X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=ee0a5462de87049f6b026546492203be630ea8d7;hb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;hp=c9fecd58ca08d9103770dd5f0e3afd7f2274c89d;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index c9fecd5..ee0a546 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -10,6 +10,55 @@
 
 #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)  {
@@ -42,12 +91,17 @@ 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; }
@@ -57,7 +111,7 @@ 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	
@@ -97,7 +151,7 @@ int PCACommand::execute(){
 		vector<string> names;
 		vector<vector<double> > D;
 	
-		fbase = outputDir + getRootName(getSimpleName(filename));
+		fbase = outputDir + m->getRootName(m->getSimpleName(filename));
 		
 		read(filename, names, D);
 		
@@ -219,11 +273,11 @@ int 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;
 		
@@ -233,21 +287,21 @@ 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) {
 		m->errorOut(e, "PCACommand", "read");
@@ -512,15 +566,17 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
 			}
 		}
 		
-		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++){