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

[mothur.git] / sracommand.h

diff --git a/sracommand.h b/sracommand.h
index 3f7f1560530f8a8903db79b7a6f98b474ce50102..dde656132ad57144f694dba1b043e66aed68ea2f 100644 (file)
--- a/sracommand.h
+++ b/sracommand.h
@@ -10,7 +10,8 @@
 #define Mothur_sracommand_h
 
 #include "command.hpp"
-
+#include "trimoligos.h"
+#include "oligos.h"
 
 /**************************************************************************************************/
 
@@ -34,14 +35,35 @@ public:
     void help() { m->mothurOut(getHelpString()); }
     
 private:
-    bool abort, isSFF;
+    bool abort, isSFF, pairedOligos;
     int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
-    string sfffile, fastqfile, platform, outputDir, groupfile, file, oligosfile;
-    vector<string> outputNames;
-    
-    int readFile(vector<string>&);
-    int parseSffFile(vector<string>&);
-    int parseFastqFile(vector<string>&);
+    string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;
+    string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType, dataType, checkorient;
+    string submissionName, lastName, firstName, email, centerName, centerType, description, website, orientation, packageType;
+    string projectName, grantId, grantTitle, grantAgency, projectTitle, inputDir;
+    vector<string> outputNames, Groups;
+    map<string, vector<string> > Group2Barcode;
+    map<string, vector<string> > Group2Primer;
+    map<string, string> Group2Organism;
+    map<string, map<string, string> > mimarks;  //group -> <field -> valueForGroup> ex.  F003D001 -> <lat_lon -> 42.282026 -83.733850>
+    set<string> uniqueNames;
+
+    bool checkCasesInstrumentModels(string&);
+    bool checkCasesPlatforms(string&);
+    bool checkCasesLibStrategy(string&);
+    bool checkCasesLibSource(string&);
+    bool checkCasesLibSelection(string&);
+    bool checkCasesDataType(string&);
+    bool sanityCheckMiMarksGroups();
+    int readFile(map<string, vector<string> >&);
+    int readContactFile();
+    int readMIMarksFile();
+    int readOligos();
+    int parseSffFile(map<string, vector<string> >&);
+    int parseFastqFile(map<string, vector<string> >&);
+    int checkGroups(map<string, vector<string> >&);
+    int mapGroupToFile(map<string, vector<string> >&, vector<string>);
+    string reverseOligo(string oligo);
     
 };