+//**********************************************************************************************************************
+vector<string> HeatMapSimCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string HeatMapSimCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n";
+ helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
+ helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
+ helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
+ helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
+ helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
+ helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+ helpString += validCalculator.printCalc("heat");
+ helpString += "The default value for calc is jclass-thetayc.\n";
+ helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
+ helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
+ helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n";
+ helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
+ helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "getHelpString");
+ exit(1);
+ }
+}