added modify names parameter to set.dir

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index fa3f559056161945021e10f9b1892db742a6116e..a9cfc102fb957ea775b14211db4e1f1e1118c50f 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -25,8 +25,9 @@ class ChopSeqsCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "chop.seqs";           }
                string getCommandCategory()             { return "Sequence Processing"; }
-               string getOutputFileNameTag(string, string);
+               
         string getHelpString();        
+        string getOutputPattern(string);       
                string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
                string getDescription()         { return "trim sequence length"; }
        
@@ -40,7 +41,7 @@ class ChopSeqsCommand : public Command {
             linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         };
     
-               string fastafile, outputDir, keep;
+               string fastafile, outputDir, keep, namefile, groupfile, countfile;
                bool abort, countGaps, Short;
                int numbases, processors;
                vector<string> outputNames;
@@ -59,7 +60,7 @@ struct chopData {
        string outFasta, outAccnos, keep; 
        unsigned long long start;
        unsigned long long end;
-       int numbases;
+       int numbases, count;
     bool countGaps, Short, wroteAccnos;
        MothurOut* m;
        string namefile;
@@ -107,7 +108,7 @@ static DWORD WINAPI MyChopThreadFunction(LPVOID lpParam){
 
                bool done = false;
         bool wroteAccnos = false;
-               int count = 0;
+               pDataArray->count = 0;
 
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
                                                
@@ -237,14 +238,14 @@ static DWORD WINAPI MyChopThreadFunction(LPVOID lpParam){
                                        outAcc << seq.getName() << endl;
                                        pDataArray->wroteAccnos = true;
                                }
-                count++;
+                pDataArray->count++;
                        }
             //report progress
-                       if((count) % 1000 == 0){        pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();           }
+                       if((pDataArray->count) % 1000 == 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
                        
                }
                //report progress
-               if((count) % 1000 != 0){        pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();           }
+               if((pDataArray->count) % 1000 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
         
                
                in.close();