added blastlocation to chimera.slayer and fixed issue with clearcut getting current...

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 0d3bc33e2e406e1a811598fee620a92f3cedc3e2..e791f0c65c88e55b8eaf7a022c3d6be454633f69 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -92,6 +92,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -157,21 +158,22 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  format = "phylip";      inputfile = phylipfile; if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
+                       else {  format = "phylip";      inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  format = "column";      inputfile = columnfile; if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+                       else {  format = "column";      inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; } 
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "shared";      inputfile = sharedfile;  if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+                       else {  format = "shared";      inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        
                        //error checking on files                       
@@ -222,6 +224,11 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                if (calc == "default")  {  calc = "jest-thetayc";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
                                
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
@@ -287,7 +294,7 @@ int HeatMapSimCommand::execute(){
                
                delete heatmap;
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } outputTypes.clear(); return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();