bugs fixes while testing for 1.5 release

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 0ee34f9432deedc6cfe9a914efc84f4b3cf8c91f..e21b14dce5afaf3744b1338416b1af3630a6830c 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -39,8 +39,8 @@ HeatMapCommand::HeatMapCommand(string option){
                        }
                        
                        //make sure the user has already run the read.otu command
-                       if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
-                                mothurOut("You must read a list, or a list and a group, or a shared before you can use the heatmap.bin command."); mothurOutEndLine(); abort = true; 
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
+                                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."); mothurOutEndLine(); abort = true; 
                        }
 
                        //check for optional parameter and set defaults
@@ -132,7 +132,7 @@ int HeatMapCommand::execute(){
        try {
        
                if (abort == true) { return 0; }
-       
+
                int count = 1;  
                string lastLabel;
        
@@ -144,14 +144,16 @@ int HeatMapCommand::execute(){
                        input = globaldata->ginput;
                        lookup = input->getSharedRAbundVectors();
                        lastLabel = lookup[0]->getLabel();
-               }else if (format == "list") {
+       
+               }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
                        //you are using just a list file and have only one group
                        read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
-                       
+               
                        rabund = globaldata->rabund;
                        lastLabel = rabund->getLabel();
-                       input = globaldata->ginput;             
+                       input = globaldata->ginput;     
+
                }
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -159,7 +161,7 @@ int HeatMapCommand::execute(){
                set<string> userLabels = labels;
                set<int> userLines = lines;
 
-               if (format != "list") { 
+               if ((format != "list") && (format != "rabund") && (format != "sabund")) {       
                
                        //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) || (userLines.size() != 0))) {
@@ -223,7 +225,7 @@ int HeatMapCommand::execute(){
                        globaldata->Groups.clear();  
                        
                }else{
-               
+       
                        while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 
                                if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){                  
@@ -282,6 +284,7 @@ int HeatMapCommand::execute(){
                
                }
                
+               globaldata->rabund = NULL;
                delete input; globaldata->ginput = NULL;
                return 0;
        }