helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.\n";
helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
helpString += "The anosim command should be in the following format: anosim(phylip=file.dist, design=file.design).\n";
- helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n";
return helpString;
}
catch(exception& e) {
exit(1);
}
}
-
+//**********************************************************************************************************************
+string AnosimCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "anosim") { outputFileName = "anosim"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "getOutputFileNameTag");
+ 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";
+ string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("anosim");
m->openOutputFile(ANOSIMFileName, ANOSIMFile);
outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
m->mothurOut("\ncomparison\tR-value\tP-value\n");