fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 9d8e7960f5c2e949f021602aaf1aa36e7d3e82e0..0f606ffb59ac884b46ac97d861aa3542786d1793 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,15 +17,28 @@ class GetSeqsCommand : public Command {
        public:
        
                GetSeqsCommand(string);
-               ~GetSeqsCommand(){};
-               int execute();
-               void help();    
-               
+               GetSeqsCommand();
+               ~GetSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
-               bool abort;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
+    
+        //for debug
+        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
                
                int readFasta();
                int readName();
@@ -34,6 +47,11 @@ class GetSeqsCommand : public Command {
                int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };