X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=e6875b6af18d71bb0f78341f2a04bfc2c002886d;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=c39b002ccfc0096197cd59ced3f4bb7fa21cce6b;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3;p=mothur.git diff --git a/hclustercommand.cpp b/hclustercommand.cpp index c39b002..e6875b6 100644 --- a/hclustercommand.cpp +++ b/hclustercommand.cpp @@ -11,7 +11,7 @@ //********************************************************************************************************************** //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen. -HClusterCommand::HClusterCommand(string option){ +HClusterCommand::HClusterCommand(string option) { try{ globaldata = GlobalData::getInstance(); abort = false; @@ -21,16 +21,17 @@ HClusterCommand::HClusterCommand(string option){ else { //valid paramters for this command - string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"}; + string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } @@ -38,6 +39,39 @@ HClusterCommand::HClusterCommand(string option){ globaldata->newRead(); + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("phylip"); + //user has given a template file + if(it != parameters.end()){ + path = 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; } + } + + it = parameters.find("column"); + //user has given a template file + if(it != parameters.end()){ + path = 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; } + } + + it = parameters.find("name"); + //user has given a template file + if(it != parameters.end()){ + path = 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; } + } + } + + //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 = ""; } + //check for required parameters phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } @@ -53,8 +87,8 @@ HClusterCommand::HClusterCommand(string option){ if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } - if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a hcluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; } - else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; } + if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; } + else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; } if (columnfile != "") { if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; } @@ -79,7 +113,7 @@ HClusterCommand::HClusterCommand(string option){ if (method == "not found") { method = "furthest"; } if ((method == "furthest") || (method == "nearest") || (method == "average")) { } - else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; } + else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; } showabund = validParameter.validFile(parameters, "showabund", false); if (showabund == "not found") { showabund = "T"; } @@ -93,8 +127,9 @@ HClusterCommand::HClusterCommand(string option){ if (abort == false) { - - fileroot = getRootName(distfile); + + if (outputDir == "") { outputDir += hasPath(distfile); } + fileroot = outputDir + getRootName(getSimpleName(distfile)); if (method == "furthest") { tag = "fn"; } else if (method == "nearest") { tag = "nn"; } @@ -103,11 +138,15 @@ HClusterCommand::HClusterCommand(string option){ openOutputFile(fileroot+ tag + ".sabund", sabundFile); openOutputFile(fileroot+ tag + ".rabund", rabundFile); openOutputFile(fileroot+ tag + ".list", listFile); + + outputNames.push_back(fileroot+ tag + ".sabund"); + outputNames.push_back(fileroot+ tag + ".rabund"); + outputNames.push_back(fileroot+ tag + ".list"); } } } catch(exception& e) { - errorOut(e, "HClusterCommand", "HClusterCommand"); + m->errorOut(e, "HClusterCommand", "HClusterCommand"); exit(1); } } @@ -116,15 +155,15 @@ HClusterCommand::HClusterCommand(string option){ void HClusterCommand::help(){ try { - mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n"); - mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n"); - mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n"); - mothurOut("The hcluster command should be in the following format: \n"); - mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"); - mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n"); + m->mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n"); + m->mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n"); + 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"); } catch(exception& e) { - errorOut(e, "HClusterCommand", "help"); + m->errorOut(e, "HClusterCommand", "help"); exit(1); } } @@ -161,14 +200,14 @@ int HClusterCommand::execute(){ list = new ListVector(globaldata->nameMap->getListVector()); } - mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine(); + m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); m->mothurOutEndLine(); estart = time(NULL); //list vector made by read contains all sequence names if(list != NULL){ rabund = new RAbundVector(list->getRAbundVector()); }else{ - mothurOut("Error: no list vector!"); mothurOutEndLine(); return 0; + m->mothurOut("Error: no list vector!"); m->mothurOutEndLine(); return 0; } float previousDist = 0.00000; @@ -230,13 +269,18 @@ int HClusterCommand::execute(){ rabundFile.close(); listFile.close(); delete cluster; - - mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine(); + + 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(); + + m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); m->mothurOutEndLine(); return 0; } catch(exception& e) { - errorOut(e, "HClusterCommand", "execute"); + m->errorOut(e, "HClusterCommand", "execute"); exit(1); } } @@ -246,8 +290,8 @@ int HClusterCommand::execute(){ void HClusterCommand::printData(string label){ try { if (isTrue(timing)) { - mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) - + "\tclusters. Updates: " + toString(loops)); mothurOutEndLine(); + m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) + + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine(); } print_start = true; loops = 0; @@ -264,7 +308,7 @@ void HClusterCommand::printData(string label){ oldList.print(listFile); } catch(exception& e) { - errorOut(e, "HClusterCommand", "printData"); + m->errorOut(e, "HClusterCommand", "printData"); exit(1); }