added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index d37d6f43b50b3b567d267ab82dd83db459f126df..79e8be96974141da315d1038a51096695212ad5c 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -25,6 +25,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "summary.seqs";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
        string getDescription()         { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
@@ -62,11 +63,11 @@ private:
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct seqSumData {
-       vector<int>* startPosition;
-       vector<int>* endPosition;
-       vector<int>* seqLength; 
-       vector<int>* ambigBases; 
-       vector<int>* longHomoPolymer; 
+       vector<int> startPosition;
+       vector<int> endPosition;
+       vector<int> seqLength; 
+       vector<int> ambigBases; 
+       vector<int> longHomoPolymer; 
        string filename; 
        string sumFile; 
        unsigned long long start;
@@ -78,12 +79,7 @@ struct seqSumData {
        
        
        seqSumData(){}
-       seqSumData(vector<int>* s, vector<int>* e, vector<int>* l, vector<int>* a, vector<int>* h, string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
-               startPosition = s;
-               endPosition = e;
-               seqLength = l;
-               ambigBases = a;
-               longHomoPolymer = h;
+       seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
                filename = f;
                sumFile = sf;
                m = mout;
@@ -96,7 +92,7 @@ struct seqSumData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){ 
        seqSumData* pDataArray;
@@ -137,11 +133,11 @@ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
                                
                                //for each sequence this sequence represents
                                for (int i = 0; i < num; i++) {
-                                       pDataArray->startPosition->push_back(current.getStartPos());
-                                       pDataArray->endPosition->push_back(current.getEndPos());
-                                       pDataArray->seqLength->push_back(current.getNumBases());
-                                       pDataArray->ambigBases->push_back(current.getAmbigBases());
-                                       pDataArray->longHomoPolymer->push_back(current.getLongHomoPolymer());
+                                       pDataArray->startPosition.push_back(current.getStartPos());
+                                       pDataArray->endPosition.push_back(current.getEndPos());
+                                       pDataArray->seqLength.push_back(current.getNumBases());
+                                       pDataArray->ambigBases.push_back(current.getAmbigBases());
+                                       pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
                                }
                                
                                outSummary << current.getName() << '\t';