X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=c982d7563c8f26066924eeab070f5fd16a5b30e5;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=c17053e29cb31812f681333078199c9abaea02fa;hpb=96b36196d49a3d1f6bc49a26a9d2aa2da7ff876e;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index c17053e..c982d75 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -12,7 +12,7 @@
 
 //**********************************************************************************************************************
 
-PCACommand::PCACommand(string option){
+PCACommand::PCACommand(string option)  {
 	try {
 		abort = false;
 		
@@ -42,7 +42,7 @@ 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;		}
 				}
@@ -57,16 +57,16 @@ PCACommand::PCACommand(string option){
 			//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	
-			if (phylipfile == "")	{ mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }		
+			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);
 	}
 }
@@ -74,10 +74,10 @@ PCACommand::PCACommand(string option){
 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);
 	}
 }
@@ -97,17 +97,11 @@ int PCACommand::execute(){
 		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 = outputDir + getRootName(getSimpleName(filename));
+		fbase = outputDir + m->getRootName(m->getSimpleName(filename));
 		
 		read(filename, names, D);
+		
+		if (m->control_pressed) { return 0; }
    	
 		double offset = 0.0000;
 		vector<double> d;
@@ -116,23 +110,31 @@ int PCACommand::execute(){
 		vector<vector<double> > copy_G;
 		//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);
 	}
 }
@@ -152,14 +154,14 @@ void PCACommand::get_comment(istream& f, char begin, char end){
 		d = f.peek();
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "get_comment");
+		m->errorOut(e, "PCACommand", "get_comment");
 		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;
@@ -176,6 +178,8 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
 				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;
@@ -192,6 +196,7 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
 				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;
@@ -199,9 +204,11 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
 				}
 			}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "read_phylip");
+		m->errorOut(e, "PCACommand", "read_phylip");
 		exit(1);
 	}
 
@@ -212,11 +219,11 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
 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;
 		
@@ -226,24 +233,24 @@ void PCACommand::read(string fname, vector<string>& names, vector<vector<double>
 			
 			//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) {
-		errorOut(e, "PCACommand", "read");
+		m->errorOut(e, "PCACommand", "read");
 		exit(1);
 	}
 }
@@ -275,7 +282,7 @@ void PCACommand::matrix_mult(vector<vector<double> > first, vector<vector<double
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "matrix_mult");
+		m->errorOut(e, "PCACommand", "matrix_mult");
 		exit(1);
 	}
 
@@ -309,7 +316,7 @@ void PCACommand::recenter(double offset, vector<vector<double> > D, vector<vecto
 		matrix_mult(A,C,G);
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "recenter");
+		m->errorOut(e, "PCACommand", "recenter");
 		exit(1);
 	}
 
@@ -402,7 +409,7 @@ void PCACommand::tred2(vector<vector<double> >& a, vector<double>& d, vector<dou
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "tred2");
+		m->errorOut(e, "PCACommand", "tred2");
 		exit(1);
 	}
 
@@ -486,7 +493,7 @@ void PCACommand::qtli(vector<double>& d, vector<double>& e, vector<vector<double
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "qtli");
+		m->errorOut(e, "PCACommand", "qtli");
 		exit(1);
 	}
 }
@@ -508,10 +515,12 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
 		ofstream pcaData((fnameRoot+"pca").c_str(), ios::trunc);
 		pcaData.setf(ios::fixed, ios::floatfield);
 		pcaData.setf(ios::showpoint);	
+		outputNames.push_back(fnameRoot+"pca");
 		
 		ofstream pcaLoadings((fnameRoot+"pca.loadings").c_str(), ios::trunc);
 		pcaLoadings.setf(ios::fixed, ios::floatfield);
-		pcaLoadings.setf(ios::showpoint);	
+		pcaLoadings.setf(ios::showpoint);
+		outputNames.push_back(fnameRoot+"pca.loadings");	
 		
 		pcaLoadings << "axis\tloading\n";
 		for(int i=0;i<rank;i++){
@@ -533,7 +542,7 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "PCACommand", "output");
+		m->errorOut(e, "PCACommand", "output");
 		exit(1);
 	}
 }