working of get.mimarkspackage and sra command

[mothur.git] / sracommand.h

diff --git a/sracommand.h b/sracommand.h
index 5cc371447ecb0b47605c642eb523afe7d2d7bac6..c53a17ddc038361c1dab613723eeef17b37e736b 100644 (file)
--- a/sracommand.h
+++ b/sracommand.h
@@ -36,27 +36,28 @@ public:
 private:
     bool abort, isSFF, pairedOligos;
     int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
-    string sfffile, fastqfile, outputDir, groupfile, file, oligosfile, contactfile, inputfile;
-    string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType;
-    string submissionName, lastName, firstName, email, centerName, centerType, description;
-    vector<string> outputNames, Groups, revPrimer;
+    string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;
+    string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType, dataType;
+    string submissionName, lastName, firstName, email, centerName, centerType, description, website, orientation, packageType;
+    string projectName, grantId, grantTitle, grantAgency, projectTitle;
+    vector<string> outputNames, Groups;
     vector<string> primerNameVector;
     vector<string> barcodeNameVector;
     map<string, string> Group2Barcode;
-    map<int, oligosPair> pairedBarcodes;
-    map<int, oligosPair> pairedPrimers;
-       map<string, int> barcodes;
-       map<string, int> primers;
-    vector<string>  linker;
-    vector<string>  spacer;
+    map<string, string> Group2Primer;
+    map<string, string> Group2Organism;
+    map<string, map<string, string> > mimarks;  //group -> <field -> valueForGroup> ex.  F003D001 -> <lat_lon -> 42.282026 -83.733850>
 
     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> >&);