X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=heatmapsimcommand.cpp;h=b9216e4a990e7818c4ed5ce8759c706a44530c26;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hp=331ff7963460ef9d952a71382615bdf54e195677;hpb=37e0d78135e32b5aa58ca163f4d416716c78b67f;p=mothur.git diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 331ff79..b9216e4 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -52,7 +52,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ //make sure the user has already run the read.otu command if (globaldata->getSharedFile() == "") { - cout << "You must read a list and a group, or a shared before you can use the heatmap.sim command." << endl; abort = true; + mothurOut("You must read a list and a group, or a shared before you can use the heatmap.sim command."); mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults @@ -72,7 +72,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ } //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } + if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } //if the user has not specified any line or labels use the ones from read.otu else if ((line == "") && (label == "")) { allLines = globaldata->allLines; @@ -132,40 +132,32 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** void HeatMapSimCommand::help(){ try { - cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n"; - cout << "The heatmap.sim command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n"; - cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n"; - cout << "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n"; - cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n"; + mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n"); + mothurOut("The heatmap.sim command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time.\n"); + mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n"); + mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes.\n"); + mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels).\n"); + mothurOut("Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund).\n"); + mothurOut("The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used.\n"); validCalculator->printCalc("heat", cout); - cout << "The default value for calc is jclass-thetayc." << "\n"; - cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n"; + mothurOut("The default value for calc is jclass-thetayc.\n"); + mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "HeatMapSimCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -189,7 +181,7 @@ int HeatMapSimCommand::execute(){ int count = 1; //if the users entered no valid calculators don't execute command - if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; } + if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; } //you have groups read = new ReadOTUFile(globaldata->inputFileName); @@ -199,7 +191,7 @@ int HeatMapSimCommand::execute(){ lookup = input->getSharedRAbundVectors(); string lastLabel = lookup[0]->getLabel(); - if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;} + if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0;} //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; @@ -212,7 +204,7 @@ int HeatMapSimCommand::execute(){ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); heatmap->getPic(lookup, heatCalculators); processedLabels.insert(lookup[0]->getLabel()); @@ -225,7 +217,7 @@ int HeatMapSimCommand::execute(){ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); heatmap->getPic(lookup, heatCalculators); processedLabels.insert(lookup[0]->getLabel()); @@ -246,12 +238,12 @@ int HeatMapSimCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; + mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - cout << ". I will use " << lastLabel<< "." << endl; + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLabel << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } @@ -260,7 +252,7 @@ int HeatMapSimCommand::execute(){ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); heatmap->getPic(lookup, heatCalculators); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } @@ -272,13 +264,9 @@ int HeatMapSimCommand::execute(){ return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "HeatMapSimCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************