5 * Created by westcott on 11/12/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "indicatorcommand.h"
11 #include "sharedutilities.h"
14 //**********************************************************************************************************************
15 vector<string> IndicatorCommand::setParameters(){
17 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
18 CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
19 CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
20 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
21 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
22 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
23 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
24 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
26 vector<string> myArray;
27 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
31 m->errorOut(e, "IndicatorCommand", "setParameters");
35 //**********************************************************************************************************************
36 string IndicatorCommand::getHelpString(){
38 string helpString = "";
39 helpString += "The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n";
40 helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
41 helpString += "The summary file lists the indicator value for each OTU for each node.\n";
42 helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
43 helpString += "The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n";
44 helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n";
45 helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
46 helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
47 helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
51 m->errorOut(e, "IndicatorCommand", "getHelpString");
56 //**********************************************************************************************************************
57 IndicatorCommand::IndicatorCommand(){
59 abort = true; calledHelp = true;
61 vector<string> tempOutNames;
62 outputTypes["tree"] = tempOutNames;
63 outputTypes["summary"] = tempOutNames;
66 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
70 //**********************************************************************************************************************
71 IndicatorCommand::IndicatorCommand(string option) {
73 abort = false; calledHelp = false;
75 //allow user to run help
76 if(option == "help") { help(); abort = true; calledHelp = true; }
77 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
80 vector<string> myArray = setParameters();
82 OptionParser parser(option);
83 map<string, string> parameters = parser.getParameters();
85 ValidParameters validParameter;
86 map<string, string>::iterator it;
88 //check to make sure all parameters are valid for command
89 for (it = parameters.begin(); it != parameters.end(); it++) {
90 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
95 m->namesOfGroups.clear();
99 vector<string> tempOutNames;
100 outputTypes["tree"] = tempOutNames;
101 outputTypes["summary"] = tempOutNames;
103 //if the user changes the input directory command factory will send this info to us in the output parameter
104 string inputDir = validParameter.validFile(parameters, "inputdir", false);
105 if (inputDir == "not found"){ inputDir = ""; }
108 it = parameters.find("tree");
109 //user has given a template file
110 if(it != parameters.end()){
111 path = m->hasPath(it->second);
112 //if the user has not given a path then, add inputdir. else leave path alone.
113 if (path == "") { parameters["tree"] = inputDir + it->second; }
116 it = parameters.find("shared");
117 //user has given a template file
118 if(it != parameters.end()){
119 path = m->hasPath(it->second);
120 //if the user has not given a path then, add inputdir. else leave path alone.
121 if (path == "") { parameters["shared"] = inputDir + it->second; }
124 it = parameters.find("relabund");
125 //user has given a template file
126 if(it != parameters.end()){
127 path = m->hasPath(it->second);
128 //if the user has not given a path then, add inputdir. else leave path alone.
129 if (path == "") { parameters["relabund"] = inputDir + it->second; }
132 it = parameters.find("design");
133 //user has given a template file
134 if(it != parameters.end()){
135 path = m->hasPath(it->second);
136 //if the user has not given a path then, add inputdir. else leave path alone.
137 if (path == "") { parameters["design"] = inputDir + it->second; }
141 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
143 //check for required parameters
144 treefile = validParameter.validFile(parameters, "tree", true);
145 if (treefile == "not open") { abort = true; }
146 else if (treefile == "not found") { //if there is a current design file, use it
147 treefile = m->getTreeFile();
148 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
149 else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
152 sharedfile = validParameter.validFile(parameters, "shared", true);
153 if (sharedfile == "not open") { abort = true; }
154 else if (sharedfile == "not found") { sharedfile = ""; }
155 else { inputFileName = sharedfile; }
157 relabundfile = validParameter.validFile(parameters, "relabund", true);
158 if (relabundfile == "not open") { abort = true; }
159 else if (relabundfile == "not found") { relabundfile = ""; }
160 else { inputFileName = relabundfile; }
162 designfile = validParameter.validFile(parameters, "design", true);
163 if (designfile == "not open") { abort = true; }
164 else if (designfile == "not found") { designfile = ""; }
166 groups = validParameter.validFile(parameters, "groups", false);
167 if (groups == "not found") { groups = ""; Groups.push_back("all"); }
168 else { m->splitAtDash(groups, Groups); }
171 label = validParameter.validFile(parameters, "label", false);
172 if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
174 if ((relabundfile == "") && (sharedfile == "")) {
175 //is there are current file available for either of these?
176 //give priority to shared, then relabund
177 sharedfile = m->getSharedFile();
178 if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
180 relabundfile = m->getRelAbundFile();
181 if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
183 m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
189 if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
193 catch(exception& e) {
194 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
198 //**********************************************************************************************************************
200 int IndicatorCommand::execute(){
203 if (abort == true) { if (calledHelp) { return 0; } return 2; }
205 //read designfile if given and set up globaldatas groups for read of sharedfiles
206 if (designfile != "") {
207 designMap = new GroupMap(designfile);
208 designMap->readDesignMap();
210 //fill Groups - checks for "all" and for any typo groups
211 SharedUtil* util = new SharedUtil();
212 util->setGroups(Groups, designMap->namesOfGroups);
215 //loop through the Groups and fill Globaldata's Groups with the design file info
216 m->Groups = designMap->getNamesSeqs(Groups);
219 /***************************************************/
220 // use smart distancing to get right sharedRabund //
221 /***************************************************/
222 if (sharedfile != "") {
224 if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
225 if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
228 if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
229 if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
232 //reset Globaldatas groups if needed
233 if (designfile != "") { m->Groups = Groups; }
235 /***************************************************/
236 // reading tree info //
237 /***************************************************/
238 string groupfile = "";
239 m->setTreeFile(treefile);
240 Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
241 treeMap = new TreeMap();
242 bool mismatch = false;
244 for (int i = 0; i < m->Treenames.size(); i++) {
245 //sanity check - is this a group that is not in the sharedfile?
246 if (designfile == "") {
247 if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
248 m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
251 treeMap->addSeq(m->Treenames[i], "Group1");
253 vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
254 vector<string> myNames = designMap->getNamesSeqs(myGroups);
256 for(int k = 0; k < myNames.size(); k++) {
257 if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
258 m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
262 treeMap->addSeq(m->Treenames[i], "Group1");
266 if ((designfile != "") && (m->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
268 if (mismatch) { //cleanup and exit
269 if (designfile != "") { delete designMap; }
270 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
271 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
276 read = new ReadNewickTree(treefile);
277 int readOk = read->read(treeMap);
279 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
281 vector<Tree*> T = read->getTrees();
285 if (m->control_pressed) {
286 if (designfile != "") { delete designMap; }
287 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
288 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
289 for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
292 T[0]->assembleTree();
294 /***************************************************/
295 // create ouptut tree - respecting pickedGroups //
296 /***************************************************/
297 Tree* outputTree = new Tree(m->Groups.size(), treeMap);
299 outputTree->getSubTree(T[0], m->Groups);
300 outputTree->assembleTree();
302 //no longer need original tree, we have output tree to use and label
303 for (int i = 0; i < T.size(); i++) { delete T[i]; }
306 if (m->control_pressed) {
307 if (designfile != "") { delete designMap; }
308 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
309 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
310 delete outputTree; delete treeMap; return 0;
313 /***************************************************/
314 // get indicator species values //
315 /***************************************************/
316 GetIndicatorSpecies(outputTree);
318 if (designfile != "") { delete designMap; }
319 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
320 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
321 delete outputTree; delete treeMap;
324 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
326 //set tree file as new current treefile
328 itTypes = outputTypes.find("tree");
329 if (itTypes != outputTypes.end()) {
330 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
333 m->mothurOutEndLine();
334 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
335 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
336 m->mothurOutEndLine();
340 catch(exception& e) {
341 m->errorOut(e, "IndicatorCommand", "execute");
345 //**********************************************************************************************************************
346 //traverse tree finding indicator species values for each otu at each node
347 //label node with otu number that has highest indicator value
348 //report all otu values to file
349 int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
352 string thisOutputDir = outputDir;
353 if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
354 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
355 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
358 m->openOutputFile(outputFileName, out);
359 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
362 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
363 else { numBins = lookupFloat[0]->getNumBins(); }
367 for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
370 string treeOutputDir = outputDir;
371 if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
372 string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
375 //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
376 map<int, set<string> > nodeToDescendants;
377 map<int, set<int> > descendantNodes;
378 for (int i = 0; i < T->getNumNodes(); i++) {
379 if (m->control_pressed) { return 0; }
381 nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
384 //you need the distances to leaf to decide grouping below
385 //this will also set branch lengths if the tree does not include them
386 map<int, float> distToRoot = getDistToRoot(T);
389 for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
391 if (m->control_pressed) { out.close(); return 0; }
393 /*****************************************************/
394 //create vectors containing rabund info //
395 /*****************************************************/
397 vector<float> indicatorValues; //size of numBins
399 if (sharedfile != "") {
400 vector< vector<SharedRAbundVector*> > groupings;
402 //get nodes that will be a valid grouping
403 //you are valid if you are not one of my descendants
404 //AND your distToRoot is >= mine
405 //AND you were not added as part of a larger grouping. Largest nodes are added first.
407 set<string> groupsAlreadyAdded;
408 //create a grouping with my grouping
409 vector<SharedRAbundVector*> subset;
411 int doneCount = nodeToDescendants[i].size();
412 for (int k = 0; k < lookup.size(); k++) {
413 //is this descendant of i
414 if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
415 subset.push_back(lookup[k]);
416 groupsAlreadyAdded.insert(lookup[k]->getGroup());
419 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
421 if (subset.size() != 0) { groupings.push_back(subset); }
424 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
427 if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
428 vector<SharedRAbundVector*> subset;
430 int doneCount = nodeToDescendants[j].size();
431 for (int k = 0; k < lookup.size(); k++) {
432 //is this descendant of j, and we didn't already add this as part of a larger grouping
433 if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
434 subset.push_back(lookup[k]);
435 groupsAlreadyAdded.insert(lookup[k]->getGroup());
438 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
441 //if subset.size == 0 then the node was added as part of a larger grouping
442 if (subset.size() != 0) { groupings.push_back(subset); }
446 if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
448 indicatorValues = getValues(groupings);
451 vector< vector<SharedRAbundFloatVector*> > groupings;
453 //get nodes that will be a valid grouping
454 //you are valid if you are not one of my descendants
455 //AND your distToRoot is >= mine
456 //AND you were not added as part of a larger grouping. Largest nodes are added first.
458 set<string> groupsAlreadyAdded;
459 //create a grouping with my grouping
460 vector<SharedRAbundFloatVector*> subset;
462 int doneCount = nodeToDescendants[i].size();
463 for (int k = 0; k < lookupFloat.size(); k++) {
464 //is this descendant of i
465 if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
466 subset.push_back(lookupFloat[k]);
467 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
470 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
472 if (subset.size() != 0) { groupings.push_back(subset); }
474 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
475 if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
476 vector<SharedRAbundFloatVector*> subset;
478 int doneCount = nodeToDescendants[j].size();
479 for (int k = 0; k < lookupFloat.size(); k++) {
480 //is this descendant of j, and we didn't already add this as part of a larger grouping
481 if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
482 subset.push_back(lookupFloat[k]);
483 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
486 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
489 //if subset.size == 0 then the node was added as part of a larger grouping
490 if (subset.size() != 0) { groupings.push_back(subset); }
494 if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
496 indicatorValues = getValues(groupings);
499 if (m->control_pressed) { out.close(); return 0; }
502 /******************************************************/
503 //output indicator values to table form + label tree //
504 /*****************************************************/
505 out << (i+1) << '\t';
506 for (int j = 0; j < indicatorValues.size(); j++) {
508 if (m->control_pressed) { out.close(); return 0; }
510 out << indicatorValues[j] << '\t';
514 T->tree[i].setLabel((i+1));
520 m->openOutputFile(outputTreeFileName, outTree);
521 outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
523 T->print(outTree, "both");
528 catch(exception& e) {
529 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
533 //**********************************************************************************************************************
534 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings){
536 vector<float> values;
539 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
541 if (m->control_pressed) { return values; }
544 float AijDenominator = 0.0;
546 //get overall abundance of each grouping
547 for (int j = 0; j < groupings.size(); j++) {
549 float totalAbund = 0;
551 for (int k = 0; k < groupings[j].size(); k++) {
552 totalAbund += groupings[j][k]->getAbundance(i);
553 if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
556 float Aij = (totalAbund / (float) groupings[j].size());
557 terms.push_back(Aij);
559 //percentage of sites represented
560 Bij.push_back(numNotZero / (float) groupings[j].size());
562 AijDenominator += Aij;
565 float maxIndVal = 0.0;
566 for (int j = 0; j < terms.size(); j++) {
567 float thisAij = (terms[j] / AijDenominator);
568 float thisValue = thisAij * Bij[j] * 100.0;
571 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
574 values.push_back(maxIndVal);
579 catch(exception& e) {
580 m->errorOut(e, "IndicatorCommand", "getValues");
584 //**********************************************************************************************************************
585 //same as above, just data type difference
586 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings){
588 vector<float> values;
590 /*for (int j = 0; j < groupings.size(); j++) {
591 cout << "grouping " << j << endl;
592 for (int k = 0; k < groupings[j].size(); k++) {
593 cout << groupings[j][k]->getGroup() << endl;
597 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
599 float AijDenominator = 0.0;
601 //get overall abundance of each grouping
602 for (int j = 0; j < groupings.size(); j++) {
604 int totalAbund = 0.0;
606 for (int k = 0; k < groupings[j].size(); k++) {
607 totalAbund += groupings[j][k]->getAbundance(i);
608 if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
612 float Aij = (totalAbund / (float) groupings[j].size());
613 terms.push_back(Aij);
615 //percentage of sites represented
616 Bij.push_back(numNotZero / (float) groupings[j].size());
618 AijDenominator += Aij;
621 float maxIndVal = 0.0;
622 for (int j = 0; j < terms.size(); j++) {
623 float thisAij = (terms[j] / AijDenominator);
624 float thisValue = thisAij * Bij[j] * 100.0;
627 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
630 values.push_back(maxIndVal);
635 catch(exception& e) {
636 m->errorOut(e, "IndicatorCommand", "getValues");
640 //**********************************************************************************************************************
641 //you need the distances to root to decide groupings
642 //this will also set branch lengths if the tree does not include them
643 map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
645 map<int, float> dists;
647 bool hasBranchLengths = false;
648 for (int i = 0; i < T->getNumNodes(); i++) {
649 if (T->tree[i].getBranchLength() > 0.0) { hasBranchLengths = true; break; }
652 //set branchlengths if needed
653 if (!hasBranchLengths) {
654 for (int i = 0; i < T->getNumNodes(); i++) {
656 int lc = T->tree[i].getLChild();
657 int rc = T->tree[i].getRChild();
659 if (lc == -1) { // you are a leaf
660 //if you are a leaf set you priliminary length to 1.0, this may adjust later
661 T->tree[i].setBranchLength(1.0);
663 }else{ // you are an internal node
664 //look at your children's length to leaf
665 float ldist = dists[lc];
666 float rdist = dists[rc];
668 float greater = ldist;
669 if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
670 else { dists[i] = rdist + 1.0; }
673 //branch length = difference + 1
674 T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
675 T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
682 for (int i = 0; i < T->getNumNodes(); i++) {
687 while(T->tree[index].getParent() != -1){
688 if (T->tree[index].getBranchLength() != -1) {
689 sum += abs(T->tree[index].getBranchLength());
691 index = T->tree[index].getParent();
699 catch(exception& e) {
700 m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
704 //**********************************************************************************************************************
705 set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
709 set<string>::iterator it;
711 int lc = T->tree[i].getLChild();
712 int rc = T->tree[i].getRChild();
714 if (lc == -1) { //you are a leaf your only descendant is yourself
715 set<int> temp; temp.insert(i);
718 if (designfile == "") {
719 names.insert(T->tree[i].getName());
721 vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
722 vector<string> myReps = designMap->getNamesSeqs(myGroup);
723 for (int k = 0; k < myReps.size(); k++) {
724 names.insert(myReps[k]);
728 }else{ //your descedants are the combination of your childrens descendants
729 names = descendants[lc];
730 nodes[i] = nodes[lc];
731 for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
734 for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
735 nodes[i].insert(*itNum);
737 //you are your own descendant
743 catch(exception& e) {
744 m->errorOut(e, "IndicatorCommand", "getDescendantList");
748 //**********************************************************************************************************************
749 int IndicatorCommand::getShared(){
751 InputData* input = new InputData(sharedfile, "sharedfile");
752 lookup = input->getSharedRAbundVectors();
753 string lastLabel = lookup[0]->getLabel();
755 if (label == "") { label = lastLabel; delete input; return 0; }
757 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
758 set<string> labels; labels.insert(label);
759 set<string> processedLabels;
760 set<string> userLabels = labels;
762 //as long as you are not at the end of the file or done wih the lines you want
763 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
764 if (m->control_pressed) { delete input; return 0; }
766 if(labels.count(lookup[0]->getLabel()) == 1){
767 processedLabels.insert(lookup[0]->getLabel());
768 userLabels.erase(lookup[0]->getLabel());
772 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
773 string saveLabel = lookup[0]->getLabel();
775 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
776 lookup = input->getSharedRAbundVectors(lastLabel);
778 processedLabels.insert(lookup[0]->getLabel());
779 userLabels.erase(lookup[0]->getLabel());
781 //restore real lastlabel to save below
782 lookup[0]->setLabel(saveLabel);
786 lastLabel = lookup[0]->getLabel();
788 //get next line to process
789 //prevent memory leak
790 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
791 lookup = input->getSharedRAbundVectors();
795 if (m->control_pressed) { delete input; return 0; }
797 //output error messages about any remaining user labels
798 set<string>::iterator it;
799 bool needToRun = false;
800 for (it = userLabels.begin(); it != userLabels.end(); it++) {
801 m->mothurOut("Your file does not include the label " + *it);
802 if (processedLabels.count(lastLabel) != 1) {
803 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
806 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
810 //run last label if you need to
811 if (needToRun == true) {
812 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
813 lookup = input->getSharedRAbundVectors(lastLabel);
819 catch(exception& e) {
820 m->errorOut(e, "IndicatorCommand", "getShared");
824 //**********************************************************************************************************************
825 int IndicatorCommand::getSharedFloat(){
827 InputData* input = new InputData(relabundfile, "relabund");
828 lookupFloat = input->getSharedRAbundFloatVectors();
829 string lastLabel = lookupFloat[0]->getLabel();
831 if (label == "") { label = lastLabel; delete input; return 0; }
833 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
834 set<string> labels; labels.insert(label);
835 set<string> processedLabels;
836 set<string> userLabels = labels;
838 //as long as you are not at the end of the file or done wih the lines you want
839 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
841 if (m->control_pressed) { delete input; return 0; }
843 if(labels.count(lookupFloat[0]->getLabel()) == 1){
844 processedLabels.insert(lookupFloat[0]->getLabel());
845 userLabels.erase(lookupFloat[0]->getLabel());
849 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
850 string saveLabel = lookupFloat[0]->getLabel();
852 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
853 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
855 processedLabels.insert(lookupFloat[0]->getLabel());
856 userLabels.erase(lookupFloat[0]->getLabel());
858 //restore real lastlabel to save below
859 lookupFloat[0]->setLabel(saveLabel);
863 lastLabel = lookupFloat[0]->getLabel();
865 //get next line to process
866 //prevent memory leak
867 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
868 lookupFloat = input->getSharedRAbundFloatVectors();
872 if (m->control_pressed) { delete input; return 0; }
874 //output error messages about any remaining user labels
875 set<string>::iterator it;
876 bool needToRun = false;
877 for (it = userLabels.begin(); it != userLabels.end(); it++) {
878 m->mothurOut("Your file does not include the label " + *it);
879 if (processedLabels.count(lastLabel) != 1) {
880 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
883 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
887 //run last label if you need to
888 if (needToRun == true) {
889 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
890 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
896 catch(exception& e) {
897 m->errorOut(e, "IndicatorCommand", "getShared");
901 /*****************************************************************/