#include "readtreecommand.h"
+
//**********************************************************************************************************************
ReadTreeCommand::ReadTreeCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
+ /*
//valid paramters for this command
string Array[] = {"tree","group","name","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
it = parameters.find("tree");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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; }
}
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);
+ 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
+
+ //read in group map info.
+ treeMap = new TreeMap();
+ for (int i = 0; i < m->Treenames.size(); i++) { treeMap->addSeq(m->Treenames[i], "Group1"); }
+
+ }else {
//read in group map info.
treeMap = new TreeMap(groupfile);
treeMap->readMap();
- globaldata->gTreemap = treeMap;
}
namefile = validParameter.validFile(parameters, "name", true);
filename = treefile;
read = new ReadNewickTree(filename);
}
-
+ */
}
}
catch(exception& e) {
}
//**********************************************************************************************************************
-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(){
- if (abort == false) { delete read; }
-}
-
-//**********************************************************************************************************************
-
int ReadTreeCommand::execute(){
try {
- if (abort == true) { return 0; }
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+ /*
int readOk;
- readOk = read->read();
+ readOk = read->read(treeMap);
if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
- vector<Tree*> T = globaldata->gTree;
+ vector<Tree*> T = read->gTree;
//assemble users trees
for (int i = 0; i < T.size(); i++) {
T[i]->assembleTree();
}
+
+ //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 (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+ if (numNamesInTree < treeMap->getNumSeqs()) {
for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
//is that name in the tree?
int count = 0;
globaldata->gTreemap = treeMap;
}
-
+ */
return 0;
}
catch(exception& e) {
/*****************************************************************/
int ReadTreeCommand::readNamesFile() {
try {
- globaldata->names.clear();
+ /*
+ m->names.clear();
+ numUniquesInName = 0;
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string first, second;
map<string, string>::iterator itNames;
while(!in.eof()) {
- in >> first >> second; gobble(in);
+ in >> first >> second; m->gobble(in);
- itNames = globaldata->names.find(first);
+ numUniquesInName++;
+
+ itNames = m->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;
- splitAtComma(second, 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; }
+ 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) {
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