#include "readtreecommand.h"
//**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(){
+ReadTreeCommand::ReadTreeCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- filename = globaldata->inputFileName;
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- //read in group map info.
- treeMap = new TreeMap(globaldata->getGroupFile());
- treeMap->readMap();
- globaldata->gTreemap = treeMap;
-
- read = new ReadNewickTree(filename);
+ else {
+ //valid paramters for this command
+ string Array[] = {"tree","group","name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+ //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();
+
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+
+ }
+
+
+ //check for required parameters
+ 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; }
+ else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ globaldata->setGroupFile(groupfile);
+ //read in group map info.
+ treeMap = new TreeMap(groupfile);
+ treeMap->readMap();
+ globaldata->gTreemap = treeMap;
+ }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { readNamesFile(); }
+
+ 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";
+ m->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 {
+ 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.\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(){
- delete read;
+ if (abort == false) { delete read; }
}
//**********************************************************************************************************************
int ReadTreeCommand::execute(){
try {
- read->read();
+ if (abort == true) { return 0; }
+
+ int readOk;
- Tree* T = globaldata->gTree;
-// T->createNewickFile();
+ readOk = read->read();
+
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->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++) {
+ if (m->control_pressed) {
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ globaldata->gTree.clear();
+ delete globaldata->gTreemap;
+ return 0;
+ }
+
+ T[i]->assembleTree();
+ }
+
+ //output any names that are in group 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++;
+ }
+
+ if (m->control_pressed) {
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ globaldata->gTree.clear();
+ delete globaldata->gTreemap;
+ return 0;
+ }
+
+ //then you did not find it so report it
+ if (count == globaldata->Treenames.size()) {
+ //if it is in your namefile then don't remove
+ map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
+
+ if (it == nameMap.end()) {
+ m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+ treeMap->removeSeq(treeMap->namesOfSeqs[i]);
+ i--; //need this because removeSeq removes name from namesOfSeqs
+ }
+ }
+ }
+
+ globaldata->gTreemap = treeMap;
+ }
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";
+ m->errorOut(e, "ReadTreeCommand", "execute");
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";
+}
+/*****************************************************************/
+int ReadTreeCommand::readNamesFile() {
+ try {
+ globaldata->names.clear();
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ itNames = globaldata->names.find(first);
+ if (itNames == globaldata->names.end()) {
+ globaldata->names[first] = second;
+
+ //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+ vector<string> dupNames;
+ m->splitAtComma(second, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; }
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadTreeCommand", "readNamesFile");
exit(1);
}
}
-//**********************************************************************************************************************
\ No newline at end of file
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff