//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();;
treefile = m->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setTreeFile(treefile); }
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") {
- //if there is a current design file, use it
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
m->setTreeFile(treefile);
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
+ if (groupfile != "") {
+ //read in group map info.
+ tmap = new TreeMap(groupfile);
+ tmap->readMap();
+ }else{ //fake out by putting everyone in one group
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ tmap = new TreeMap();
+
+ for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+ }
if (namefile != "") { readNamesFile(); }
if (m->control_pressed) {
delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
m->Groups.clear();
return 0;
}
}
SharedUtil* util = new SharedUtil();
- util->setGroups(m->Groups, tmap->namesOfGroups, "treegroup"); //sets the groups the user wants to analyze
+ util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity"); //sets the groups the user wants to analyze
delete util;
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
//for each of the users trees
for(int i = 0; i < trees.size(); i++) {
- if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
ofstream outSum, outRare, outCollect;
string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.summary";
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
in.close();
- remove(inTemp.c_str());
+ m->mothurRemove(inTemp);
}
#endif