X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.cpp;h=d88bec0147095a1ed8e57e14c7e771548f86ffe6;hb=f37a59b81c339f574d97042ff6e364146feb457a;hp=3b0d7984bc1d0be02cb66c9d816f72df94e48f36;hpb=49b8297d25caae7ad4cf1e5208a4a66fdfe071fe;p=mothur.git diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 3b0d798..d88bec0 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -27,7 +27,6 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ globaldata = GlobalData::getInstance(); abort = false; allLines = 1; - lines.clear(); labels.clear(); Groups.clear(); Estimators.clear(); @@ -37,7 +36,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ else { //valid paramters for this command - string AlignArray[] = {"groups","line","label", "calc"}; + string AlignArray[] = {"groups","label", "calc"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -52,18 +51,11 @@ 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 // ...at some point should added some additional type checking... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - } - label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { @@ -71,13 +63,10 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ else { allLines = 1; } } - //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 the user has not specified any line or labels use the ones from read.otu - else if ((line == "") && (label == "")) { + //if the user has not specified any labels use the ones from read.otu + if (label == "") { allLines = globaldata->allLines; labels = globaldata->labels; - lines = globaldata->lines; } calc = validParameter.validFile(parameters, "calc", false); @@ -132,49 +121,43 @@ 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 and label. No parameters are required.\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 label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n"); + mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n"); + mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n"); + mothurOut("The default value for groups is all the groups in your groupfile, and all labels 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 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); - } } //********************************************************************************************************************** HeatMapSimCommand::~HeatMapSimCommand(){ - delete input; - delete read; - delete heatmap; - delete validCalculator; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete heatmap; + delete validCalculator; + } } //********************************************************************************************************************** @@ -184,10 +167,8 @@ int HeatMapSimCommand::execute(){ if (abort == true) { return 0; } - 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); @@ -195,66 +176,70 @@ int HeatMapSimCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; + 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; set userLabels = labels; - set userLines = lines; - //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); heatmap->getPic(lookup, heatCalculators); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - heatmap->getPic(lastLookup, heatCalculators); + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + heatmap->getPic(lookup, heatCalculators); - processedLabels.insert(lastLookup[0]->getLabel()); - userLabels.erase(lastLookup[0]->getLabel()); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); } //prevent memory leak - if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } - lastLookup = lookup; + + lastLabel = lookup[0]->getLabel(); //get next line to process + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); - count++; } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastLookup[0]->getLabel()) != 1) { - cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl; + mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - heatmap->getPic(lastLookup, heatCalculators); + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + heatmap->getPic(lookup, heatCalculators); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } //reset groups parameter globaldata->Groups.clear(); @@ -262,13 +247,9 @@ 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); - } } //**********************************************************************************************************************