fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 38e344dfea67fdcfe89ce80a0476300d8ff50e3a..de35075e98ee938e67f1880cada0ebfb1e0ba26a 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -30,6 +30,7 @@ vector<string> HeatMapSimCommand::setParameters(){
                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);
+               CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -47,11 +48,12 @@ string HeatMapSimCommand::getHelpString(){
        try {
                string helpString = "";
                ValidCalculators validCalculator;
-               helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label.  shared or phylip or column and name are required unless valid current files exist.\n";
+               helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label.  shared or phylip or column and name are required unless valid current files exist.\n";
                helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
                helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
                helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
                helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
+               helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
                helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
                helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
                helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
@@ -113,9 +115,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        outputTypes["svg"] = tempOutNames;
                        
                        format = "";
-                       //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
-                       
+                               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -208,6 +208,10 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                }
                        }
                        
+                       
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
+
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                                                        
@@ -234,9 +238,11 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
+                       string temp = validParameter.validFile(parameters, "fontsize", false);                          if (temp == "not found") { temp = "24"; }
+                       m->mothurConvert(temp, fontsize);
                        
                        if (abort == false) {
                                ValidCalculators validCalculator;
@@ -286,7 +292,7 @@ int HeatMapSimCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               heatmap = new HeatMapSim(outputDir, inputfile);
+               heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
                
                if (format == "shared") {
                        runCommandShared();
@@ -294,7 +300,7 @@ 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();
@@ -325,12 +331,12 @@ 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){                  
        
@@ -370,7 +376,7 @@ 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;
@@ -385,7 +391,7 @@ 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)  {
@@ -399,10 +405,10 @@ 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;