#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; }
//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.
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { treefile = ""; }
+ else if (namefile == "not found") { namefile = ""; }
else { readNamesFile(); }
if (abort == false) {
}
}
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 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("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();
}
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()) {
- mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
+ 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);
}
}
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);
}
}