small mods to sensspec command

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 82922ededbff38fd76909d1694742c6adac7666b..55d90bdd2ce1debc857ddb33a47969e0c3f66933 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -19,7 +19,7 @@ vector<string> SensSpecCommand::setParameters(){
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -256,7 +256,9 @@ int SensSpecCommand::processPhylip(){
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
+                       if(m->control_pressed){
+                for (int i = 0; i < outputNames.size(); i++){  m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
+            }
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                
@@ -324,7 +326,9 @@ int SensSpecCommand::processPhylip(){
                exit(1);
        }
 }
+
 //***************************************************************************************************************
+
 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
        try {
                //for each otu
@@ -387,7 +391,7 @@ int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
                return numSeqs;
        }
        catch(exception& e) {
-               m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+               m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
                exit(1);
        }
 }
@@ -401,7 +405,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                ifstream phylipFile;
                m->openInputFile(distFile, phylipFile);
                phylipFile >> pNumSeqs;
-               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
+               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
                
                string seqName;
                double distance;
@@ -426,7 +430,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                
                m->mothurOut(label); m->mothurOutEndLine();
                
-               for(int i=0;i<lNumSeqs;i++){
+               for(int i=0;i<pNumSeqs;i++){
                        
                        if (m->control_pressed) { return 0; }