else {
//valid paramters for this command
- string Array[] = {"phylip"};
+ 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 = 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 += 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; }
-
-
}
}
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 += ".";
- }
+ //fbase = filename;
+ //if(fbase.find_last_of(".")!=string::npos){
+ // fbase.erase(fbase.find_last_of(".")+1);
+ //}
+ //else{
+ // fbase += ".";
+ //}
+
+ fbase = outputDir + getRootName(getSimpleName(filename));
+
read(filename, names, D);
double offset = 0.0000;
/*********************************************************************************************************************************/
-void PCACommand::read_mega(istream& f, 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){
try {
// int count1=0;
try {
ifstream f;
openInputFile(fname, f);
+
+ //check whether matrix is square
+ char d;
+ int m = 1;
+ int numSeqs;
+ string name;
- char test = f.peek();
+ f >> numSeqs >> name;
- if(test == '#'){
- read_mega(f, names, D);
- }
- else{
- //check whether matrix is square
- char d;
- int m = 1;
- int numSeqs;
- string name;
+ while((d=f.get()) != EOF){
- f >> numSeqs >> name;
-
- while((d=f.get()) != EOF){
-
- //is d a number meaning its square
- if(isalnum(d)){
- m = 1;
- break;
- }
-
- //is d a line return meaning its lower triangle
- if(d == '\n'){
- m = 2;
- break;
- }
+ //is d a number meaning its square
+ if(isalnum(d)){
+ m = 1;
+ break;
}
- f.close();
- //reopen to get back to beginning
- openInputFile(fname, f);
- read_phylip(f, m, names, D);
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ m = 2;
+ break;
+ }
}
+ f.close();
- //int rank = D.size();
+ //reopen to get back to beginning
+ openInputFile(fname, f);
+ read_phylip(f, m, names, D);
}
- catch(exception& e) {
+ catch(exception& e) {
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){
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;
}
/*********************************************************************************************************************************/
-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