#include "readphylipvector.h"
//**********************************************************************************************************************
-vector<string> NMDSCommand::getValidParameters(){
+vector<string> NMDSCommand::setParameters(){
try {
- string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(paxes);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","nmds-stress",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmaxdim);
+ CommandParameter pmindim("mindim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmindim);
+ CommandParameter piters("iters", "Number", "", "10", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "","",false,false); parameters.push_back(pmaxiters);
+ CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "","",false,false); parameters.push_back(pepsilon);
+ 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, "NMDSCommand", "getValidParameters");
+ m->errorOut(e, "NMDSCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-NMDSCommand::NMDSCommand(){
+string NMDSCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["nmds"] = tempOutNames;
- outputTypes["stress"] = tempOutNames;
- outputTypes["iters"] = tempOutNames;
+ string helpString = "";
+ helpString += "The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling.\n";
+ helpString += "The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon.\n";
+ helpString += "The phylip parameter allows you to enter your distance file.\n";
+ helpString += "The axes parameter allows you to enter a file containing a starting configuration.\n";
+ helpString += "The maxdim parameter allows you to select the maximum dimensions to use. Default=2\n";
+ helpString += "The mindim parameter allows you to select the minimum dimensions to use. Default=2\n";
+ helpString += "The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500\n";
+ helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n";
+ helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n";
+ helpString += "Example nmds(phylip=yourDistanceFile).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "NMDSCommand", "NMDSCommand");
+ m->errorOut(e, "NMDSCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> NMDSCommand::getRequiredParameters(){
- try {
- string Array[] = {"phylip"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "NMDSCommand", "getRequiredParameters");
- exit(1);
- }
+string NMDSCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "nmds") { pattern = "[filename],nmds.axes"; }
+ else if (type == "stress") { pattern = "[filename],nmds.stress"; }
+ else if (type == "iters") { pattern = "[filename],nmds.iters"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
-vector<string> NMDSCommand::getRequiredFiles(){
+NMDSCommand::NMDSCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["nmds"] = tempOutNames;
+ outputTypes["stress"] = tempOutNames;
+ outputTypes["iters"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "NMDSCommand", "getRequiredFiles");
+ m->errorOut(e, "NMDSCommand", "NMDSCommand");
exit(1);
}
}
//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 Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
+ else if (phylipfile == "not found") {
+ //if there is a current phylip file, use it
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " 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(phylipfile); }
axesfile = validParameter.validFile(parameters, "axes", true);
if (axesfile == "not open") { axesfile = ""; abort = true; }
}
string temp = validParameter.validFile(parameters, "mindim", false); if (temp == "not found") { temp = "2"; }
- convert(temp, mindim);
+ m->mothurConvert(temp, mindim);
temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") { temp = "500"; }
- convert(temp, maxIters);
+ m->mothurConvert(temp, maxIters);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "maxdim", false); if (temp == "not found") { temp = "2"; }
- convert(temp, maxdim);
+ m->mothurConvert(temp, maxdim);
temp = validParameter.validFile(parameters, "epsilon", false); if (temp == "not found") { temp = "0.000000000001"; }
- convert(temp, epsilon);
+ m->mothurConvert(temp, epsilon);
if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
- if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
+ if (maxdim < mindim) { maxdim = mindim; }
}
}
}
}
//**********************************************************************************************************************
-void NMDSCommand::help(){
- try {
- m->mothurOut("The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling."); m->mothurOutEndLine();
- m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine();
- m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
- m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
- m->mothurOut("The maxdim parameter allows you to select the maximum dimensions to use. Default=2"); m->mothurOutEndLine();
- m->mothurOut("The mindim parameter allows you to select the minimum dimensions to use. Default=2"); m->mothurOutEndLine();
- m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
- m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
- m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
- m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "NMDSCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-NMDSCommand::~NMDSCommand(){}
-//**********************************************************************************************************************
int NMDSCommand::execute(){
try {
vector< vector<double> > axes;
if (axesfile != "") { axes = readAxes(names); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
- string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ string outputFileName = getOutputFileName("iters",variables);
+ string stressFileName = getOutputFileName("stress",variables);
outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
vector< vector<double> > thisConfig;
if (axesfile == "") { thisConfig = generateStartingConfiguration(names.size(), i); }
else { thisConfig = getConfiguration(axes, i); }
- if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
//calc nmds for this dimension
double stress;
vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
- if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
//calc euclid distances for new config
vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
- if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
//calc correlation between original distances and euclidean distances from this config
double rsquared = linearCalc.calcPearson(newEuclid, matrix);
rsquared *= rsquared;
- if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
//output results
out << "Config" << (j+1) << '\t';
bestConfig = endConfig;
}
- if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
}
}
out.close(); out2.close();
//output best config
- string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+ string BestFileName = getOutputFileName("nmds",variables);
outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
outBest.close();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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