X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=d63930d071da178e5ddcfdb82950ae37b03718cd;hb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;hp=40b911bb8c844ad252a714383ce93109772209a0;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 40b911b..d63930d 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -33,9 +33,76 @@ #include "whittaker.h" - //********************************************************************************************************************** - +vector CollectSharedCommand::getValidParameters(){ + try { + string AlignArray[] = {"freq","label","calc","groups","all","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "CollectSharedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector CollectSharedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "CollectSharedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector CollectSharedCommand::getRequiredFiles(){ + try { + string AlignArray[] = {"shared"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "CollectSharedCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +CollectSharedCommand::CollectSharedCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["sharedchao"] = tempOutNames; + outputTypes["sharedsobs"] = tempOutNames; + outputTypes["sharedace"] = tempOutNames; + outputTypes["jabund"] = tempOutNames; + outputTypes["sorabund"] = tempOutNames; + outputTypes["jclass"] = tempOutNames; + outputTypes["sorclass"] = tempOutNames; + outputTypes["jest"] = tempOutNames; + outputTypes["sorest"] = tempOutNames; + outputTypes["thetayc"] = tempOutNames; + outputTypes["thetan"] = tempOutNames; + outputTypes["kstest"] = tempOutNames; + outputTypes["whittaker"] = tempOutNames; + outputTypes["sharednseqs"] = tempOutNames; + outputTypes["ochiai"] = tempOutNames; + outputTypes["anderberg"] = tempOutNames; + outputTypes["skulczynski"] = tempOutNames; + outputTypes["kulczynskicody"] = tempOutNames; + outputTypes["lennon"] = tempOutNames; + outputTypes["morisitahorn"] = tempOutNames; + outputTypes["braycurtis"] = tempOutNames; + + } + catch(exception& e) { + m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** CollectSharedCommand::CollectSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); @@ -63,6 +130,31 @@ CollectSharedCommand::CollectSharedCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["sharedchao"] = tempOutNames; + outputTypes["sharedsobs"] = tempOutNames; + outputTypes["sharedace"] = tempOutNames; + outputTypes["jabund"] = tempOutNames; + outputTypes["sorabund"] = tempOutNames; + outputTypes["jclass"] = tempOutNames; + outputTypes["sorclass"] = tempOutNames; + outputTypes["jest"] = tempOutNames; + outputTypes["sorest"] = tempOutNames; + outputTypes["thetayc"] = tempOutNames; + outputTypes["thetan"] = tempOutNames; + outputTypes["kstest"] = tempOutNames; + outputTypes["whittaker"] = tempOutNames; + outputTypes["sharednseqs"] = tempOutNames; + outputTypes["ochiai"] = tempOutNames; + outputTypes["anderberg"] = tempOutNames; + outputTypes["skulczynski"] = tempOutNames; + outputTypes["kulczynskicody"] = tempOutNames; + outputTypes["lennon"] = tempOutNames; + outputTypes["morisitahorn"] = tempOutNames; + outputTypes["braycurtis"] = tempOutNames; + + //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 = ""; } @@ -79,7 +171,7 @@ CollectSharedCommand::CollectSharedCommand(string option) { 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; } } @@ -94,12 +186,12 @@ CollectSharedCommand::CollectSharedCommand(string option) { else { if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); } globaldata->Groups = Groups; @@ -108,12 +200,12 @@ CollectSharedCommand::CollectSharedCommand(string option) { convert(temp, freq); temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; } - all = isTrue(temp); + all = m->isTrue(temp); if (abort == false) { - if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); } - string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName)); + if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); } + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)); format = globaldata->getFormat(); int i; @@ -124,67 +216,67 @@ CollectSharedCommand::CollectSharedCommand(string option) { if (validCalculator->isValidCalculator("shared", Estimators[i]) == true) { if (Estimators[i] == "sharedchao") { cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao"))); - outputNames.push_back(fileNameRoot+"shared.chao"); + outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao"); }else if (Estimators[i] == "sharedsobs") { cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs"))); - outputNames.push_back(fileNameRoot+"shared.sobs"); + outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs"); }else if (Estimators[i] == "sharedace") { cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace"))); - outputNames.push_back(fileNameRoot+"shared.ace"); + outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace"); }else if (Estimators[i] == "jabund") { cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund"))); - outputNames.push_back(fileNameRoot+"jabund"); + outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund"); }else if (Estimators[i] == "sorabund") { cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund"))); - outputNames.push_back(fileNameRoot+"sorabund"); + outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund"); }else if (Estimators[i] == "jclass") { cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass"))); - outputNames.push_back(fileNameRoot+"jclass"); + outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass"); }else if (Estimators[i] == "sorclass") { cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass"))); - outputNames.push_back(fileNameRoot+"sorclass"); + outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass"); }else if (Estimators[i] == "jest") { cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest"))); - outputNames.push_back(fileNameRoot+"jest"); + outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest"); }else if (Estimators[i] == "sorest") { cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest"))); - outputNames.push_back(fileNameRoot+"sorest"); + outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest"); }else if (Estimators[i] == "thetayc") { cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc"))); - outputNames.push_back(fileNameRoot+"thetayc"); + outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc"); }else if (Estimators[i] == "thetan") { cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan"))); - outputNames.push_back(fileNameRoot+"thetan"); + outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan"); }else if (Estimators[i] == "kstest") { cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest"))); - outputNames.push_back(fileNameRoot+"kstest"); + outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest"); }else if (Estimators[i] == "whittaker") { cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker"))); - outputNames.push_back(fileNameRoot+"whittaker"); + outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker"); }else if (Estimators[i] == "sharednseqs") { cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs"))); - outputNames.push_back(fileNameRoot+"shared.nseqs"); + outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs"); }else if (Estimators[i] == "ochiai") { cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai"))); - outputNames.push_back(fileNameRoot+"ochiai"); + outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai"); }else if (Estimators[i] == "anderberg") { cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg"))); - outputNames.push_back(fileNameRoot+"anderberg"); + outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg"); }else if (Estimators[i] == "skulczynski") { cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski"))); - outputNames.push_back(fileNameRoot+"kulczynski"); + outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski"); }else if (Estimators[i] == "kulczynskicody") { cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody"))); - outputNames.push_back(fileNameRoot+"kulczynskicody"); + outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody"); }else if (Estimators[i] == "lennon") { cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon"))); - outputNames.push_back(fileNameRoot+"lennon"); + outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon"); }else if (Estimators[i] == "morisitahorn") { cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn"))); - outputNames.push_back(fileNameRoot+"morisitahorn"); + outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn"); }else if (Estimators[i] == "braycurtis") { cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis"))); - outputNames.push_back(fileNameRoot+"braycurtis"); + outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis"); } } } @@ -263,7 +355,7 @@ int CollectSharedCommand::execute(){ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if (m->control_pressed) { - 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(); for(int i=0;iGroups.clear(); @@ -283,7 +375,7 @@ int CollectSharedCommand::execute(){ } //you have a label the user want that is smaller than this label and the last label has not already been processed - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = order->getLabel(); delete order; @@ -311,7 +403,7 @@ int CollectSharedCommand::execute(){ } if (m->control_pressed) { - 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(); for(int i=0;iGroups.clear(); return 0; @@ -341,7 +433,7 @@ int CollectSharedCommand::execute(){ delete cCurve; if (m->control_pressed) { - 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(); for(int i=0;iGroups.clear();