#include "readtreecommand.h"
//**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(string option){
+ReadTreeCommand::ReadTreeCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
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; }
}
//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 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 = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); 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.
}
}
catch(exception& e) {
- errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
+ m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
exit(1);
}
}
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");
+ 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) {
- errorOut(e, "ReadTreeCommand", "help");
+ m->errorOut(e, "ReadTreeCommand", "help");
exit(1);
}
}
readOk = read->read();
- if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); 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();
}
+
+// Sarah, isn't this checking already done when assigning the sequences to the groups? it makes read.tree
+// wicked slow... For some reason my tree is coming in here eventhough the number of sequences in the tree
+// agrees with the number of lines in the name file and the number of sequences represented by the name file
+// agrees with the number of sequences in the group file
+
//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++;
- }
-
- //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()) {
- mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
- treeMap->removeSeq(treeMap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
- }
- }
- }
+
+// if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+// cout << "in here" << endl;
+// 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) {
- errorOut(e, "ReadTreeCommand", "execute");
+ m->errorOut(e, "ReadTreeCommand", "execute");
exit(1);
}
}
globaldata->names.clear();
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);
if (itNames == globaldata->names.end()) {
//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 { mothurOut(first + " has already been seen in namefile, disregarding names file."); mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }
+ }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) {
- errorOut(e, "ReadTreeCommand", "readNamesFile");
+ m->errorOut(e, "ReadTreeCommand", "readNamesFile");
exit(1);
}
}
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