X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=helpcommand.cpp;h=47d04f9d528ab14053f468f2eacc7e150db736c0;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=f1cf89367b2c62dfead85d70547cfb94a53c50db;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/helpcommand.cpp b/helpcommand.cpp index f1cf893..47d04f9 100644 --- a/helpcommand.cpp +++ b/helpcommand.cpp @@ -11,143 +11,22 @@ //********************************************************************************************************************** -HelpCommand::HelpCommand(){} - -//********************************************************************************************************************** - -HelpCommand::~HelpCommand(){} - +HelpCommand::HelpCommand(string option) { + validCommands = CommandFactory::getInstance(); +} //********************************************************************************************************************** - int HelpCommand::execute(){ - - globaldata = GlobalData::getInstance(); + try { + validCommands->printCommands(cout); + m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine(); - if (globaldata->helpRequest == "read.phylip") { - cout << "The read.phylip command parameter options are distfile, namefile, cutoff and precision" << "\n"; - cout << "The read.phylip command should be in the following format: " << "\n"; - cout << "read.phylip(distfile=yourDistFile, namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; - cout << "The distfile parameter is required. If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. distfile), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "read.column") { - cout << "The read.column command parameter options are distfile, namefile, cutoff and precision" << "\n"; - cout << "The read.column command should be in the following format: " << "\n"; - cout << "read.column(distfile=yourDistFile, namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; - cout << "The distfile and namefile parameters are required. If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. distfile), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "read.list") { - cout << "The read.list command parameter options are listfile and orderfile." << "\n"; - cout << "The read.list command should be in the following format: " << "\n"; - cout << "read.list(listfile=yourListFile, orderfile=yourOrderFile) " << "\n"; - cout << "The listfile parameter is required." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "read.rabund") { - cout << "The read.rabund command parameter options are rabundfile and orderfile." << "\n"; - cout << "The read.rabund command should be in the following format: " << "\n"; - cout << "read.rabund(rabundfile=yourRAbundFile, orderfile=yourOrderFile) " << "\n"; - cout << "The rabundfile parameter is required." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. rabundfile), '=' and parameters (i.e.yourRAbundfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "read.sabund") { - cout << "The read.sabund command parameter options are sabundfile and orderfile." << "\n"; - cout << "The read.sabund command should be in the following format: " << "\n"; - cout << "read.sabund(sabundfile=yourSAbundFile, orderfile=yourOrderFile) " << "\n"; - cout << "The sabundfile parameter is required." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. sabundfile), '=' and parameters (i.e.yourSAbundfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "read.shared") { - cout << "The read.shared command parameter options are listfile and groupfile." << "\n"; - cout << "The read.shared command should be in the following format: " << "\n"; - cout << "read.shared(listfile=yourListFile, groupfile=yourGroupFile) " << "\n"; - cout << "The listfile parameter and groupfile paramaters are required." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "cluster") { - cout << "The cluster command can only be executed after a successful read.phylip or read.column command." << "\n"; - cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n"; - cout << "The cluster command should be in the following format: " << "\n"; - cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; - cout << "The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed." << "\n" << "\n"; - }else if (globaldata->helpRequest == "collect.single") { - cout << "The collect.single command can only be executed after a successful read.list read.rabund or rad.sabund command. WITH ONE EXECEPTION. " << "\n"; - cout << "The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; - cout << "The collect.single command parameters are label, line, freq, single. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n"; - cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, single=yourEstimators)." << "\n"; - cout << "Example collect(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, single=collect-chao-ace-jack)." << "\n"; - cout << "The default values for freq is 100, and single are sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "collect.shared") { - cout << "The collect.shared command can only be executed after a successful read.shared command." << "\n"; - cout << "The collect.shared command parameters are label, line, freq, jumble, shared. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n"; - cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, shared=yourEstimators)." << "\n"; - cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, shared=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n"; - cout << "The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "rarefaction.single") { - cout << "The rarefaction.single command can only be executed after a successful read.list, read.rabund or read.sabund. WTIH ONE EXECEPTION." << "\n"; - cout << "The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; - cout << "The rarefaction.single command parameters are label, line, iters, freq, rarefaction. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n"; - cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators)." << "\n"; - cout << "Example rarefaction.single(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n"; - cout << "The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness." << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "rarefaction.shared") { - cout << "The rarefaction.shared command can only be executed after a successful read.shared command." << "\n"; - cout << "The rarefaction.shared command parameters are label, line, iters, jumble and sharedrarefaction. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n"; - cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, sharedrarefaction=yourEstimators)." << "\n"; - cout << "Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, jumble=1, sharedrarefaction=sharedobserved)." << "\n"; - cout << "The default values for iters is 1000, jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), freq is 100, and sharedrarefaction is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "summary.single") { - cout << "The summary.single command can only be executed after a successful read.list, read.rabund or read.sabund. WTIH ONE EXECEPTION." << "\n"; - cout << "The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; - cout << "The summary.single command parameters are label, line, summary. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n"; - cout << "summary.single(label=yourLabel, line=yourLines, summary=yourEstimators)." << "\n"; - cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, summary=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n"; - cout << "The default value summary is sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson" << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "summary.shared") { - cout << "The summary.shared command can only be executed after a successful read.shared command." << "\n"; - cout << "The summary.shared command parameters are label, line, jumble and sharedsummary. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n"; - cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, sharedsummary=yourEstimators)." << "\n"; - cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, sharedsummary=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n"; - cout << "The default value for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble) and sharedsummary is sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN" << "\n"; - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "shared") { - cout << "The shared command can only be executed after a successful read.shared command." << "\n"; - cout << "The shared command parses a list file and separates it into groups." << "\n"; - cout << "It outputs a shared file containing the otu information for each group. There are no shared command parameters." << "\n"; - cout << "The shared command should be in the following format: shared()." << "\n"; - cout << "Example shared()." << "\n"; - }else if (globaldata->helpRequest == "parselist") { - cout << "The parselist command parses a list file and separates it into groups." << "\n"; - cout << "It outputs a list file for each group." << "\n"; - cout << "The parselist command parameter options are listfile and groupfile." << "\n"; - cout << "The parselist command should be in the following format: " << "\n"; - cout << "parselist(listfile=yourListFile, groupfile=yourGroupFile) " << "\n"; - cout << "The listfile parameter and groupfile paramater are required." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. listfile), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - }else if (globaldata->helpRequest == "quit") { - cout << "The quit command will terminate Dotur and should be in the following format: " << "\n"; - cout << "quit()" << "\n" << "\n"; - }else if (globaldata->helpRequest == "") { - cout << "Valid commands are read.phylip(), read.column(), read.list(), read.rabund(), read.sabund(), cluster(), collect.single(), rarefaction.single(), summary.single(), collect.shared(), rarefaction.shared(), summary.shared(), shared(), pareselist(), quit(), help()." << "\n"; - cout << "For more information about a specific command type 'help(commandName)' i.e. 'help(read.phylip)'" << endl; - }else { - cout << "not a valid command" << endl; - } + m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n"); - cout << endl << "For further assistance please refer to the Mothur manual, or contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - return 0; + return 0; + } + catch(exception& e) { + m->errorOut(e, "HelpCommand", "execute"); + exit(1); + } } - //**********************************************************************************************************************/