#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->newRead();
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { abort = true; }
+ else if (treefile == "not found") { treefile = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); 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 = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); 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";
+ errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReadTreeCommand class function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void ReadTreeCommand::help(){
+ try {
+ mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
+ mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
+ mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
+ mothurOut("The tree and group parameters are both required.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "ReadTreeCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
ReadTreeCommand::~ReadTreeCommand(){
- delete read;
+ if (abort == false) { delete read; }
}
//**********************************************************************************************************************
int ReadTreeCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
int readOk;
readOk = read->read();
- if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
+ if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
vector<Tree*> T = globaldata->gTree;
-
+
//assemble users trees
for (int i = 0; i < T.size(); i++) {
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()) {
+ mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
+ }
+ }
+ }
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadTreeCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReadTreeCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff