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; }
79 vector<string> myArray = setParameters();
81 OptionParser parser(option);
82 map<string, string> parameters = parser.getParameters();
84 ValidParameters validParameter;
85 map<string, string>::iterator it;
87 //check to make sure all parameters are valid for command
88 for (it = parameters.begin(); it != parameters.end(); it++) {
89 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
94 vector<string> tempOutNames;
95 outputTypes["tree"] = tempOutNames;
96 outputTypes["summary"] = tempOutNames;
98 //if the user changes the input directory command factory will send this info to us in the output parameter
99 string inputDir = validParameter.validFile(parameters, "inputdir", false);
100 if (inputDir == "not found"){ inputDir = ""; }
103 it = parameters.find("tree");
104 //user has given a template file
105 if(it != parameters.end()){
106 path = m->hasPath(it->second);
107 //if the user has not given a path then, add inputdir. else leave path alone.
108 if (path == "") { parameters["tree"] = inputDir + it->second; }
111 it = parameters.find("shared");
112 //user has given a template file
113 if(it != parameters.end()){
114 path = m->hasPath(it->second);
115 //if the user has not given a path then, add inputdir. else leave path alone.
116 if (path == "") { parameters["shared"] = inputDir + it->second; }
119 it = parameters.find("relabund");
120 //user has given a template file
121 if(it != parameters.end()){
122 path = m->hasPath(it->second);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { parameters["relabund"] = inputDir + it->second; }
127 it = parameters.find("design");
128 //user has given a template file
129 if(it != parameters.end()){
130 path = m->hasPath(it->second);
131 //if the user has not given a path then, add inputdir. else leave path alone.
132 if (path == "") { parameters["design"] = inputDir + it->second; }
136 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
138 //check for required parameters
139 treefile = validParameter.validFile(parameters, "tree", true);
140 if (treefile == "not open") { abort = true; }
141 else if (treefile == "not found") { //if there is a current design file, use it
142 treefile = m->getTreeFile();
143 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
144 else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
147 sharedfile = validParameter.validFile(parameters, "shared", true);
148 if (sharedfile == "not open") { abort = true; }
149 else if (sharedfile == "not found") { sharedfile = ""; }
150 else { inputFileName = sharedfile; }
152 relabundfile = validParameter.validFile(parameters, "relabund", true);
153 if (relabundfile == "not open") { abort = true; }
154 else if (relabundfile == "not found") { relabundfile = ""; }
155 else { inputFileName = relabundfile; }
157 designfile = validParameter.validFile(parameters, "design", true);
158 if (designfile == "not open") { abort = true; }
159 else if (designfile == "not found") { designfile = ""; }
161 groups = validParameter.validFile(parameters, "groups", false);
162 if (groups == "not found") { groups = ""; Groups.push_back("all"); }
163 else { m->splitAtDash(groups, Groups); }
166 label = validParameter.validFile(parameters, "label", false);
167 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=""; }
169 if ((relabundfile == "") && (sharedfile == "")) {
170 //is there are current file available for either of these?
171 //give priority to shared, then relabund
172 sharedfile = m->getSharedFile();
173 if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
175 relabundfile = m->getRelAbundFile();
176 if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
178 m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
184 if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
188 catch(exception& e) {
189 m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
193 //**********************************************************************************************************************
195 int IndicatorCommand::execute(){
198 if (abort == true) { if (calledHelp) { return 0; } return 2; }
200 //read designfile if given and set up globaldatas groups for read of sharedfiles
201 if (designfile != "") {
202 designMap = new GroupMap(designfile);
203 designMap->readDesignMap();
205 //fill Groups - checks for "all" and for any typo groups
206 SharedUtil* util = new SharedUtil();
207 util->setGroups(Groups, designMap->namesOfGroups);
210 //loop through the Groups and fill Globaldata's Groups with the design file info
211 m->Groups = designMap->getNamesSeqs(Groups);
214 /***************************************************/
215 // use smart distancing to get right sharedRabund //
216 /***************************************************/
217 if (sharedfile != "") {
219 if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
220 if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
223 if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
224 if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
227 //reset Globaldatas groups if needed
228 if (designfile != "") { m->Groups = Groups; }
230 /***************************************************/
231 // reading tree info //
232 /***************************************************/
233 string groupfile = "";
234 Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
235 treeMap = new TreeMap();
236 bool mismatch = false;
238 for (int i = 0; i < m->Treenames.size(); i++) {
239 //sanity check - is this a group that is not in the sharedfile?
240 if (designfile == "") {
241 if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
242 m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
245 treeMap->addSeq(m->Treenames[i], "Group1");
247 vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
248 vector<string> myNames = designMap->getNamesSeqs(myGroups);
250 for(int k = 0; k < myNames.size(); k++) {
251 if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
252 m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
256 treeMap->addSeq(m->Treenames[i], "Group1");
260 if ((designfile != "") && (m->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
262 if (mismatch) { //cleanup and exit
263 if (designfile != "") { delete designMap; }
264 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
265 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
270 read = new ReadNewickTree(treefile);
271 int readOk = read->read(treeMap);
273 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
275 vector<Tree*> T = read->getTrees();
279 if (m->control_pressed) {
280 if (designfile != "") { delete designMap; }
281 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
282 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
283 for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
286 T[0]->assembleTree();
288 /***************************************************/
289 // create ouptut tree - respecting pickedGroups //
290 /***************************************************/
291 Tree* outputTree = new Tree(m->Groups.size(), treeMap);
293 outputTree->getSubTree(T[0], m->Groups);
294 outputTree->assembleTree();
296 //no longer need original tree, we have output tree to use and label
297 for (int i = 0; i < T.size(); i++) { delete T[i]; }
300 if (m->control_pressed) {
301 if (designfile != "") { delete designMap; }
302 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
303 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
304 delete outputTree; delete treeMap; return 0;
307 /***************************************************/
308 // get indicator species values //
309 /***************************************************/
310 GetIndicatorSpecies(outputTree);
312 if (designfile != "") { delete designMap; }
313 if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
314 else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
315 delete outputTree; delete treeMap;
318 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
320 //set tree file as new current treefile
322 itTypes = outputTypes.find("tree");
323 if (itTypes != outputTypes.end()) {
324 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
327 m->mothurOutEndLine();
328 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
329 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
330 m->mothurOutEndLine();
334 catch(exception& e) {
335 m->errorOut(e, "IndicatorCommand", "execute");
339 //**********************************************************************************************************************
340 //traverse tree finding indicator species values for each otu at each node
341 //label node with otu number that has highest indicator value
342 //report all otu values to file
343 int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
346 string thisOutputDir = outputDir;
347 if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
348 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
349 outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
352 m->openOutputFile(outputFileName, out);
353 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
356 if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
357 else { numBins = lookupFloat[0]->getNumBins(); }
361 for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
364 string treeOutputDir = outputDir;
365 if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
366 string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
369 //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
370 map<int, set<string> > nodeToDescendants;
371 map<int, set<int> > descendantNodes;
372 for (int i = 0; i < T->getNumNodes(); i++) {
373 if (m->control_pressed) { return 0; }
375 nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
378 //you need the distances to leaf to decide grouping below
379 //this will also set branch lengths if the tree does not include them
380 map<int, float> distToRoot = getDistToRoot(T);
383 for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
385 if (m->control_pressed) { out.close(); return 0; }
387 /*****************************************************/
388 //create vectors containing rabund info //
389 /*****************************************************/
391 vector<float> indicatorValues; //size of numBins
393 if (sharedfile != "") {
394 vector< vector<SharedRAbundVector*> > groupings;
396 //get nodes that will be a valid grouping
397 //you are valid if you are not one of my descendants
398 //AND your distToRoot is >= mine
399 //AND you were not added as part of a larger grouping. Largest nodes are added first.
401 set<string> groupsAlreadyAdded;
402 //create a grouping with my grouping
403 vector<SharedRAbundVector*> subset;
405 int doneCount = nodeToDescendants[i].size();
406 for (int k = 0; k < lookup.size(); k++) {
407 //is this descendant of i
408 if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
409 subset.push_back(lookup[k]);
410 groupsAlreadyAdded.insert(lookup[k]->getGroup());
413 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
415 if (subset.size() != 0) { groupings.push_back(subset); }
418 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
421 if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
422 vector<SharedRAbundVector*> subset;
424 int doneCount = nodeToDescendants[j].size();
425 for (int k = 0; k < lookup.size(); k++) {
426 //is this descendant of j, and we didn't already add this as part of a larger grouping
427 if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
428 subset.push_back(lookup[k]);
429 groupsAlreadyAdded.insert(lookup[k]->getGroup());
432 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
435 //if subset.size == 0 then the node was added as part of a larger grouping
436 if (subset.size() != 0) { groupings.push_back(subset); }
440 if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
442 indicatorValues = getValues(groupings);
445 vector< vector<SharedRAbundFloatVector*> > groupings;
447 //get nodes that will be a valid grouping
448 //you are valid if you are not one of my descendants
449 //AND your distToRoot is >= mine
450 //AND you were not added as part of a larger grouping. Largest nodes are added first.
452 set<string> groupsAlreadyAdded;
453 //create a grouping with my grouping
454 vector<SharedRAbundFloatVector*> subset;
456 int doneCount = nodeToDescendants[i].size();
457 for (int k = 0; k < lookupFloat.size(); k++) {
458 //is this descendant of i
459 if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
460 subset.push_back(lookupFloat[k]);
461 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
464 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
466 if (subset.size() != 0) { groupings.push_back(subset); }
468 for (int j = (T->getNumNodes()-1); j >= 0; j--) {
469 if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
470 vector<SharedRAbundFloatVector*> subset;
472 int doneCount = nodeToDescendants[j].size();
473 for (int k = 0; k < lookupFloat.size(); k++) {
474 //is this descendant of j, and we didn't already add this as part of a larger grouping
475 if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
476 subset.push_back(lookupFloat[k]);
477 groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
480 if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
483 //if subset.size == 0 then the node was added as part of a larger grouping
484 if (subset.size() != 0) { groupings.push_back(subset); }
488 if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
490 indicatorValues = getValues(groupings);
493 if (m->control_pressed) { out.close(); return 0; }
496 /******************************************************/
497 //output indicator values to table form + label tree //
498 /*****************************************************/
499 out << (i+1) << '\t';
500 for (int j = 0; j < indicatorValues.size(); j++) {
502 if (m->control_pressed) { out.close(); return 0; }
504 out << indicatorValues[j] << '\t';
508 T->tree[i].setLabel((i+1));
514 m->openOutputFile(outputTreeFileName, outTree);
515 outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
517 T->print(outTree, "both");
522 catch(exception& e) {
523 m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
527 //**********************************************************************************************************************
528 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings){
530 vector<float> values;
533 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
535 if (m->control_pressed) { return values; }
538 float AijDenominator = 0.0;
540 //get overall abundance of each grouping
541 for (int j = 0; j < groupings.size(); j++) {
543 float totalAbund = 0;
545 for (int k = 0; k < groupings[j].size(); k++) {
546 totalAbund += groupings[j][k]->getAbundance(i);
547 if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
550 float Aij = (totalAbund / (float) groupings[j].size());
551 terms.push_back(Aij);
553 //percentage of sites represented
554 Bij.push_back(numNotZero / (float) groupings[j].size());
556 AijDenominator += Aij;
559 float maxIndVal = 0.0;
560 for (int j = 0; j < terms.size(); j++) {
561 float thisAij = (terms[j] / AijDenominator);
562 float thisValue = thisAij * Bij[j] * 100.0;
565 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
568 values.push_back(maxIndVal);
573 catch(exception& e) {
574 m->errorOut(e, "IndicatorCommand", "getValues");
578 //**********************************************************************************************************************
579 //same as above, just data type difference
580 vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings){
582 vector<float> values;
584 /*for (int j = 0; j < groupings.size(); j++) {
585 cout << "grouping " << j << endl;
586 for (int k = 0; k < groupings[j].size(); k++) {
587 cout << groupings[j][k]->getGroup() << endl;
591 for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
593 float AijDenominator = 0.0;
595 //get overall abundance of each grouping
596 for (int j = 0; j < groupings.size(); j++) {
598 int totalAbund = 0.0;
600 for (int k = 0; k < groupings[j].size(); k++) {
601 totalAbund += groupings[j][k]->getAbundance(i);
602 if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
606 float Aij = (totalAbund / (float) groupings[j].size());
607 terms.push_back(Aij);
609 //percentage of sites represented
610 Bij.push_back(numNotZero / (float) groupings[j].size());
612 AijDenominator += Aij;
615 float maxIndVal = 0.0;
616 for (int j = 0; j < terms.size(); j++) {
617 float thisAij = (terms[j] / AijDenominator);
618 float thisValue = thisAij * Bij[j] * 100.0;
621 if (thisValue > maxIndVal) { maxIndVal = thisValue; }
624 values.push_back(maxIndVal);
629 catch(exception& e) {
630 m->errorOut(e, "IndicatorCommand", "getValues");
634 //**********************************************************************************************************************
635 //you need the distances to root to decide groupings
636 //this will also set branch lengths if the tree does not include them
637 map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
639 map<int, float> dists;
641 bool hasBranchLengths = false;
642 for (int i = 0; i < T->getNumNodes(); i++) {
643 if (T->tree[i].getBranchLength() > 0.0) { hasBranchLengths = true; break; }
646 //set branchlengths if needed
647 if (!hasBranchLengths) {
648 for (int i = 0; i < T->getNumNodes(); i++) {
650 int lc = T->tree[i].getLChild();
651 int rc = T->tree[i].getRChild();
653 if (lc == -1) { // you are a leaf
654 //if you are a leaf set you priliminary length to 1.0, this may adjust later
655 T->tree[i].setBranchLength(1.0);
657 }else{ // you are an internal node
658 //look at your children's length to leaf
659 float ldist = dists[lc];
660 float rdist = dists[rc];
662 float greater = ldist;
663 if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
664 else { dists[i] = rdist + 1.0; }
667 //branch length = difference + 1
668 T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
669 T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
676 for (int i = 0; i < T->getNumNodes(); i++) {
681 while(T->tree[index].getParent() != -1){
682 if (T->tree[index].getBranchLength() != -1) {
683 sum += abs(T->tree[index].getBranchLength());
685 index = T->tree[index].getParent();
693 catch(exception& e) {
694 m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
698 //**********************************************************************************************************************
699 set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
703 set<string>::iterator it;
705 int lc = T->tree[i].getLChild();
706 int rc = T->tree[i].getRChild();
708 if (lc == -1) { //you are a leaf your only descendant is yourself
709 set<int> temp; temp.insert(i);
712 if (designfile == "") {
713 names.insert(T->tree[i].getName());
715 vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
716 vector<string> myReps = designMap->getNamesSeqs(myGroup);
717 for (int k = 0; k < myReps.size(); k++) {
718 names.insert(myReps[k]);
722 }else{ //your descedants are the combination of your childrens descendants
723 names = descendants[lc];
724 nodes[i] = nodes[lc];
725 for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
728 for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
729 nodes[i].insert(*itNum);
731 //you are your own descendant
737 catch(exception& e) {
738 m->errorOut(e, "IndicatorCommand", "getDescendantList");
742 //**********************************************************************************************************************
743 int IndicatorCommand::getShared(){
745 InputData* input = new InputData(sharedfile, "sharedfile");
746 lookup = input->getSharedRAbundVectors();
747 string lastLabel = lookup[0]->getLabel();
749 if (label == "") { label = lastLabel; delete input; return 0; }
751 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
752 set<string> labels; labels.insert(label);
753 set<string> processedLabels;
754 set<string> userLabels = labels;
756 //as long as you are not at the end of the file or done wih the lines you want
757 while((lookup[0] != NULL) && (userLabels.size() != 0)) {
758 if (m->control_pressed) { delete input; return 0; }
760 if(labels.count(lookup[0]->getLabel()) == 1){
761 processedLabels.insert(lookup[0]->getLabel());
762 userLabels.erase(lookup[0]->getLabel());
766 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
767 string saveLabel = lookup[0]->getLabel();
769 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
770 lookup = input->getSharedRAbundVectors(lastLabel);
772 processedLabels.insert(lookup[0]->getLabel());
773 userLabels.erase(lookup[0]->getLabel());
775 //restore real lastlabel to save below
776 lookup[0]->setLabel(saveLabel);
780 lastLabel = lookup[0]->getLabel();
782 //get next line to process
783 //prevent memory leak
784 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
785 lookup = input->getSharedRAbundVectors();
789 if (m->control_pressed) { delete input; return 0; }
791 //output error messages about any remaining user labels
792 set<string>::iterator it;
793 bool needToRun = false;
794 for (it = userLabels.begin(); it != userLabels.end(); it++) {
795 m->mothurOut("Your file does not include the label " + *it);
796 if (processedLabels.count(lastLabel) != 1) {
797 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
800 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
804 //run last label if you need to
805 if (needToRun == true) {
806 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
807 lookup = input->getSharedRAbundVectors(lastLabel);
813 catch(exception& e) {
814 m->errorOut(e, "IndicatorCommand", "getShared");
818 //**********************************************************************************************************************
819 int IndicatorCommand::getSharedFloat(){
821 InputData* input = new InputData(relabundfile, "relabund");
822 lookupFloat = input->getSharedRAbundFloatVectors();
823 string lastLabel = lookupFloat[0]->getLabel();
825 if (label == "") { label = lastLabel; delete input; return 0; }
827 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
828 set<string> labels; labels.insert(label);
829 set<string> processedLabels;
830 set<string> userLabels = labels;
832 //as long as you are not at the end of the file or done wih the lines you want
833 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
835 if (m->control_pressed) { delete input; return 0; }
837 if(labels.count(lookupFloat[0]->getLabel()) == 1){
838 processedLabels.insert(lookupFloat[0]->getLabel());
839 userLabels.erase(lookupFloat[0]->getLabel());
843 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
844 string saveLabel = lookupFloat[0]->getLabel();
846 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
847 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
849 processedLabels.insert(lookupFloat[0]->getLabel());
850 userLabels.erase(lookupFloat[0]->getLabel());
852 //restore real lastlabel to save below
853 lookupFloat[0]->setLabel(saveLabel);
857 lastLabel = lookupFloat[0]->getLabel();
859 //get next line to process
860 //prevent memory leak
861 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
862 lookupFloat = input->getSharedRAbundFloatVectors();
866 if (m->control_pressed) { delete input; return 0; }
868 //output error messages about any remaining user labels
869 set<string>::iterator it;
870 bool needToRun = false;
871 for (it = userLabels.begin(); it != userLabels.end(); it++) {
872 m->mothurOut("Your file does not include the label " + *it);
873 if (processedLabels.count(lastLabel) != 1) {
874 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
877 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
881 //run last label if you need to
882 if (needToRun == true) {
883 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
884 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
890 catch(exception& e) {
891 m->errorOut(e, "IndicatorCommand", "getShared");
895 /*****************************************************************/