X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=c97e92ed7253cf1cdf00882a6e1155c1b86fe60a;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=b87e9c0b1ea0f5e84cbdf87a341c2fc6d393699d;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index b87e9c0..c97e92e 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -9,6 +9,54 @@ #include "parsimonycommand.h" +//********************************************************************************************************************** +vector ParsimonyCommand::getValidParameters(){ + try { + string Array[] = {"random","groups","iters","processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ParsimonyCommand::ParsimonyCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParsimonyCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParsimonyCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getRequiredFiles"); + exit(1); + } +} /***********************************************************/ ParsimonyCommand::ParsimonyCommand(string option) { try { @@ -21,7 +69,7 @@ ParsimonyCommand::ParsimonyCommand(string option) { else { //valid paramters for this command - string Array[] = {"random","groups","iters","outputdir","inputdir"}; + string Array[] = {"random","groups","processors","iters","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -34,6 +82,11 @@ ParsimonyCommand::ParsimonyCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; } //are you trying to use parsimony without reading a tree or saying you want random distribution @@ -43,19 +96,22 @@ ParsimonyCommand::ParsimonyCommand(string option) { } //if the user changes the output directory command factory will send this info to us in the output parameter - string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; if (randomtree == "") { outputDir += m->hasPath(globaldata->inputFileName); } } //check for optional parameter and set defaults // ...at some point should added some additional type checking... groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; globaldata->Groups.clear(); } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } convert(itersString, iters); + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); if (abort == false) { //randomtree will tell us if user had their own treefile or if they just want the random distribution @@ -64,20 +120,23 @@ ParsimonyCommand::ParsimonyCommand(string option) { T = globaldata->gTree; tmap = globaldata->gTreemap; - if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); } - output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString); - outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony"); + if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); } + output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString); + outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony"); + outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony"); - sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary"; - openOutputFile(sumFile, outSum); + sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary"; + m->openOutputFile(sumFile, outSum); outputNames.push_back(sumFile); + outputTypes["psummary"].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)); + if(outputDir == "") { outputDir += m->hasPath(randomtree); } + output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString); + outputNames.push_back(outputDir+ m->getSimpleName(randomtree)); + outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree)); } //set users groups to analyze @@ -106,10 +165,11 @@ ParsimonyCommand::ParsimonyCommand(string option) { void ParsimonyCommand::help(){ try { 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 parsimony command parameters are random, groups, processors 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("The processors parameter allows you to specify the number of processors to use. The default is 1.\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"); @@ -134,7 +194,7 @@ int ParsimonyCommand::execute() { 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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } @@ -153,12 +213,12 @@ int ParsimonyCommand::execute() { if (randomtree == "") { //get pscores for users trees for (int i = 0; i < T.size(); i++) { - userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC. + userData = pars->getValues(T[i], processors, outputDir); //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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } @@ -191,12 +251,12 @@ int ParsimonyCommand::execute() { randT->assembleRandomTree(); //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars->getValues(randT, processors, outputDir); 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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } @@ -233,19 +293,19 @@ int ParsimonyCommand::execute() { 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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars->getValues(randT, processors, outputDir); 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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } @@ -302,7 +362,7 @@ int ParsimonyCommand::execute() { 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()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); globaldata->Groups.clear(); return 0; } @@ -327,7 +387,7 @@ int ParsimonyCommand::execute() { if (m->control_pressed) { delete pars; delete util; delete output; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }