added list.labels command. started work on make.contigs command. fixed fastq.info...

[mothur.git] / makecontigscommand.h

diff --git a/makecontigscommand.h b/makecontigscommand.h
new file mode 100644 (file)
index 0000000..5d123d5
--- /dev/null
+++ b/makecontigscommand.h
@@ -0,0 +1,63 @@
+#ifndef Mothur_makecontigscommand_h
+#define Mothur_makecontigscommand_h
+
+//
+//  makecontigscommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 5/15/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "command.hpp"
+
+struct fastqRead {
+       vector<int> scores;
+       string name;
+       string sequence;
+       
+       fastqRead() { name = ""; sequence = ""; scores.clear(); };
+       fastqRead(string n, string s, vector<int> sc) : name(n), sequence(s), scores(sc) {};
+       ~fastqRead() {};
+};
+
+/**************************************************************************************************/
+
+class MakeContigsCommand : public Command {
+public:
+    MakeContigsCommand(string);
+    MakeContigsCommand();
+    ~MakeContigsCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "make.contigs";                        }
+    string getCommandCategory()                { return "Sequence Processing";         } 
+    //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
+    string getHelpString();    
+    string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
+    string getDescription()            { return "description"; }
+    
+    int execute(); 
+    void help() { m->mothurOut(getHelpString()); }     
+    
+private:
+    bool abort;
+    string outputDir, ffastqfile, rfastqfile, align;
+       float match, misMatch, gapOpen, gapExtend;
+       int processors, longestBase;
+    vector<string> outputNames;
+    
+    fastqRead readFastq(ifstream&);
+    vector< vector<string> > readFastqFiles();
+    bool checkReads(fastqRead&, fastqRead&);
+};
+
+/**************************************************************************************************/
+
+
+
+
+
+
+
+#endif