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);
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label. shared or phylip or column and name are required unless valid current files exist.\n";
+ 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";
outputTypes["svg"] = tempOutNames;
format = "";
- //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 = ""; }
-
+
//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 = ""; }
}
}
+
+ //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 = m->hasPath(inputfile); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
+ string temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontsize);
if (abort == false) {
ValidCalculators validCalculator;
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- heatmap = new HeatMapSim(outputDir, inputfile);
+ heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
if (format == "shared") {
runCommandShared();
delete heatmap;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
delete input;