X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=69dbef6d15791466813ba0ecdde87f6a68a55664;hb=5e5253ff472de3c6349e562d2580873287be0c65;hp=dc14e1670c5221599dd14929dd6d08fde6c6b766;hpb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;p=mothur.git diff --git a/hclustercommand.cpp b/hclustercommand.cpp index dc14e16..69dbef6 100644 --- a/hclustercommand.cpp +++ b/hclustercommand.cpp @@ -9,6 +9,56 @@ #include "hclustercommand.h" +//********************************************************************************************************************** +vector HClusterCommand::getValidParameters(){ + try { + string Array[] = {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HClusterCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +HClusterCommand::HClusterCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "HClusterCommand", "HClusterCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector HClusterCommand::getRequiredParameters(){ + try { + string Array[] = {"phylip","column","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HClusterCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector HClusterCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HClusterCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen. HClusterCommand::HClusterCommand(string option) { @@ -37,6 +87,12 @@ HClusterCommand::HClusterCommand(string option) { } } + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + globaldata->newRead(); //if the user changes the input directory command factory will send this info to us in the output parameter @@ -47,7 +103,7 @@ HClusterCommand::HClusterCommand(string option) { it = parameters.find("phylip"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["phylip"] = inputDir + it->second; } } @@ -55,7 +111,7 @@ HClusterCommand::HClusterCommand(string option) { it = parameters.find("column"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["column"] = inputDir + it->second; } } @@ -63,7 +119,7 @@ HClusterCommand::HClusterCommand(string option) { it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } @@ -105,25 +161,25 @@ HClusterCommand::HClusterCommand(string option) { convert(temp, precision); temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; } - hard = isTrue(temp); + hard = m->isTrue(temp); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } convert(temp, cutoff); - if (!hard) { cutoff += (5 / (precision * 10.0)); } + cutoff += (5 / (precision * 10.0)); method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; } - if ((method == "furthest") || (method == "nearest") || (method == "average")) { } - else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; } + if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { } + else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average or weighted."); m->mothurOutEndLine(); abort = true; } showabund = validParameter.validFile(parameters, "showabund", false); if (showabund == "not found") { showabund = "T"; } sort = validParameter.validFile(parameters, "sorted", false); if (sort == "not found") { sort = "F"; } - sorted = isTrue(sort); + sorted = m->isTrue(sort); timing = validParameter.validFile(parameters, "timing", false); if (timing == "not found") { timing = "F"; } @@ -131,20 +187,21 @@ HClusterCommand::HClusterCommand(string option) { if (abort == false) { - if (outputDir == "") { outputDir += hasPath(distfile); } - fileroot = outputDir + getRootName(getSimpleName(distfile)); + if (outputDir == "") { outputDir += m->hasPath(distfile); } + fileroot = outputDir + m->getRootName(m->getSimpleName(distfile)); if (method == "furthest") { tag = "fn"; } else if (method == "nearest") { tag = "nn"; } + else if (method == "weighted") { tag = "wn"; } else { tag = "an"; } - openOutputFile(fileroot+ tag + ".sabund", sabundFile); - openOutputFile(fileroot+ tag + ".rabund", rabundFile); - openOutputFile(fileroot+ tag + ".list", listFile); + m->openOutputFile(fileroot+ tag + ".sabund", sabundFile); + m->openOutputFile(fileroot+ tag + ".rabund", rabundFile); + m->openOutputFile(fileroot+ tag + ".list", listFile); - outputNames.push_back(fileroot+ tag + ".sabund"); - outputNames.push_back(fileroot+ tag + ".rabund"); - outputNames.push_back(fileroot+ tag + ".list"); + outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund"); + outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund"); + outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list"); } } } @@ -163,7 +220,7 @@ void HClusterCommand::help(){ m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n"); m->mothurOut("The hcluster command should be in the following format: \n"); m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"); - m->mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n"); + m->mothurOut("The acceptable hcluster methods are furthest, nearest, weighted and average.\n\n"); } catch(exception& e) { m->errorOut(e, "HClusterCommand", "help"); @@ -201,7 +258,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } @@ -217,7 +274,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } @@ -247,7 +304,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } @@ -261,7 +318,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } @@ -275,12 +332,18 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } - - float rndDist = roundDist(seqs[i].dist, precision); + + float rndDist; + if (hard) { + rndDist = m->ceilDist(seqs[i].dist, precision); + }else{ + rndDist = m->roundDist(seqs[i].dist, precision); + } + if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){ printData("unique"); @@ -302,7 +365,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - 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(); return 0; } @@ -330,7 +393,7 @@ int HClusterCommand::execute(){ delete cluster; 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(); return 0; } @@ -354,7 +417,7 @@ int HClusterCommand::execute(){ void HClusterCommand::printData(string label){ try { - if (isTrue(timing)) { + if (m->isTrue(timing)) { m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine(); } @@ -363,7 +426,7 @@ void HClusterCommand::printData(string label){ start = time(NULL); oldRAbund.setLabel(label); - if (isTrue(showabund)) { + if (m->isTrue(showabund)) { oldRAbund.getSAbundVector().print(cout); } oldRAbund.print(rabundFile);