X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=b8956ecd6b495525d922c296484a433cd97ebdc9;hb=d01397212a287495d3d0ec00beea93759bf25402;hp=74327ba684a535d0dd62125a5848e159bf6ddcc9;hpb=71b2121662daae3f9044252887d1c16eeddd85bb;p=mothur.git diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 74327ba..b8956ec 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -35,12 +35,11 @@ //********************************************************************************************************************** -SummarySharedCommand::SummarySharedCommand(string option){ +SummarySharedCommand::SummarySharedCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; allLines = 1; - lines.clear(); labels.clear(); Estimators.clear(); @@ -49,7 +48,7 @@ SummarySharedCommand::SummarySharedCommand(string option){ else { //valid paramters for this command - string Array[] = {"line","label","calc","groups"}; + string Array[] = {"label","calc","groups","all","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -64,18 +63,17 @@ SummarySharedCommand::SummarySharedCommand(string option){ //make sure the user has already run the read.otu command if (globaldata->getSharedFile() == "") { - mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true; + m->mothurOut("You must read a list and a group, or a shared before you can use the summary.shared 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 += hasPath(globaldata->getSharedFile()); //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 { @@ -83,13 +81,10 @@ SummarySharedCommand::SummarySharedCommand(string option){ 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; } calc = validParameter.validFile(parameters, "calc", false); @@ -106,6 +101,9 @@ SummarySharedCommand::SummarySharedCommand(string option){ globaldata->Groups = Groups; } + string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; } + all = isTrue(temp); + if (abort == false) { validCalculator = new ValidCalculators(); @@ -159,14 +157,16 @@ SummarySharedCommand::SummarySharedCommand(string option){ } } - outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); + outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary"; openOutputFile(outputFileName, outputFileHandle); + outputNames.push_back(outputFileName); + mult = false; } } } catch(exception& e) { - errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); + m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); exit(1); } } @@ -175,20 +175,22 @@ SummarySharedCommand::SummarySharedCommand(string option){ void SummarySharedCommand::help(){ try { - mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n"); - mothurOut("The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use \n"); - mothurOut("both the line and label parameters at the same time. The summary.shared command should be in the following format: \n"); - mothurOut("summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups).\n"); - mothurOut("Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"); + m->mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n"); + m->mothurOut("The summary.shared command parameters are label, calc and all. No parameters are required.\n"); + m->mothurOut("The summary.shared command should be in the following format: \n"); + m->mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n"); + m->mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"); validCalculator->printCalc("sharedsummary", cout); - mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n"); - mothurOut("The default value for groups is all the groups in your groupfile.\n"); - mothurOut("The label and line parameters are used to analyze specific lines in your input.\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 2 valid groups.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n"); + m->mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n"); + m->mothurOut("The default value for groups is all the groups in your groupfile.\n"); + m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); + m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n"); + m->mothurOut("If you use sharedchao and run into memory issues, set all to false. \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 2 valid groups.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); } catch(exception& e) { - errorOut(e, "SummarySharedCommand", "help"); + m->errorOut(e, "SummarySharedCommand", "help"); exit(1); } } @@ -209,14 +211,14 @@ int SummarySharedCommand::execute(){ if (abort == true) { return 0; } - int count = 1; - //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } //check if any calcs can do multiples else{ - for (int i = 0; i < sumCalculators.size(); i++) { - if (sumCalculators[i]->getMultiple() == true) { mult = true; } + if (all){ + for (int i = 0; i < sumCalculators.size(); i++) { + if (sumCalculators[i]->getMultiple() == true) { mult = true; } + } } } @@ -239,6 +241,7 @@ int SummarySharedCommand::execute(){ if (mult == true) { outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary"); openOutputFile(outAllFileName, outAll); + outputNames.push_back(outAllFileName); outAll << "label" <<'\t' << "comparison" << '\t'; for(int i=0;imothurOut("I cannot run the command without at least 2 valid groups."); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } //close files and clean up @@ -262,37 +265,60 @@ int SummarySharedCommand::execute(){ mult = false; outAll.close(); remove(outAllFileName.c_str()); + outputNames.pop_back(); } - + + if (m->control_pressed) { + if (mult) { outAll.close(); remove(outAllFileName.c_str()); } + outputFileHandle.close(); remove(outputFileName.c_str()); + delete input; globaldata->ginput = NULL; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for(int i=0;iGroups.clear(); + 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 (m->control_pressed) { + if (mult) { outAll.close(); remove(outAllFileName.c_str()); } + outputFileHandle.close(); remove(outputFileName.c_str()); + delete input; globaldata->ginput = NULL; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for(int i=0;iGroups.clear(); + return 0; + } + - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ - mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } if ((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()); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } - - lastLabel = lookup[0]->getLabel(); @@ -300,33 +326,41 @@ int SummarySharedCommand::execute(){ //prevent memory leak for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); - count++; } + if (m->control_pressed) { + if (mult) { outAll.close(); remove(outAllFileName.c_str()); } + outputFileHandle.close(); remove(outputFileName.c_str()); + delete input; globaldata->ginput = NULL; + for(int i=0;iGroups.clear(); + 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()); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - + //reset groups parameter globaldata->Groups.clear(); @@ -335,19 +369,29 @@ int SummarySharedCommand::execute(){ if (mult == true) { outAll.close(); } for(int i=0;iginput = NULL; + + if (m->control_pressed) { + remove(outAllFileName.c_str()); + remove(outputFileName.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, "SummarySharedCommand", "execute"); + m->errorOut(e, "SummarySharedCommand", "execute"); exit(1); } } /***********************************************************/ -void SummarySharedCommand::process(vector thisLookup) { +int SummarySharedCommand::process(vector thisLookup) { try { //loop through calculators and add to file all for all calcs that can do mutiple groups if (mult == true) { @@ -365,6 +409,9 @@ void SummarySharedCommand::process(vector thisLookup) { for(int i=0;igetMultiple() == true) { sumCalculators[i]->getValues(thisLookup); + + if (m->control_pressed) { return 1; } + outAll << '\t'; sumCalculators[i]->print(outAll); } @@ -393,6 +440,9 @@ void SummarySharedCommand::process(vector thisLookup) { for(int i=0;igetValues(subset); //saves the calculator outputs + + if (m->control_pressed) { return 1; } + outputFileHandle << '\t'; sumCalculators[i]->print(outputFileHandle); } @@ -400,10 +450,10 @@ void SummarySharedCommand::process(vector thisLookup) { } n++; } - + return 0; } catch(exception& e) { - errorOut(e, "SummarySharedCommand", "process"); + m->errorOut(e, "SummarySharedCommand", "process"); exit(1); } }