1.22.0

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index dd8fa4c7ecf647f4cc3ab9b8657cb7c3f019d1ac..1b6fc5bc427f48e68171f47654b18363afc21e9e 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -23,10 +23,10 @@
 //**********************************************************************************************************************
 vector<string> HeatMapSimCommand::setParameters(){     
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);    
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+               CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);        
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);              
+               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);          
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
@@ -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                       
@@ -222,12 +224,17 @@ 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 = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(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();
@@ -318,12 +325,12 @@ int HeatMapSimCommand::runCommandShared() {
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->clearGroups(); return 0; }
                
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0; }
 
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
        
@@ -363,7 +370,7 @@ int HeatMapSimCommand::runCommandShared() {
                }
                
                        
-               if (m->control_pressed) {  delete input;  m->Groups.clear();  return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups();  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -378,7 +385,7 @@ int HeatMapSimCommand::runCommandShared() {
                        }
                }
                
-               if (m->control_pressed) {  delete input;  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
                
                //run last label if you need to
                if (needToRun == true)  {
@@ -392,10 +399,10 @@ int HeatMapSimCommand::runCommandShared() {
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               if (m->control_pressed) {  delete input;  m->Groups.clear(); return 0; }
+               if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
                        
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                        
                delete input;