broke up globaldata and moved error checking and help into commands

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 19ab67531dc96e8929b258eef2a41b4d24538bc4..6e5742ddbbc35cdc6d01b9d57b3d58a8c7856816 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -10,24 +10,55 @@
 #include "readtreecommand.h"
 
 //**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(){
+ReadTreeCommand::ReadTreeCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
-               filename = globaldata->inputFileName;
+               abort = false;
                
-               //read in group map info.
-               treeMap = new TreeMap(globaldata->getGroupFile());
-               treeMap->readMap();
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
                
-               //memory leak prevention
-               //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
-               globaldata->gTreemap = treeMap;
-               
-               //get names in tree
-               globaldata->parseTreeFile();
-
-               read = new ReadNewickTree(filename);
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"tree","group"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       parser = new OptionParser();
+                       parser->parse(option, parameters);  delete parser;
+                       
+                       ValidParameters* validParameter = new ValidParameters();
                
+                       //check to make sure all parameters are valid for command
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       globaldata->newRead();
+                       
+                       //check for required parameters
+                       treefile = validParameter->validFile(parameters, "tree", true);
+                       if (treefile == "not open") { abort = true; }
+                       else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true;  }  
+                       else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
+                       
+                       groupfile = validParameter->validFile(parameters, "group", true);
+                       if (groupfile == "not open") { abort = true; }  
+                       else if (groupfile == "not found") { groupfile = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true;  }
+                       else {  
+                               globaldata->setGroupFile(groupfile); 
+                               //read in group map info.
+                               treeMap = new TreeMap(groupfile);
+                               treeMap->readMap();
+                               globaldata->gTreemap = treeMap;
+                       }
+                       
+                       if (abort == false) {
+                               filename = treefile;
+                               read = new ReadNewickTree(filename);
+                       }
+                                               
+                       delete validParameter;
+               }
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -38,6 +69,25 @@ ReadTreeCommand::ReadTreeCommand(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+
+void ReadTreeCommand::help(){
+       try {
+               cout << "The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. " << "\n";
+               cout << "It also must be run before using the parsimony command, unless you are using the randomtree parameter." << "\n";
+               cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
+               cout << "The tree and group parameters are both required." << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ReadTreeCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
 
 //**********************************************************************************************************************
 
@@ -49,6 +99,9 @@ ReadTreeCommand::~ReadTreeCommand(){
 
 int ReadTreeCommand::execute(){
        try {
+       
+               if (abort == true) { return 0; }
+               
                int readOk;
                
                readOk = read->read();