X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensuscommand.cpp;h=e522b098f0703d6909f1906c3039fb4459e99854;hb=ae9c5b48da9047548f86fc84897926d9f5102312;hp=8c34068bba76f4347d8783b35c74af69979921ea;hpb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;p=mothur.git diff --git a/consensuscommand.cpp b/consensuscommand.cpp index 8c34068..e522b09 100644 --- a/consensuscommand.cpp +++ b/consensuscommand.cpp @@ -10,63 +10,94 @@ #include "consensuscommand.h" //********************************************************************************************************************** - -ConcensusCommand::ConcensusCommand(string fileroot){ +vector ConcensusCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - abort = false; - - filename = fileroot; - - t = globaldata->gTree; - + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "ConcensusCommand"); + m->errorOut(e, "ConcensusCommand", "setParameters"); exit(1); } } - //********************************************************************************************************************** - -void ConcensusCommand::help(){ +string ConcensusCommand::getHelpString(){ try { - mothurOut("The consensus command can only be executed after a successful read.tree command.\n"); - mothurOut("The consensus command has no parameters.\n"); - mothurOut("The consensus command should be in the following format: consensus().\n"); - mothurOut("The consensus command output two files: .consensus.tre and .consensuspairs.\n"); - mothurOut("The .consensus.tre file contains the consensus tree of the trees in your input file.\n"); - mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n"); - mothurOut("The .consensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the consensus tree \n"); - mothurOut("is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n\n"); + string helpString = ""; + helpString += "The consensus command can only be executed after a successful read.tree command.\n"; + helpString += "The consensus command has no parameters.\n"; + helpString += "The consensus command should be in the following format: consensus().\n"; + helpString += "The consensus command output two files: .consensus.tre and .consensuspairs.\n"; + helpString += "The .consensus.tre file contains the consensus tree of the trees in your input file.\n"; + helpString += "The branch lengths are the percentage of trees in your input file that had the given pair.\n"; + helpString += "The .consensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the consensus tree \n"; + helpString += "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n"; + return helpString; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "help"); + m->errorOut(e, "ConcensusCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +ConcensusCommand::ConcensusCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + outputTypes["nodepairs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ConcensusCommand", "ConcensusCommand"); exit(1); } } - //********************************************************************************************************************** -ConcensusCommand::~ConcensusCommand(){} - +ConcensusCommand::ConcensusCommand(string fileroot) { + try { + abort = false; calledHelp = false; + + setParameters(); + + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + outputTypes["nodepairs"] = tempOutNames; + + filename = fileroot; + + } + catch(exception& e) { + m->errorOut(e, "ConcensusCommand", "ConcensusCommand"); + exit(1); + } +} //********************************************************************************************************************** int ConcensusCommand::execute(){ try { - if (abort == true) { return 0; } - else { - numNodes = t[0]->getNumNodes(); - numLeaves = t[0]->getNumLeaves(); - } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + + m->mothurOut("This command is not currently in use."); m->mothurOutEndLine(); + /* + t = globaldata->gTree; + numNodes = t[0]->getNumNodes(); + numLeaves = t[0]->getNumLeaves(); + //get the possible pairings - getSets(); + getSets(); + + if (m->control_pressed) { return 0; } //open file for pairing not included in the tree - notIncluded = filename + ".cons.pairs"; - openOutputFile(notIncluded, out2); + notIncluded = filename + ".cons.pairs"; outputNames.push_back(notIncluded); outputTypes["nodepairs"].push_back(notIncluded); + m->openOutputFile(notIncluded, out2); consensusTree = new Tree(); @@ -82,8 +113,12 @@ int ConcensusCommand::execute(){ buildConcensusTree(treeSet); + if (m->control_pressed) { delete consensusTree; return 0; } + consensusTree->assembleTree(); + if (m->control_pressed) { delete consensusTree; return 0; } + //output species in order out2 << "Species in Order: " << endl << endl; for (int i = 0; i < treeSet.size(); i++) { out2 << i+1 << ". " << treeSet[i] << endl; } @@ -91,8 +126,13 @@ int ConcensusCommand::execute(){ //output sets included out2 << endl << "Sets included in the consensus tree:" << endl << endl; + if (m->control_pressed) { delete consensusTree; return 0; } + vector temp; for (it2 = nodePairsInTree.begin(); it2 != nodePairsInTree.end(); it2++) { + + if (m->control_pressed) { delete consensusTree; return 0; } + //only output pairs not leaves if (it2->first.size() > 1) { temp.clear(); @@ -118,6 +158,9 @@ int ConcensusCommand::execute(){ //output sets not included out2 << endl << "Sets NOT included in the consensus tree:" << endl << endl; for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) { + + if (m->control_pressed) { delete consensusTree; return 0; } + temp.clear(); //initialize temp to all "." temp.resize(treeSet.size(), "."); @@ -136,19 +179,26 @@ int ConcensusCommand::execute(){ out2 << '\t' << it2->second << endl; } - outputFile = filename + ".cons.tre"; - openOutputFile(outputFile, out); + outputFile = filename + ".cons.tre"; outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); + m->openOutputFile(outputFile, out); - consensusTree->printForBoot(out); + consensusTree->print(out, "boot"); out.close(); out2.close(); delete consensusTree; + //set first tree file as new current treefile + string currentTree = ""; + itTypes = outputTypes.find("tree"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); } + } + */ return 0; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "execute"); + m->errorOut(e, "ConcensusCommand", "execute"); exit(1); } } @@ -159,6 +209,8 @@ int ConcensusCommand::buildConcensusTree(vector nodeSet) { vector leftChildSet; vector rightChildSet; + if (m->control_pressed) { return 1; } + //if you are at a leaf if (nodeSet.size() == 1) { //return the vector index of the leaf you are at @@ -180,13 +232,13 @@ int ConcensusCommand::buildConcensusTree(vector nodeSet) { } catch(exception& e) { - errorOut(e, "ConcensusCommand", "buildConcensusTree"); + m->errorOut(e, "ConcensusCommand", "buildConcensusTree"); exit(1); } } //********************************************************************************************************************** -void ConcensusCommand::getSets() { +int ConcensusCommand::getSets() { try { vector temp; treeSet.clear(); @@ -196,6 +248,9 @@ void ConcensusCommand::getSets() { //for each non-leaf node get descendant info. for (int j = numLeaves; j < numNodes; j++) { + + if (m->control_pressed) { return 1; } + temp.clear(); //go through pcounts and pull out descendants for (it = t[i]->tree[j].pcount.begin(); it != t[i]->tree[j].pcount.end(); it++) { @@ -219,6 +274,8 @@ void ConcensusCommand::getSets() { //you want the leaves in there but with insignifigant sightings value so it is added last //for each leaf node get descendant info. for (int j = 0; j < numLeaves; j++) { + + if (m->control_pressed) { return 1; } //only need the first one since leaves have no descendants but themselves it = t[0]->tree[j].pcount.begin(); @@ -239,19 +296,21 @@ void ConcensusCommand::getSets() { //set initial rating on pairs to sightings + subgroup sightings while (nodePairsCopy.size() != 0) { + if (m->control_pressed) { return 1; } - vector small = getSmallest(nodePairsCopy); + vector smallOne = getSmallest(nodePairsCopy); - int subgrouprate = getSubgroupRating(small); + int subgrouprate = getSubgroupRating(smallOne); - nodePairsInitialRate[small] = nodePairs[small] + subgrouprate; + nodePairsInitialRate[smallOne] = nodePairs[smallOne] + subgrouprate; - nodePairsCopy.erase(small); + nodePairsCopy.erase(smallOne); } + return 0; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "getSets"); + m->errorOut(e, "ConcensusCommand", "getSets"); exit(1); } } @@ -268,7 +327,7 @@ vector ConcensusCommand::getSmallest(map< vector, int> nodes) { return smallest; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "getSmallest"); + m->errorOut(e, "ConcensusCommand", "getSmallest"); exit(1); } } @@ -306,7 +365,7 @@ vector ConcensusCommand::getNextAvailableSet(vector bigset, vect } catch(exception& e) { - errorOut(e, "ConcensusCommand", "getNextAvailableSet"); + m->errorOut(e, "ConcensusCommand", "getNextAvailableSet"); exit(1); } } @@ -373,7 +432,7 @@ int ConcensusCommand::getSubgroupRating(vector group) { return rate; } catch(exception& e) { - errorOut(e, "ConcensusCommand", "getSubgroupRating"); + m->errorOut(e, "ConcensusCommand", "getSubgroupRating"); exit(1); } } @@ -397,7 +456,7 @@ vector ConcensusCommand::getRestSet(vector bigset, vectorerrorOut(e, "ConcensusCommand", "getRestSet"); exit(1); } } @@ -424,7 +483,7 @@ bool ConcensusCommand::isSubset(vector bigset, vector subset) { } catch(exception& e) { - errorOut(e, "ConcensusCommand", "isSubset"); + m->errorOut(e, "ConcensusCommand", "isSubset"); exit(1); } } @@ -442,7 +501,7 @@ int ConcensusCommand::findSpot(string node) { } catch(exception& e) { - errorOut(e, "ConcensusCommand", "findSpot"); + m->errorOut(e, "ConcensusCommand", "findSpot"); exit(1); } }