommonHeader(ofstream&, CommonHeader&); 
        int printHeader(ofstream&, Header&);
@@ -108,7 +67,8 @@ 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);
     
        //parsesfftxt file functions