//**********************************************************************************************************************
vector<string> AnosimCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pphylip);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ 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); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string AnosimCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "anosim") { pattern = "[filename],anosim"; } //makes file like: amazon.align
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
AnosimCommand::AnosimCommand(){
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setPhylipFile(phylipFileName); }
//check for required parameters
designFileName = validParameter.validFile(parameters, "design", true);
- if (designFileName == "not open") { abort = true; }
+ if (designFileName == "not open") { designFileName = ""; abort = true; }
else if (designFileName == "not found") {
//if there is a current design file, use it
designFileName = m->getDesignFile();
if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setDesignFile(designFileName); }
string temp = validParameter.validFile(parameters, "iters", false);
if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "alpha", false);
if (temp == "not found") { temp = "0.05"; }
- convert(temp, experimentwiseAlpha);
+ m->mothurConvert(temp, experimentwiseAlpha);
}
}
//link designMap to rows/columns in distance matrix
map<string, vector<int> > origGroupSampleMap;
for(int i=0;i<sampleNames.size();i++){
- origGroupSampleMap[designMap->getGroup(sampleNames[i])].push_back(i);
+ string group = designMap->getGroup(sampleNames[i]);
+
+ if (group == "not found") {
+ m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+ }else { origGroupSampleMap[group].push_back(i); }
}
int numGroups = origGroupSampleMap.size();
+ if (m->control_pressed) { delete designMap; return 0; }
+
//create a new filename
ofstream ANOSIMFile;
- string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "anosim";
+ map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+ string ANOSIMFileName = getOutputFileName("anosim", variables);
+
m->openOutputFile(ANOSIMFileName, ANOSIMFile);
outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
m->mothurOut("\ncomparison\tR-value\tP-value\n");