X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.cpp;h=608c0a06a93b955c6021dbb565df7b3d98cb13ea;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=38cf8cb6a1c189c2f2d3451d63c3891c65dbe499;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git diff --git a/venncommand.cpp b/venncommand.cpp index 38cf8cb..608c0a0 100644 --- a/venncommand.cpp +++ b/venncommand.cpp @@ -19,20 +19,19 @@ //********************************************************************************************************************** -VennCommand::VennCommand(string option){ +VennCommand::VennCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; allLines = 1; - lines.clear(); labels.clear(); - + //allow user to run help if(option == "help") { help(); abort = true; } else { //valid paramters for this command - string AlignArray[] = {"groups","line","label","calc", "abund"}; + string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -47,38 +46,34 @@ VennCommand::VennCommand(string option){ //make sure the user has already run the read.otu command if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) { - mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true; + m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); abort = true; + } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } //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 { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - //make sure user did not use both the line and label parameters - 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 == "")) { + //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; } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -94,7 +89,7 @@ VennCommand::VennCommand(string option){ else { calc = "sharedsobs"; } } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } @@ -133,15 +128,18 @@ VennCommand::VennCommand(string option){ } } - venn = new Venn(); + //if the users entered no valid calculators don't execute command + if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true; } + else { venn = new Venn(outputDir); } } + } } catch(exception& e) { - errorOut(e, "VennCommand", "VennCommand"); + m->errorOut(e, "VennCommand", "VennCommand"); exit(1); } } @@ -150,21 +148,21 @@ VennCommand::VennCommand(string option){ void VennCommand::help(){ try { - mothurOut("The venn command can only be executed after a successful read.otu command.\n"); - mothurOut("The venn command parameters are groups, calc, abund, 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 venn diagram, you may only use a maximum of 4 groups.\n"); - mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n"); - mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund).\n"); - mothurOut("Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20).\n"); - mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used.\n"); - mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n"); - mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n"); - mothurOut("The only estmiator available four 4 groups is sharedsobs.\n"); - mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + m->mothurOut("The venn command can only be executed after a successful read.otu command.\n"); + m->mothurOut("The venn command parameters are groups, calc, abund and label. No parameters are required.\n"); + m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n"); + m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n"); + m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n"); + m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n"); + m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n"); + m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n"); + m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n"); + m->mothurOut("The only estmiator available four 4 groups is sharedsobs.\n"); + m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); } catch(exception& e) { - errorOut(e, "VennCommand", "help"); + m->errorOut(e, "VennCommand", "help"); exit(1); } } @@ -178,6 +176,7 @@ VennCommand::~VennCommand(){ delete read; delete venn; globaldata->sabund = NULL; + delete validCalculator; } } @@ -189,11 +188,8 @@ int VennCommand::execute(){ if (abort == true) { return 0; } - int count = 1; string lastLabel; - - //if the users entered no valid calculators don't execute command - if (vennCalculators.size() == 0) { return 0; } + vector outputNames; if (format == "sharedfile") { //you have groups @@ -216,39 +212,53 @@ int VennCommand::execute(){ //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; if (format != "list") { //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 (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); if (lookup.size() > 4) { - mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine(); + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine(); for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor } - venn->getPic(lookup, vennCalculators); + + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); if (lookup.size() > 4) { - mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine(); + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine(); for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor } - venn->getPic(lookup, vennCalculators); + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } @@ -257,36 +267,45 @@ int VennCommand::execute(){ //get next line to process for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); - count++; } + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } lookup = input->getSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); if (lookup.size() > 4) { - mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine(); + m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine(); for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor } - venn->getPic(lookup, vennCalculators); + vector outfilenames = venn->getPic(lookup, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } @@ -294,69 +313,110 @@ int VennCommand::execute(){ //reset groups parameter globaldata->Groups.clear(); + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + }else{ - while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + delete sabund; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } - if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){ + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ - mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine(); - venn->getPic(sabund, vennCalculators); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } + processedLabels.insert(sabund->getLabel()); userLabels.erase(sabund->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + delete sabund; sabund = input->getSAbundVector(lastLabel); - mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine(); - venn->getPic(sabund, vennCalculators); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } + processedLabels.insert(sabund->getLabel()); userLabels.erase(sabund->getLabel()); + + //restore real lastlabel to save below + sabund->setLabel(saveLabel); } lastLabel = sabund->getLabel(); delete sabund; sabund = input->getSAbundVector(); - count++; + } + + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - delete sabund; + if (sabund != NULL) { delete sabund; } sabund = input->getSAbundVector(lastLabel); - mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine(); - venn->getPic(sabund, vennCalculators); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + vector outfilenames = venn->getPic(sabund, vennCalculators); + for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } } + delete sabund; } + if (m->control_pressed) { + for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } } for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + + 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, "VennCommand", "execute"); + m->errorOut(e, "VennCommand", "execute"); exit(1); } }