added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index ea93b5a1c4e0427cc43157a5d77f995bb3f2308b..4561d28614c62686c42e29a9747b84d853537fd0 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -18,20 +18,24 @@ class GetSeqsCommand : public Command {
        
                GetSeqsCommand(string);
                GetSeqsCommand();
-               ~GetSeqsCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+               ~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;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
-               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();
@@ -40,6 +44,8 @@ class GetSeqsCommand : public Command {
                int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
                
 };