1.22.0

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 629eca965b3ca1c084c3d837b6a2870ea8fa43ec..f15581f271382f671505dc708a9ffa2545e32eeb 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -532,6 +532,11 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
                        if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 
+                       //until we resolve the issue 10-18-11
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+                       processors=1;
+#endif
                }
        }
        catch(exception& e) {
@@ -561,7 +566,6 @@ int ChimeraSlayerCommand::execute(){
                        map<string, map<string, int> > fileToPriority; 
                        map<string, map<string, int> >::iterator itFile;
                        map<string, string> fileGroup;
-                       map<string, int> priority;
                        fileToPriority[fastaFileNames[s]] = priority; //default
                        fileGroup[fastaFileNames[s]] = "noGroup";
                        SequenceParser* parser = NULL;
@@ -582,11 +586,15 @@ int ChimeraSlayerCommand::execute(){
                                priority = sortFastaFile(fastaFileNames[s], nameFile);
                                m->mothurOut("Done."); m->mothurOutEndLine();
                                
+                               fileToPriority.clear();
+                               fileGroup.clear();
                                fileToPriority[fastaFileNames[s]] = priority;
+                               fileGroup[fastaFileNames[s]] = "noGroup";
                                if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        }  return 0;    }
                        }else if ((templatefile == "self") && (groupFile != "")) {
                                fileGroup.clear();
                                fileToPriority.clear();
+                               if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
                                string nameFile = "";
                                if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
                                        nameFile = nameFileNames[s];
@@ -978,7 +986,7 @@ int ChimeraSlayerCommand::deconvoluteResults(SequenceParser* parser, string outp
                                        
                                        if (print) {
                                                out << name << '\t';
-                                               cout << name<< endl;
+                                               
                                                namesInFile.insert(name);
 
                                                //output parent1's name
@@ -1406,7 +1414,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                        pDataArray.push_back(tempslayer);
                        processIDS.push_back(i);
                        
-                       //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+                       //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
                        hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
                }