X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=b87e9c0b1ea0f5e84cbdf87a341c2fc6d393699d;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=da997c13b0c150369e15d94ccabb95f8dc3b8d26;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index da997c1..b87e9c0 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -10,12 +10,12 @@ #include "parsimonycommand.h" /***********************************************************/ -ParsimonyCommand::ParsimonyCommand(string option) { +ParsimonyCommand::ParsimonyCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; Groups.clear(); - + //allow user to run help if(option == "help") { help(); abort = true; } @@ -39,7 +39,7 @@ ParsimonyCommand::ParsimonyCommand(string option) { //are you trying to use parsimony without reading a tree or saying you want random distribution if (randomtree == "") { if (globaldata->gTree.size() == 0) { - mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); mothurOutEndLine(); abort = true; } + m->mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); m->mothurOutEndLine(); abort = true; } } //if the user changes the output directory command factory will send this info to us in the output parameter @@ -66,15 +66,18 @@ ParsimonyCommand::ParsimonyCommand(string option) { if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); } output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString); + outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony"); sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary"; openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); }else { //user wants random distribution savetmap = globaldata->gTreemap; getUserInput(); if(outputDir == "") { outputDir += hasPath(randomtree); } output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString); + outputNames.push_back(outputDir+ getSimpleName(randomtree)); } //set users groups to analyze @@ -93,7 +96,7 @@ ParsimonyCommand::ParsimonyCommand(string option) { } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); exit(1); } } @@ -102,18 +105,18 @@ ParsimonyCommand::ParsimonyCommand(string option) { void ParsimonyCommand::help(){ try { - mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n"); - mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n"); - mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n"); - mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n"); - mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n"); - mothurOut("Example parsimony(random=out, iters=500).\n"); - mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n"); - mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n"); + m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n"); + m->mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n"); + m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n"); + m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n"); + m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n"); + m->mothurOut("Example parsimony(random=out, iters=500).\n"); + m->mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n"); + m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n"); } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "help"); + m->errorOut(e, "ParsimonyCommand", "help"); exit(1); } } @@ -128,6 +131,15 @@ int ParsimonyCommand::execute() { Progress* reading; reading = new Progress("Comparing to random:", iters); + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } + + //get pscore for users tree userData.resize(numComp,0); //data = AB, AC, BC, ABC. randomData.resize(numComp,0); //data = AB, AC, BC, ABC. @@ -142,6 +154,15 @@ int ParsimonyCommand::execute() { //get pscores for users trees for (int i = 0; i < T.size(); i++) { userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC. + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } + //output scores for each combination for(int k = 0; k < numComp; k++) { @@ -162,6 +183,7 @@ int ParsimonyCommand::execute() { //get pscores for random trees for (int j = 0; j < iters; j++) { + //create new tree with same num nodes and leaves as users randT = new Tree(); @@ -170,6 +192,14 @@ int ParsimonyCommand::execute() { //get pscore of random tree randomData = pars->getValues(randT); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores @@ -193,14 +223,32 @@ int ParsimonyCommand::execute() { }else { //get pscores for random trees for (int j = 0; j < iters; j++) { + //create new tree with same num nodes and leaves as users randT = new Tree(); //create random relationships between nodes randT->assembleRandomTree(); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + globaldata->gTreemap = savetmap; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } + //get pscore of random tree randomData = pars->getValues(randT); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + globaldata->gTreemap = savetmap; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores @@ -250,6 +298,15 @@ int ParsimonyCommand::execute() { } } + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + else { globaldata->gTreemap = savetmap; } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + globaldata->Groups.clear(); + return 0; + } + //finish progress bar reading->finish(); delete reading; @@ -268,11 +325,23 @@ int ParsimonyCommand::execute() { //reset groups parameter globaldata->Groups.clear(); + if (m->control_pressed) { + delete pars; delete util; delete output; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "execute"); + m->errorOut(e, "ParsimonyCommand", "execute"); exit(1); } } @@ -305,16 +374,16 @@ void ParsimonyCommand::printParsimonyFile() { } } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "printParsimonyFile"); + m->errorOut(e, "ParsimonyCommand", "printParsimonyFile"); exit(1); } } /***********************************************************/ -void ParsimonyCommand::printUSummaryFile() { +int ParsimonyCommand::printUSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; - mothurOut("Tree#\tGroups\tParsScore\tParsSig"); mothurOutEndLine(); + m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -323,22 +392,24 @@ void ParsimonyCommand::printUSummaryFile() { //print each line for (int i = 0; i< T.size(); i++) { for(int a = 0; a < numComp; a++) { + if (m->control_pressed) { outSum.close(); return 0; } if (UScoreSig[a][i] > (1/(float)iters)) { outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl; cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl; - mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine(); }else { outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl; cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl; - mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine(); } } } outSum.close(); + return 0; } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "printUSummaryFile"); + m->errorOut(e, "ParsimonyCommand", "printUSummaryFile"); exit(1); } } @@ -350,18 +421,18 @@ void ParsimonyCommand::getUserInput() { //create treemap tmap = new TreeMap(); - mothurOut("Please enter the number of groups you would like to analyze: "); + m->mothurOut("Please enter the number of groups you would like to analyze: "); cin >> numGroups; - mothurOutJustToLog(toString(numGroups)); mothurOutEndLine(); + m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine(); int num, count; count = 1; numEachGroup.resize(numGroups, 0); for (int i = 1; i <= numGroups; i++) { - mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); + m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; - mothurOutJustToLog(toString(num)); mothurOutEndLine(); + m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine(); //set tmaps seqsPerGroup tmap->seqsPerGroup[toString(i)] = num; @@ -387,7 +458,7 @@ void ParsimonyCommand::getUserInput() { } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "getUserInput"); + m->errorOut(e, "ParsimonyCommand", "getUserInput"); exit(1); } }