X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=47136938a19e6c5d4b8dd2b8110849249ac50b06;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hp=503bc48273069f829103788ce2711bc12d56ea42;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/hclustercommand.cpp b/hclustercommand.cpp index 503bc48..4713693 100644 --- a/hclustercommand.cpp +++ b/hclustercommand.cpp @@ -17,8 +17,8 @@ vector HClusterCommand::setParameters(){ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn); CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff); CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision); - CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod); - CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard); + CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod); + CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard); CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psorted); CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund); CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming); @@ -74,11 +74,10 @@ HClusterCommand::HClusterCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -136,16 +135,17 @@ HClusterCommand::HClusterCommand(string option) { phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } else if (phylipfile == "not found") { phylipfile = ""; } - else { distfile = phylipfile; format = "phylip"; } + else { distfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); } columnfile = validParameter.validFile(parameters, "column", true); if (columnfile == "not open") { abort = true; } else if (columnfile == "not found") { columnfile = ""; } - else { distfile = columnfile; format = "column"; } + else { distfile = columnfile; format = "column"; m->setColumnFile(columnfile); } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these? @@ -182,18 +182,18 @@ HClusterCommand::HClusterCommand(string option) { if (temp == "not found") { temp = "100"; } //saves precision legnth for formatting below length = temp.length(); - convert(temp, precision); + m->mothurConvert(temp, precision); - temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; } + temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; } hard = m->isTrue(temp); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); cutoff += (5 / (precision * 10.0)); method = validParameter.validFile(parameters, "method", false); - if (method == "not found") { method = "furthest"; } + if (method == "not found") { method = "average"; } 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; } @@ -260,7 +260,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -276,7 +276,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -306,35 +306,41 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + float saveCutoff = cutoff; while (seqs.size() != 0){ seqs = cluster->getSeqs(); + //to account for cutoff change in average neighbor + if (seqs.size() != 0) { + if (seqs[0].dist > cutoff) { break; } + } + if (m->control_pressed) { delete cluster; sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } for (int i = 0; i < seqs.size(); i++) { //-1 means skip me if (seqs[i].seq1 != seqs[i].seq2) { - cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); + cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); if (m->control_pressed) { delete cluster; sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -367,7 +373,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -384,10 +390,18 @@ int HClusterCommand::execute(){ delete cluster; if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + + if (saveCutoff != cutoff) { + if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); } + else { saveCutoff = m->roundDist(saveCutoff, precision); } + + m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); + } + //set list file as new current listfile string current = ""; itTypes = outputTypes.find("list");