added sharedRabundFloatVector class to represent the relabund file. modified read...

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 1ca894fb391eae4e604736d0cb7102986ed3569d..c6345328e6d5ac5b0e577d03a797d35448446227 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -44,8 +44,8 @@ HeatMapCommand::HeatMapCommand(string option) {
                        }
                        
                        //make sure the user has already run the read.otu command
-                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
-                                m->mothurOut("You must read a list, rabund, sabund, or a list and a group, or a shared before you can use the heatmap.bin command."); m->mothurOutEndLine(); abort = true; 
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
+                                m->mothurOut("You must read a list, rabund, sabund, or a list and a group, shared, or relabund file before you can use the heatmap.bin command."); m->mothurOutEndLine(); abort = true; 
                        }
 
                        //check for optional parameter and set defaults
@@ -152,13 +152,17 @@ int HeatMapCommand::execute(){
                        //you are using just a list file and have only one group
                        rabund = globaldata->rabund;
                        lastLabel = rabund->getLabel();
+               }else if (format == "relabund") {
+                       //you have groups
+                       lookupFloat = input->getSharedRAbundFloatVectors();
+                       lastLabel = lookupFloat[0]->getLabel();
                }
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;
 
-               if ((format != "list") && (format != "rabund") && (format != "sabund")) {       
+               if (format == "sharedfile") {   
                
                        //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))) {
@@ -235,7 +239,7 @@ int HeatMapCommand::execute(){
                        //reset groups parameter
                        globaldata->Groups.clear();  
                        
-               }else{
+               }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
        
                        while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                if (m->control_pressed) {   
@@ -304,6 +308,83 @@ int HeatMapCommand::execute(){
                                delete rabund; globaldata->rabund = NULL;
                        }
                
+               }else {
+               
+                       //as long as you are not at the end of the file or done wih the lines you want
+                       while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                               if (m->control_pressed) {
+                                       for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                                       globaldata->Groups.clear(); 
+                                       delete read; delete heatmap; return 0;
+                               }
+               
+                               if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){                     
+       
+                                       m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+                                       outputNames.push_back(heatmap->getPic(lookupFloat));
+                                       
+                                       processedLabels.insert(lookupFloat[0]->getLabel());
+                                       userLabels.erase(lookupFloat[0]->getLabel());
+                               }
+                               
+                               if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       string saveLabel = lookupFloat[0]->getLabel();
+                               
+                                       for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  
+                                       lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+                                       m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+                                       
+                                       outputNames.push_back(heatmap->getPic(lookupFloat));
+                                       
+                                       processedLabels.insert(lookupFloat[0]->getLabel());
+                                       userLabels.erase(lookupFloat[0]->getLabel());
+                                       
+                                       //restore real lastlabel to save below
+                                       lookupFloat[0]->setLabel(saveLabel);
+                               }
+                               
+                               lastLabel = lookupFloat[0]->getLabel();
+                               //prevent memory leak
+                               for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
+                                                       
+                               //get next line to process
+                               lookupFloat = input->getSharedRAbundFloatVectors();                             
+                       }
+                       
+                       
+                       if (m->control_pressed) {
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                               globaldata->Groups.clear(); 
+                               delete read; delete heatmap; return 0;
+                       }
+
+                       //output error messages about any remaining user labels
+                       set<string>::iterator it;
+                       bool needToRun = false;
+                       for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                               m->mothurOut("Your file does not include the label " + *it); 
+                               if (processedLabels.count(lastLabel) != 1) {
+                                       m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+                                       needToRun = true;
+                               }else {
+                                       m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+                               }
+                       }
+               
+                       //run last label if you need to
+                       if (needToRun == true)  {
+                               for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }  
+                               lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+                               
+                               m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+                               outputNames.push_back(heatmap->getPic(lookupFloat));
+                               for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
+                       }
+               
+                       //reset groups parameter
+                       globaldata->Groups.clear();  
+
                }
                
                globaldata->rabund = NULL;
@@ -318,7 +399,7 @@ int HeatMapCommand::execute(){
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                m->mothurOutEndLine();
-               
+       
                delete read;
                delete heatmap;