#include "pcacommand.h"
+//**********************************************************************************************************************
+vector<string> PCACommand::getValidParameters(){
+ try {
+ string Array[] = {"phylip", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredParameters(){
+ try {
+ string Array[] = {"phylip"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PCACommand::PCACommand(string option) {
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
}
-
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(phylipfile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
}
//error checking on files
vector<string> names;
vector<vector<double> > D;
- fbase = outputDir + getRootName(getSimpleName(filename));
+ fbase = outputDir + m->getRootName(m->getSimpleName(filename));
read(filename, names, D);
void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
try {
ifstream f;
- openInputFile(fname, f);
+ m->openInputFile(fname, f);
//check whether matrix is square
char d;
- int m = 1;
+ int q = 1;
int numSeqs;
string name;
//is d a number meaning its square
if(isalnum(d)){
- m = 1;
+ q = 1;
break;
}
//is d a line return meaning its lower triangle
if(d == '\n'){
- m = 2;
+ q = 2;
break;
}
}
f.close();
//reopen to get back to beginning
- openInputFile(fname, f);
- read_phylip(f, m, names, D);
+ m->openInputFile(fname, f);
+ read_phylip(f, q, names, D);
}
catch(exception& e) {
m->errorOut(e, "PCACommand", "read");
}
}
- ofstream pcaData((fnameRoot+"pca").c_str(), ios::trunc);
+ ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pca");
+ outputNames.push_back(fnameRoot+"pcoa");
+ outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
- ofstream pcaLoadings((fnameRoot+"pca.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pca.loadings");
+ outputNames.push_back(fnameRoot+"pcoa.loadings");
+ outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){