//**********************************************************************************************************************
-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.dist") {
- cout << "The read.dist command parameter options are phylip or column, name, cutoff and precision" << "\n";
- cout << "The read.dist command should be in the following format: " << "\n";
- cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
- cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n";
- cout << "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. dist), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "read.otu") {
- cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
- cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
- cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, group and order." << "\n";
- cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
- cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile)." << "\n";
- cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
- cout << "The second way to use the read.otu command is to read a list and a group so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
- cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile). " << "\n";
- cout << "The list parameter and group paramaters are required. When using the command the second way read.otu command parses the .list file" << "\n";
- cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
- cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "cluster") {
- cout << "The cluster command can only be executed after a successful read.dist 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 == "deconvolute") {
- cout << "The deconvolute command reads a fastafile and creates a namesfile." << "\n";
- cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
- cout << "If the sequence is unique the second column will just contain its name. " << "\n";
- cout << "The deconvolute command parameter is fasta and it is required." << "\n";
- cout << "The deconvolute command should be in the following format: " << "\n";
- cout << "deconvolute(fasta=yourFastaFile) " << "\n";
- }else if (globaldata->helpRequest == "collect.single") {
- cout << "The collect.single command can only be executed after a successful read.otu 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. list), '=' 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.otu 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 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and shared are sharedsobs-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. list), '=' 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.otu 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=sobs-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. list), '=' 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.otu 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 1 (meaning jumble, if it’s set to 0 then it will not 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. list), '=' 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.otu 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. list), '=' 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.otu 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 1 (meaning jumble, if it’s set to 0 then it will not jumble) and sharedsummary is sharedsobs-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. list), '=' 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.dist(), read.otu(), cluster(), deconvolute(), collect.single(), rarefaction.single(), summary.single(), collect.shared(), rarefaction.shared(), summary.shared(), quit(), help()." << "\n";
- cout << "For more information about a specific command type 'help(commandName)' i.e. 'help(read.dist)'" << endl;
- }else {
- cout << globaldata->helpRequest << " is 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);
+ }
}
-
//**********************************************************************************************************************/
projects / mothur.git / blobdiff