removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 05a65b736f93c376525b1cf64e2ed8275fc9c486..c476f5a89928cf131593178b40eb50d60130a7bd 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -9,51 +9,17 @@
 
 #include "readtreecommand.h"
 
-//**********************************************************************************************************************
-vector<string> ReadTreeCommand::getValidParameters(){  
-       try {
-               string Array[] =  {"tree","group","name","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadTreeCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ReadTreeCommand::getRequiredParameters(){       
-       try {
-               string Array[] =  {"tree"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadTreeCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ReadTreeCommand::getRequiredFiles(){    
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadTreeCommand", "getRequiredFiles");
-               exit(1);
-       }
-}
+
 //**********************************************************************************************************************
 ReadTreeCommand::ReadTreeCommand(string option)  {
        try {
-               globaldata = GlobalData::getInstance();
                abort = false; calledHelp = false;   
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
+                       /*
                        //valid paramters for this command
                        string Array[] =  {"tree","group","name","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -107,7 +73,6 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                        treefile = validParameter.validFile(parameters, "tree", true);
                        if (treefile == "not open") { abort = true; }
                        else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;  }     
-                       else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -118,18 +83,14 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                                
                                if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
                                
-                               globaldata->setGroupFile(groupfile); 
                                //read in group map info.
                                treeMap = new TreeMap();
-                               for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
-                               globaldata->gTreemap = treeMap;
+                               for (int i = 0; i < m->Treenames.size(); i++) { treeMap->addSeq(m->Treenames[i], "Group1"); }
                                        
                        }else {  
-                               globaldata->setGroupFile(groupfile); 
                                //read in group map info.
                                treeMap = new TreeMap(groupfile);
                                treeMap->readMap();
-                               globaldata->gTreemap = treeMap;
                        }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
@@ -141,7 +102,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                                filename = treefile;
                                read = new ReadNewickTree(filename);
                        }
-                                               
+                       */                      
                }
        }
        catch(exception& e) {
@@ -151,42 +112,19 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void ReadTreeCommand::help(){
-       try {
-               m->mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
-               m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
-               m->mothurOut("The read.tree command parameters are tree, group and name.\n");
-               m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
-               m->mothurOut("The tree and group parameters are both required, if no group file is given then one group is assumed.\n");
-               m->mothurOut("The name parameter allows you to enter a namefile.\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadTreeCommand", "help");      
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-ReadTreeCommand::~ReadTreeCommand(){
-       if (abort == false) { delete read; }
-}
-
-//**********************************************************************************************************************
-
 int ReadTreeCommand::execute(){
        try {
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
-               
+               m->mothurOut(getHelpString()); m->mothurOutEndLine();
+               /*
                int readOk;
                
-               readOk = read->read(); 
+               readOk = read->read(treeMap); 
                
                if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
                
-               vector<Tree*> T = globaldata->gTree;
+               vector<Tree*> T = read->gTree;
 
                //assemble users trees
                for (int i = 0; i < T.size(); i++) {
@@ -241,7 +179,7 @@ int ReadTreeCommand::execute(){
                        
                        globaldata->gTreemap = treeMap;
                }
-
+                */
                return 0;
        }
        catch(exception& e) {
@@ -252,7 +190,8 @@ int ReadTreeCommand::execute(){
 /*****************************************************************/
 int ReadTreeCommand::readNamesFile() {
        try {
-               globaldata->names.clear();
+               /*
+               m->names.clear();
                numUniquesInName = 0;
                
                ifstream in;
@@ -266,7 +205,7 @@ int ReadTreeCommand::readNamesFile() {
                        
                        numUniquesInName++;
 
-                       itNames = globaldata->names.find(first);
+                       itNames = m->names.find(first);
                        if (itNames == globaldata->names.end()) {  
                                globaldata->names[first] = second; 
                                
@@ -278,7 +217,7 @@ int ReadTreeCommand::readNamesFile() {
                        }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }                 
                }
                in.close();
-               
+               */
                return 0;
        }
        catch(exception& e) {