*/
#include "pcoacommand.h"
+#include "readphylipvector.h"
+
//**********************************************************************************************************************
-vector<string> PCOACommand::getValidParameters(){
+vector<string> PCOACommand::setParameters(){
try {
- string Array[] = {"phylip", "metric","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+ 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, "PCOACommand", "getValidParameters");
+ m->errorOut(e, "PCOACommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-PCOACommand::PCOACommand(){
+string PCOACommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["pcoa"] = tempOutNames;
- outputTypes["loadings"] = tempOutNames;
+ string helpString = "";
+ helpString += "The pcoa command parameters are phylip and metric";
+ helpString += "The phylip parameter allows you to enter your distance file.";
+ helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True";
+ helpString += "Example pcoa(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, "PCOACommand", "PCOACommand");
+ m->errorOut(e, "PCOACommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> PCOACommand::getRequiredParameters(){
- try {
- string Array[] = {"phylip"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "getRequiredParameters");
- exit(1);
- }
+string PCOACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "pcoa") { pattern = "[filename],pcoa.axes"; }
+ else if (type == "loadings") { pattern = "[filename],pcoa.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCOACommand", "getOutputPattern");
+ exit(1);
+ }
}
+
+
//**********************************************************************************************************************
-vector<string> PCOACommand::getRequiredFiles(){
+PCOACommand::PCOACommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "PCOACommand", "getRequiredFiles");
+ m->errorOut(e, "PCOACommand", "PCOACommand");
exit(1);
}
}
PCOACommand::PCOACommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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","metric","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") { abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; abort = true; }
- else { filename = phylipfile; }
+ 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); }
+
+ filename = phylipfile;
//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 += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
}
- //error checking on files
- if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pcoa command."); m->mothurOutEndLine(); abort = true; }
-
string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; }
metric = m->isTrue(temp);
}
}
}
//**********************************************************************************************************************
-void PCOACommand::help(){
- try {
-
- m->mothurOut("The pcoa command parameters are phylip and metric"); m->mothurOutEndLine();
- m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
- m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
- m->mothurOut("Example pcoa(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, "PCOACommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-PCOACommand::~PCOACommand(){}
-//**********************************************************************************************************************
int PCOACommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
fbase = outputDir + m->getRootName(m->getSimpleName(filename));
- read(filename, names, D);
+ ReadPhylipVector readFile(filename);
+ names = readFile.read(D);
if (m->control_pressed) { return 0; }
vector<double> d;
vector<double> e;
vector<vector<double> > G = D;
- vector<vector<double> > copy_G;
+ //vector<vector<double> > copy_G;
- m->mothurOut("\nProcessing...\n\n");
+ m->mothurOut("\nProcessing...\n");
for(int count=0;count<2;count++){
- recenter(offset, D, G); if (m->control_pressed) { return 0; }
+ linearCalc.recenter(offset, D, G); if (m->control_pressed) { return 0; }
linearCalc.tred2(G, d, e); if (m->control_pressed) { return 0; }
linearCalc.qtli(d, e, G); if (m->control_pressed) { return 0; }
offset = d[d.size()-1];
output(fbase, names, G, d);
- 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; }
if (metric) {
vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
- 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; }
double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
- m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+ m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
- 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; }
}
}
exit(1);
}
}
-
-/*********************************************************************************************************************************/
-
-int PCOACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
- try {
- // int count1=0;
- // int count2=0;
-
- int rank;
- f >> rank;
-
- name_list.resize(rank);
- d.resize(rank);
- if(square_m == 1){
- for(int i=0;i<rank;i++)
- d[i].resize(rank);
- for(int i=0;i<rank;i++) {
- f >> name_list[i];
- // cout << i << "\t" << name_list[i] << endl;
- for(int j=0;j<rank;j++) {
- if (m->control_pressed) { return 0; }
-
- f >> d[i][j];
- if (d[i][j] == -0.0000)
- d[i][j] = 0.0000;
- }
- }
- }
- else if(square_m == 2){
- for(int i=0;i<rank;i++){
- d[i].resize(rank);
- }
- d[0][0] = 0.0000;
- f >> name_list[0];
- for(int i=1;i<rank;i++){
- f >> name_list[i];
- d[i][i]=0.0000;
- for(int j=0;j<i;j++){
- if (m->control_pressed) { return 0; }
- f >> d[i][j];
- if (d[i][j] == -0.0000)
- d[i][j] = 0.0000;
- d[j][i]=d[i][j];
- }
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "read_phylip");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCOACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
- try {
- ifstream f;
- m->openInputFile(fname, f);
-
- //check whether matrix is square
- char d;
- int q = 1;
- int numSeqs;
- string name;
-
- f >> numSeqs >> name;
-
- while((d=f.get()) != EOF){
-
- //is d a number meaning its square
- if(isalnum(d)){
- q = 1;
- break;
- }
-
- //is d a line return meaning its lower triangle
- if(d == '\n'){
- q = 2;
- break;
- }
- }
- f.close();
-
- //reopen to get back to beginning
- m->openInputFile(fname, f);
- read_phylip(f, q, names, D);
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "read");
- exit(1);
- }
-}
-
-/*********************************************************************************************************************************/
-
-void PCOACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){
- try {
- int rank = D.size();
-
- vector<vector<double> > A(rank);
- vector<vector<double> > C(rank);
- for(int i=0;i<rank;i++){
- A[i].resize(rank);
- C[i].resize(rank);
- }
-
- double scale = -1.0000 / (double) rank;
-
- for(int i=0;i<rank;i++){
- A[i][i] = 0.0000;
- C[i][i] = 1.0000 + scale;
- for(int j=i+1;j<rank;j++){
- A[i][j] = A[j][i] = -0.5 * D[i][j] * D[i][j] + offset;
- C[i][j] = C[j][i] = scale;
- }
- }
-
- A = linearCalc.matrix_mult(C,A);
- G = linearCalc.matrix_mult(A,C);
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "recenter");
- exit(1);
- }
-
-}
-
/*********************************************************************************************************************************/
void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
}
}
- ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
+ ofstream pcaData;
+ map<string, string> variables;
+ variables["[filename]"] = fnameRoot;
+ string pcoaDataFile = getOutputFileName("pcoa",variables);
+ m->openOutputFile(pcoaDataFile, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa");
- outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
+ outputNames.push_back(pcoaDataFile);
+ outputTypes["pcoa"].push_back(pcoaDataFile);
- ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings;
+ string loadingsFile = getOutputFileName("loadings",variables);
+ m->openOutputFile(loadingsFile, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa.loadings");
- outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
+ outputNames.push_back(loadingsFile);
+ outputTypes["loadings"].push_back(loadingsFile);
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){
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