added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 79e8be96974141da315d1038a51096695212ad5c..3926e25f3c2ebb484b357464d1514dfc957c4000 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -34,7 +34,7 @@ public:
        void help() { m->mothurOut(getHelpString()); }          
 private:
        bool abort;
-       string fastafile, outputDir, namefile;
+       string fastafile, outputDir, namefile, countfile;
        int processors;
        vector<string> outputNames;
        map<string, int> nameMap;
@@ -74,18 +74,18 @@ struct seqSumData {
        unsigned long long end;
        int count;
        MothurOut* m;
-       string namefile;
+       bool hasNameMap;
        map<string, int> nameMap;
        
        
        seqSumData(){}
-       seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
+       seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, bool na, map<string, int> nam) {
                filename = f;
                sumFile = sf;
                m = mout;
                start = st;
                end = en;
-               namefile = na;
+               hasNameMap = na;
                nameMap = nam;
                count = 0;
        }
@@ -123,11 +123,11 @@ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
                        if (current.getName() != "") {
                                
                                int num = 1;
-                               if (pDataArray->namefile != "") {
+                               if (pDataArray->hasNameMap){
                                        //make sure this sequence is in the namefile, else error 
                                        map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
                                        
-                                       if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+                                       if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your name or count file, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
                                        else { num = it->second; }
                                }