#include "readtreecommand.h"
//**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(string option){
+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;
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string Array[] = {"tree","group"};
+ 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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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 = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true; }
-// else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
+ 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 = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true; }
- else {
+ else if (groupfile == "not found") {
+ groupfile = "";
+
+ m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine();
+
+ 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;
+
+ }else {
globaldata->setGroupFile(groupfile);
//read in group map info.
treeMap = new TreeMap(groupfile);
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";
- 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";
+ m->errorOut(e, "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";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadTreeCommand", "help");
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);
- }
}
//**********************************************************************************************************************
ReadTreeCommand::~ReadTreeCommand(){
- delete read;
+ if (abort == false) { delete read; }
}
//**********************************************************************************************************************
readOk = read->read();
- if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
+ 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 names file but not in tree
- if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+
+ //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+ int numNamesInTree;
+ if (namefile != "") {
+ if (numUniquesInName == globaldata->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ else { numNamesInTree = globaldata->Treenames.size(); }
+ }else { numNamesInTree = globaldata->Treenames.size(); }
+
+
+ //output any names that are in group file but not in tree
+ if (numNamesInTree < treeMap->getNumSeqs()) {
for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
//is that name in the tree?
int count = 0;
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()) {
- cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
+ //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();
+ numUniquesInName = 0;
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ numUniquesInName++;
+
+ 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]; if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); } }
+ }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) {
+ m->errorOut(e, "ReadTreeCommand", "readNamesFile");
exit(1);
}
}
projects / mothur.git / blobdiff