#include "mantelcommand.h"
#include "readphylipvector.h"
+
//**********************************************************************************************************************
-vector<string> MantelCommand::getValidParameters(){
+vector<string> MantelCommand::setParameters(){
try {
- string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip1);
+ CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip2);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+ 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, "MantelCommand", "getValidParameters");
+ m->errorOut(e, "MantelCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MantelCommand::getRequiredParameters(){
+string MantelCommand::getHelpString(){
try {
- string Array[] = {"phylip1", "phylip2"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n";
+ helpString += "The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n";
+ helpString += "The mantel command parameters are phylip1, phylip2, iters and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n";
+ helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
+ helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
+ helpString += "The mantel command outputs a .mantel file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "MantelCommand", "getRequiredParameters");
+ m->errorOut(e, "MantelCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
+string MantelCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "mantel") { pattern = "[filename],mantel"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MantelCommand::MantelCommand(){
try {
- abort = true; calledHelp = true;
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["mantel"] = tempOutNames;
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-vector<string> MantelCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MantelCommand", "getRequiredFiles");
- exit(1);
- }
-}
//**********************************************************************************************************************
MantelCommand::MantelCommand(string option) {
try {
//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[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
}
}
//**********************************************************************************************************************
-void MantelCommand::help(){
- try {
- m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n");
- m->mothurOut("The mantel command parameters are phylip1, phylip2 and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n");
- m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n");
- m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n");
- m->mothurOut("The mantel command outputs a .mantel file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "MantelCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-MantelCommand::~MantelCommand(){}
-
-//**********************************************************************************************************************
-
int MantelCommand::execute(){
try {
//read phylip2
ReadPhylipVector readMatrix2(phylipfile2);
- vector<seqDist> temp; //seqDist - int, int, float
- vector<string> names2 = readMatrix2.read(temp);
+ vector< vector<double> > matrix2;
+ vector<string> names2 = readMatrix2.read(matrix2);
if (m->control_pressed) { return 0; }
- //fill matrix2 making sure to make sure the distances are in the same order as matrix1
- vector< vector<double> > matrix2;
+ //make sure matrix2 and matrix1 are in the same order
if (names1 == names2) { //then everything is in same order and same size
-
- //initialize space
- matrix2.resize(names2.size());
- for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-
- //fill matrix2
- for (int i = 0; i < temp.size(); i++) {
- matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
- matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
- }
-
}else if (names1.size() != names2.size()) { //wrong size no need to order, abort
m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
m->control_pressed = true;
}else { //sizes are the same, but either the names are different or they are in different order
-
- //map location of name in names1 to location of name in names2
- map<string, int> names1Map;
- map<string, int>::iterator it;
- for (int i = 0; i < names1.size(); i++) { names1Map[names1[i]] = i; }
-
- map<string, int> names2Map;
- bool nameError = false;
- for (int i = 0; i < names2.size(); i++) {
-
- //if you find one name error stop looking
- if (!nameError) {
- it = names1Map.find(names2[i]);
- if (it == names1Map.end()) { nameError = true; }
- }
-
- //are names different
- names2Map[names2[i]] = i;
- }
-
- //initialize space
- matrix2.resize(names2.size());
- for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-
- //fill matrix2
- //are we comparing apples to apples?
- if (nameError) {
- m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
-
- for (int i = 0; i < temp.size(); i++) {
- matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
- matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
- }
-
- }else { //no name error just different orders, so reorder
-
- for (int i = 0; i < temp.size(); i++) {
-
- //what's the location of this distance comparison in matrix1
- string matrix2NameI = names2[temp[i].seq1];
- string matrix2NameJ = names2[temp[i].seq2];
- int locationI = names1Map[matrix2NameI];
- int locationJ = names1Map[matrix2NameJ];
-
- matrix2[locationI][locationJ] = temp[i].dist;
- matrix2[locationJ][locationI] = temp[i].dist;
- }
- }
-
- }
-
- //frees up space
- temp.clear();
+ m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
+ }
if (m->control_pressed) { return 0; }
if (m->control_pressed) { return 0; }
- string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile1));
+ string outputFile = getOutputFileName("mantel",variables);
outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
ofstream out;
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