added calcs to tree.shared. working on remove.rare command

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index d04c9604170cf0d5c0f440132d25747b9193ba4c..2018170648761a91b5b9026fada7079b0b4e73e1 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -13,6 +13,56 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){  
+       try {
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"taxonomy"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /**********************************************************************************************************************/
 PhylotypeCommand::PhylotypeCommand(string option)  {
        try {
@@ -38,6 +88,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       
                        //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 = "";          }
@@ -46,7 +102,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                it = parameters.find("taxonomy");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
                                }
@@ -54,7 +110,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                it = parameters.find("name");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
@@ -75,7 +131,7 @@ PhylotypeCommand::PhylotypeCommand(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 = ""; 
-                               outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it   
+                               outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it        
                        }
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);
@@ -85,7 +141,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; allLines = 1; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -127,8 +183,6 @@ int PhylotypeCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               vector<string> outputNames;
-               
                //reads in taxonomy file and makes all the taxonomies the same length 
                //by appending the last taxon to a given taxonomy as many times as needed to 
                //make it as long as the longest taxonomy in the file 
@@ -152,21 +206,21 @@ int PhylotypeCommand::execute(){
                
                if (m->control_pressed) { delete tree; return 0; }
                
-               string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+               string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
                
                ofstream outList;
                string outputListFile = fileroot + "tx.list";
-               openOutputFile(outputListFile, outList);
+               m->openOutputFile(outputListFile, outList);
                ofstream outSabund;
                string outputSabundFile = fileroot + "tx.sabund";
-               openOutputFile(outputSabundFile, outSabund);
+               m->openOutputFile(outputSabundFile, outSabund);
                ofstream outRabund;
                string outputRabundFile = fileroot + "tx.rabund";
-               openOutputFile(outputRabundFile, outRabund);
+               m->openOutputFile(outputRabundFile, outRabund);
                
-               outputNames.push_back(outputListFile);
-               outputNames.push_back(outputSabundFile);
-               outputNames.push_back(outputRabundFile);
+               outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
+               outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
+               outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
                
                int count = 1;          
                //start at leaves of tree and work towards root, processing the labels the user wants
@@ -270,13 +324,13 @@ int PhylotypeCommand::readNamesFile() {
        try {
                                
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                
                string first, second;
                map<string, string>::iterator itNames;
                
                while(!in.eof()) {
-                       in >> first >> second; gobble(in);
+                       in >> first >> second; m->gobble(in);
                        
                        itNames = namemap.find(first);
                        if (itNames == namemap.end()) {