//**********************************************************************************************************************
-PCACommand::PCACommand(string option){
+PCACommand::PCACommand(string option) {
try {
abort = false;
else {
//valid paramters for this command
- string Array[] = {"phylip","lt"};
+ string Array[] = {"phylip","outputdir", "inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+ }
+
//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; }
- //columnfile = validParameter.validFile(parameters, "column", true);
- //if (columnfile == "not open") { abort = true; }
- //else if (columnfile == "not found") { columnfile = ""; }
- //else { format = "column"; }
-
- //namefile = validParameter.validFile(parameters, "name", true);
- //if (namefile == "not open") { abort = true; }
- //else if (namefile == "not found") { namefile = ""; }
-
+ //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 += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
+ }
//error checking on files
- if (phylipfile == "") { mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }
- //if ((phylipfile == "") && (columnfile == "")) { mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }
- //else if ((phylipfile != "") && (columnfile != "")) { mothurOut("You may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
-
- //if (columnfile != "") {
- // if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
- //}
-
- string temp = validParameter.validFile(parameters, "lt", false); if (temp == "not found") { temp = "false"; }
- bool lt = isTrue(temp);
-
- if (lt) { matrix = 2; }
- else { matrix = 1; }
-
-
+ if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; }
}
}
catch(exception& e) {
- errorOut(e, "PCACommand", "PCACommand");
+ m->errorOut(e, "PCACommand", "PCACommand");
exit(1);
}
}
void PCACommand::help(){
try {
- mothurOut("The pca command..."); mothurOutEndLine();
+ m->mothurOut("The pca command..."); m->mothurOutEndLine();
}
catch(exception& e) {
- errorOut(e, "PCACommand", "help");
+ m->errorOut(e, "PCACommand", "help");
exit(1);
}
}
vector<string> names;
vector<vector<double> > D;
- fbase = filename;
- if(fbase.find_last_of(".")!=string::npos){
- fbase.erase(fbase.find_last_of(".")+1);
- }
- else{
- fbase += ".";
- }
- read(filename, matrix, names, D);
+ fbase = outputDir + m->getRootName(m->getSimpleName(filename));
+
+ read(filename, names, D);
+
+ if (m->control_pressed) { return 0; }
double offset = 0.0000;
vector<double> d;
vector<double> e;
vector<vector<double> > G = D;
vector<vector<double> > copy_G;
- int rank = D.size();
+ //int rank = D.size();
- cout << "\nProcessing...\n";
+ m->mothurOut("\nProcessing...\n");
for(int count=0;count<2;count++){
- recenter(offset, D, G);
- tred2(G, d, e);
- qtli(d, e, G);
+ recenter(offset, D, G); if (m->control_pressed) { return 0; }
+ tred2(G, d, e); if (m->control_pressed) { return 0; }
+ qtli(d, e, G); if (m->control_pressed) { return 0; }
offset = d[d.size()-1];
if(offset > 0.0) break;
}
+ if (m->control_pressed) { return 0; }
output(fbase, names, G, d);
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "PCACommand", "execute");
+ m->errorOut(e, "PCACommand", "execute");
exit(1);
}
}
d = f.peek();
}
catch(exception& e) {
- errorOut(e, "PCACommand", "get_comment");
+ m->errorOut(e, "PCACommand", "get_comment");
exit(1);
}
}
/*********************************************************************************************************************************/
-void PCACommand::read_mega(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
- try {
- get_comment(f, '#', '\n');
-
- char test = f.peek();
-
- while(test == '!'){ //get header comments
- get_comment(f, '!', ';');
- while(isspace(test=f.get())) {;}
- f.putback(test);
- test = f.peek();
- }
- while(test != '\n'){ //get sequence names
- get_comment(f, '[', ']');
- char d = f.get();
- d = f.get();
- if(d == '#'){
- string name;
- f >> name;
- name_list.push_back(name);
- while(isspace(test=f.get())) {;}
- f.putback(test);
- }
- else{
- break;
- }
- }
- int rank = name_list.size();
- d.resize(rank);
- for(int i=0;i<rank;i++){ d[i].resize(rank); }
-
- d[0][0] = 0.0000;
- get_comment(f, '[', ']');
- for(int i=1;i<rank;i++){
- get_comment(f, '[', ']');
- d[i][i]=0.0000;
- for(int j=0;j<i;j++){
- f >> d[i][j];
- if (d[i][j] == -0.0000)
- d[i][j] = 0.0000;
- d[j][i]=d[i][j];
- }
- }
- }
- catch(exception& e) {
- errorOut(e, "PCACommand", "read_mega");
- exit(1);
- }
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
+int PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
try {
// int count1=0;
// int count2=0;
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;
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;
}
}
}
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "PCACommand", "read_phylip");
+ m->errorOut(e, "PCACommand", "read_phylip");
exit(1);
}
/*********************************************************************************************************************************/
-void PCACommand::read(string fname, int m, vector<string>& names, vector<vector<double> >& D){
+void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
try {
- ifstream f(fname.c_str());
- if(!f) {
- cerr << "Error: Could not open " << fname << endl;
- exit(1);
- }
- char test = f.peek();
+ ifstream f;
+ m->openInputFile(fname, f);
+
+ //check whether matrix is square
+ char d;
+ int q = 1;
+ int numSeqs;
+ string name;
- if(test == '#'){
- read_mega(f, m, names, D);
- }
- else{
- read_phylip(f, m, names, D);
+ 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();
- int rank = D.size();
+ //reopen to get back to beginning
+ m->openInputFile(fname, f);
+ read_phylip(f, q, names, D);
}
- catch(exception& e) {
- errorOut(e, "PCACommand", "read");
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "read");
exit(1);
}
}
/*********************************************************************************************************************************/
-double PCACommand::pythag(double a, double b){
- return(pow(a*a+b*b,0.5));
-}
+
+double PCACommand::pythag(double a, double b) { return(pow(a*a+b*b,0.5)); }
+
/*********************************************************************************************************************************/
void PCACommand::matrix_mult(vector<vector<double> > first, vector<vector<double> > second, vector<vector<double> >& product){
}
}
catch(exception& e) {
- errorOut(e, "PCACommand", "matrix_mult");
+ m->errorOut(e, "PCACommand", "matrix_mult");
exit(1);
}
matrix_mult(A,C,G);
}
catch(exception& e) {
- errorOut(e, "PCACommand", "recenter");
+ m->errorOut(e, "PCACommand", "recenter");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "PCACommand", "tred2");
+ m->errorOut(e, "PCACommand", "tred2");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "PCACommand", "qtli");
+ m->errorOut(e, "PCACommand", "qtli");
exit(1);
}
}
}
}
- 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+"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);
+ pcaLoadings.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+"pcoa.loadings");
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){
pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
}
- pcaData << "SeqName";
+ pcaData << "group";
for(int i=0;i<rank;i++){
pcaData << '\t' << "axis" << i+1;
}
}
}
catch(exception& e) {
- errorOut(e, "PCACommand", "output");
+ m->errorOut(e, "PCACommand", "output");
exit(1);
}
}
/*********************************************************************************************************************************/
-void PCACommand::print_matrix(vector<vector<double> > A) {
- try {
- int rank = A.size();
- for(int i=0;i<rank;i++){
- for(int j=0;j<rank;j++){
- cout << A[i][j] << " ";
- }
- cout << endl;
- }
- }
- catch(exception& e) {
- errorOut(e, "PCACommand", "print_matrix");
- exit(1);
- }
-}
-/*********************************************************************************************************************************/
-
projects / mothur.git / blobdiff