#include "readphylipvector.h"
#include "groupmap.h"
+
//**********************************************************************************************************************
-vector<string> AmovaCommand::getValidParameters(){
+vector<string> AmovaCommand::setParameters(){
try {
- string Array[] = {"outputdir","iters","phylip","design","alpha", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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);
+
+ 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, "AmovaCommand", "getValidParameters");
+ m->errorOut(e, "AmovaCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-AmovaCommand::AmovaCommand(){
+string AmovaCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["amova"] = tempOutNames;
+ string helpString = "";
+ helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
+ helpString += "The amova command outputs a .amova file.";
+ helpString += "The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.";
+ helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
+ 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.";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
+ helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "AmovaCommand");
+ m->errorOut(e, "AmovaCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> AmovaCommand::getRequiredParameters(){
- try {
- string Array[] = {"design"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> AmovaCommand::getRequiredFiles(){
+AmovaCommand::AmovaCommand(){
try {
- string Array[] = {};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["amova"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "getRequiredFiles");
+ m->errorOut(e, "AmovaCommand", "AmovaCommand");
exit(1);
}
}
//**********************************************************************************************************************
-
AmovaCommand::AmovaCommand(string option) {
try {
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"design","outputdir","iters","phylip","alpha", "inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
phylipFileName = validParameter.validFile(parameters, "phylip", true);
if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
- else if (phylipFileName == "not found") { phylipFileName = ""; }
- else if (designFileName == "not found") {
- designFileName = "";
- m->mothurOut("You must provide an phylip file.");
- m->mothurOutEndLine();
- abort = true;
- }
+ else if (phylipFileName == "not found") {
+ //if there is a current phylip file, use it
+ phylipFileName = m->getPhylipFile();
+ 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") {
- designFileName = "";
- m->mothurOut("You must provide an design file.");
- m->mothurOutEndLine();
- abort = true;
- }
+ //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);
}
}
catch(exception& e) {
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void AmovaCommand::help(){
- try {
- m->mothurOut("Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n");
- m->mothurOut("The amova command outputs a .amova file. \n");
- m->mothurOut("The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required.\n");
- m->mothurOut("The design parameter allows you to assign your samples to groups when you are running amova. It is required. \n");
- m->mothurOut("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");
- m->mothurOut("The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n");
- m->mothurOut("The amova command should be in the following format: amova(phylip=file.dist, design=file.design).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-AmovaCommand::~AmovaCommand(){}
-
//**********************************************************************************************************************
int AmovaCommand::execute(){
//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 AMOVAFile;
string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "amova";
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