fixed some bugs and added scriptengine

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 8124d53415bda6035a3f6686d8ebc50a3ecb1419..88e34ff5c7e3f2c243eb7e0dac56b7d11fcb39b4 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -10,21 +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;
-
-               read = new ReadNewickTree(filename);
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"tree","group"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       OptionParser parser(option);
+                       map<string, string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
                
+                       //check to make sure all parameters are valid for command
+                       for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       globaldata->runParse = 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);
+                       }
+                                               
+               }
        }
        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";
@@ -35,6 +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);
+       }       
+}
 
 //**********************************************************************************************************************
 
@@ -46,6 +99,9 @@ ReadTreeCommand::~ReadTreeCommand(){
 
 int ReadTreeCommand::execute(){
        try {
+       
+               if (abort == true) { return 0; }
+               
                int readOk;
                
                readOk = read->read(); 
@@ -59,6 +115,23 @@ int ReadTreeCommand::execute(){
                        T[i]->assembleTree();
                }
 
+               //output any names that are in names file but not in tree
+               if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+                       for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
+                               //is that name in the tree?
+                               int count = 0;
+                               for (int j = 0; j < globaldata->Treenames.size(); j++) {
+                                       if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
+                                       count++;
+                               }
+                               
+                               //then you did not find it so report it 
+                               if (count == globaldata->Treenames.size()) { 
+                                       cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
+                               }
+                       }
+               }
+               
                return 0;
        }
        catch(exception& e) {