exit(1);
}
}
-
+//**********************************************************************************************************************
+string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "tree") { outputFileName = "indicator.tre"; }
+ else if (type == "summary") { outputFileName = "indicator.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
util.setGroups(Groups, nameGroups);
designMap->setNamesOfGroups(nameGroups);
- //loop through the Groups and fill Globaldata's Groups with the design file info
vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
m->setGroups(namesSeqs);
}
string groupfile = "";
m->setTreeFile(treefile);
Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- treeMap = new TreeMap();
+ ct = new CountTable();
bool mismatch = false;
-
- for (int i = 0; i < m->Treenames.size(); i++) {
- //sanity check - is this a group that is not in the sharedfile?
+
+ set<string> nameMap;
+ map<string, string> groupMap;
+ set<string> gps;
+ for (int i = 0; i < m->Treenames.size(); i++) {
+ nameMap.insert(m->Treenames[i]);
+ //sanity check - is this a group that is not in the sharedfile?
if (designfile == "") {
+ if (i == 0) { gps.insert("Group1"); }
if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
mismatch = true;
}
- treeMap->addSeq(m->Treenames[i], "Group1");
+ groupMap[m->Treenames[i]] = "Group1";
}else{
vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
vector<string> myNames = designMap->getNamesSeqs(myGroups);
mismatch = true;
}
}
- treeMap->addSeq(m->Treenames[i], "Group1");
+ groupMap[m->Treenames[i]] = "Group1";
}
- }
+ }
+ ct->createTable(nameMap, groupMap, gps);
if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete treeMap;
+ delete ct;
return 0;
}
read = new ReadNewickTree(treefile);
- int readOk = read->read(treeMap);
+ int readOk = read->read(ct);
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete ct; delete read; return 0; }
vector<Tree*> T = read->getTrees();
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete ct; return 0;
}
- map<string, string> nameMap;
- T[0]->assembleTree(nameMap);
+ T[0]->assembleTree();
/***************************************************/
// create ouptut tree - respecting pickedGroups //
/***************************************************/
- Tree* outputTree = new Tree(m->getNumGroups(), treeMap);
+ Tree* outputTree = new Tree(m->getNumGroups(), ct);
outputTree->getSubTree(T[0], m->getGroups());
- outputTree->assembleTree(nameMap);
+ outputTree->assembleTree();
//no longer need original tree, we have output tree to use and label
for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete outputTree; delete treeMap; return 0;
+ delete outputTree; delete ct; return 0;
}
/***************************************************/
// get indicator species values //
/***************************************************/
GetIndicatorSpecies(outputTree);
- delete outputTree; delete treeMap;
+ delete outputTree; delete ct;
}else { //run with design file only
//get indicator species
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+ string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
projects / mothur.git / blobdiff