*/
#include "deuniquetreecommand.h"
+#include "treereader.h"
//**********************************************************************************************************************
vector<string> DeuniqueTreeCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string DeuniqueTreeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "tree") { pattern = "[filename],deunique.tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DeuniqueTreeCommand::DeuniqueTreeCommand(){
try {
abort = true; calledHelp = true;
}
}
- m->runParse = true;
- m->clearGroups();
- m->clearAllGroups();
- m->Treenames.clear();
- m->names.clear();
-
- //check for required parameters
+ //check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (treefile == "not open") { abort = true; }
else if (treefile == "not found") { //if there is a current design file, use it
m->setTreeFile(treefile);
- //extracts names from tree to make faked out groupmap
- Tree* tree = new Tree(treefile); delete tree;
- tmap = new TreeMap();
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
-
- if (m->control_pressed) { delete tmap; return 0; }
-
- readNamesFile();
-
- if (m->control_pressed) { delete tmap; return 0; }
-
- ReadTree* read = new ReadNewickTree(treefile);
- int readOk = read->read(tmap);
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
-
- read->AssembleTrees();
- vector<Tree*> T = read->getTrees();
- delete read;
-
- //make sure all files match
- //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 (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
- else { numNamesInTree = m->Treenames.size(); }
-
- //output any names that are in group file but not in tree
- if (numNamesInTree < tmap->getNumSeqs()) {
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
- //is that name in the tree?
- int count = 0;
- for (int j = 0; j < m->Treenames.size(); j++) {
- if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
- count++;
- }
-
- if (m->control_pressed) {
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- m->clearGroups();
- return 0;
- }
-
- //then you did not find it so report it
- if (count == m->Treenames.size()) {
- //if it is in your namefile then don't remove
- map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-
- if (it == nameMap.end()) {
- m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
- }
- }
- }
-
+ TreeReader* reader = new TreeReader(treefile, "", namefile);
+ vector<Tree*> T = reader->getTrees();
+ map<string, string> nameMap;
+ m->readNames(namefile, nameMap);
+ delete reader;
//print new Tree
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputFile = getOutputFileName("tree", variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream out;
m->openOutputFile(outputFile, out);
- T[0]->print(out, "deunique");
+ T[0]->print(out, nameMap);
out.close();
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ delete (T[0]->getCountTable());
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
//set phylip file as new current phylipfile
string current = "";
exit(1);
}
}
-/*****************************************************************/
-int DeuniqueTreeCommand::readNamesFile() {
- try {
- m->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 = m->names.find(first);
- if (itNames == m->names.end()) {
- m->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 (i != 0) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, aborting."); m->mothurOutEndLine(); in.close(); m->names.clear(); m->control_pressed = true; return 1; }
- }
- in.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "DeuniqueTreeCommand", "readNamesFile");
- exit(1);
- }
-}
/***********************************************************/
projects / mothur.git / blobdiff