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

[mothur.git] / oligos.h

diff --git a/oligos.h b/oligos.h
new file mode 100644 (file)
index 0000000..d5bc303
--- /dev/null
+++ b/oligos.h
@@ -0,0 +1,92 @@
+//
+//  oligos.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 4/4/14.
+//  Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_oligos_h
+#define Mothur_oligos_h
+
+
+#include "mothurout.h"
+
+
+/**************************************************************************************************/
+
+class Oligos {
+    
+public:
+       Oligos(string);
+       Oligos();
+    ~Oligos() {}
+    
+    int read(string);
+    int read(string, bool); //read without reversing the paired barcodes, for make.contigs.
+    bool hasPairedPrimers() { return hasPPrimers; }
+    bool hasPairedBarcodes() { return hasPBarcodes; }
+    
+    //for processing with trimOligos class
+    map<int, oligosPair> getPairedPrimers()                 { return pairedPrimers;     }
+    map<int, oligosPair> getPairedBarcodes()                { return pairedBarcodes;    }
+    map<string, int> getPrimers()                           { return primers;           }
+    map<string, int> getBarcodes()                          { return barcodes;          }
+    
+    map<int, oligosPair> getReorientedPairedPrimers();
+    map<int, oligosPair> getReorientedPairedBarcodes();
+    map<string, int> getReorientedPrimers();
+    map<string, int> getReorientedBarcodes();
+    
+    
+    vector<string> getLinkers()                             { return linker;            }
+    vector<string> getSpacers()                             { return spacer;            }
+    vector<string> getReversePrimers()                      { return revPrimer;         }
+    vector<string> getPrimerNames()                         { return primerNameVector;  }
+    vector<string> getBarcodeNames()                        { return barcodeNameVector; }
+    vector<string> getGroupNames()                          { return Groups;            }
+        
+    
+    //for printing and other formatting uses
+    vector<string> getBarcodes(string); //get barcodes for a group. For paired barcodes will return forward.reverse
+    vector<string> getPrimers(string); //get primers for a group. For paired primers will return forward.reverse
+    string getBarcodeName(int);
+    string getPrimerName(int);
+    string getGroupName(int, int);
+    
+               
+private:
+    
+    set<string> uniqueNames; 
+    vector<string> Groups;
+       vector<string> revPrimer;
+    map<string, vector<string> > Group2Barcode;
+    map<string, vector<string> > Group2Primer;
+    map<int, oligosPair> pairedBarcodes;
+    map<int, oligosPair> pairedPrimers;
+    map<string, int> primers;
+       map<string, int> barcodes;
+    vector<string>  linker;
+    vector<string>  spacer;
+       vector<string> primerNameVector;
+       vector<string> barcodeNameVector;
+    bool hasPPrimers, hasPBarcodes, pairedOligos, reversePairs;
+    string oligosfile;
+    int numBarcodes, numFPrimers;
+    MothurOut* m;
+    
+    int indexPrimer;
+    int indexBarcode;
+    int indexPairedPrimer;
+    int indexPairedBarcode;
+    set<string> uniquePrimers;
+    set<string> uniqueBarcodes;
+    
+    int readOligos();
+    string reverseOligo(string);
+};
+
+/**************************************************************************************************/
+
+
+#endif