added sorted option to get.rabund command

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 73862a85eda66077fdc51b9bbebc1dc579c8da02..b0bf81980a54d7bb6f8992b49f0af83d3169f4f8 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -24,7 +24,7 @@ GetRAbundCommand::GetRAbundCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label"};
+                       string Array[] =  {"line","label","sorted"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -42,6 +42,11 @@ GetRAbundCommand::GetRAbundCommand(string option){
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
+                       
+                       string temp;
+                       temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
+                       sorted = isTrue(temp);
+                       
                        line = validParameter.validFile(parameters, "line", false);                             
                        if (line == "not found") { line = "";  }
                        else { 
@@ -82,10 +87,11 @@ GetRAbundCommand::GetRAbundCommand(string option){
 void GetRAbundCommand::help(){
        try {
                mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
-               mothurOut("The get.rabund command parameters are line and label.  No parameters are required, and you may not use line and label at the same time.\n");
+               mothurOut("The get.rabund command parameters are line, label and sorted.  No parameters are required, and you may not use line and label at the same time.\n");
                mothurOut("The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
-               mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels).\n");
-               mothurOut("Example get.rabund(line=1-3-5).\n");
+               mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
+               mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels, sorted=yourSorted).\n");
+               mothurOut("Example get.rabund(line=1-3-5, sorted=F).\n");
                mothurOut("The default value for line and label are all lines in your inputfile.\n");
                mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
@@ -129,9 +135,12 @@ int GetRAbundCommand::execute(){
                        
                        if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
                                        mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
-                                       rabund = new RAbundVector();
+                                       rabund = new RAbundVector();                            
                                        *rabund = (list->getRAbundVector());
-                                       rabund->print(out);
+                                       
+                                       if(sorted)      {   rabund->print(out);                         }
+                                       else            {       rabund->nonSortedPrint(out);    }
+                                       
                                        delete rabund;
                                                                                                                        
                                        processedLabels.insert(list->getLabel());
@@ -146,7 +155,10 @@ int GetRAbundCommand::execute(){
                                        mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
                                        rabund = new RAbundVector();
                                        *rabund = (list->getRAbundVector());
-                                       rabund->print(out);
+                                       
+                                       if(sorted)      {   rabund->print(out);                         }
+                                       else            {       rabund->nonSortedPrint(out);    }
+
                                        delete rabund;
 
                                        processedLabels.insert(list->getLabel());
@@ -181,7 +193,10 @@ int GetRAbundCommand::execute(){
                        mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
                        rabund = new RAbundVector();
                        *rabund = (list->getRAbundVector());
-                       rabund->print(out);
+                       
+                       if(sorted)      {   rabund->print(out);                         }
+                       else            {       rabund->nonSortedPrint(out);    }
+
                        delete rabund;
                        delete list;
                }