sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 6e2cce79736a9f01edbaa44bd31e145921850a30..7103adb8a150a3e6f9871989ba94bd45d2b6a542 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -13,13 +13,13 @@
 //**********************************************************************************************************************
 vector<string> PCACommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);    
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared);        
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(prelabund);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               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);          }
@@ -48,6 +48,23 @@ string PCACommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string PCACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "pca") {  pattern = "[filename],[distance],pca.axes"; } 
+        else if (type == "loadings") {  pattern = "[filename],[distance],pca.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, "PCACommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 PCACommand::PCACommand(){      
        try {
@@ -70,6 +87,7 @@ PCACommand::PCACommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -116,12 +134,12 @@ PCACommand::PCACommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  mode = "sharedfile"; inputFile = sharedfile; }
+                       else {  mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { relabundfile = ""; abort = true; }    
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else {  mode = "relabund"; inputFile = relabundfile; }
+                       else {  mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        
                        if ((sharedfile == "") && (relabundfile == "")) { 
@@ -156,7 +174,7 @@ PCACommand::PCACommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  }
                        else { m->splitAtDash(groups, Groups);  }                       
-                       m->Groups = Groups;                     
+                       m->setGroups(Groups);                   
                        
                }
                
@@ -202,7 +220,7 @@ int PCACommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
                        
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
                        
                        if(labels.count(lookupFloat[0]->getLabel()) == 1){
                                processedLabels.insert(lookupFloat[0]->getLabel());
@@ -235,7 +253,7 @@ int PCACommand::execute(){
                }
                
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -263,7 +281,7 @@ int PCACommand::execute(){
                for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } } lookupFloat.clear();
                delete input;
                
-               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; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -318,7 +336,6 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
                vector< vector<double> > matrix(numSamples);
                vector<double> colMeans(numOTUs);
                
-                               
                //fill matrix with shared relative abundances, re-center
                for (int i = 0; i < lookupFloat.size(); i++) {
                        matrix[i].resize(numOTUs, 0);
@@ -364,8 +381,8 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
                if (m->control_pressed) { return 0; }
                
                string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
-               string outputFileName = fbase + lookupFloat[0]->getLabel();
-               output(outputFileName, m->Groups, X, d);
+               //string outputFileName = fbase + lookupFloat[0]->getLabel();
+               output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d);
                
                if (metric) {   
                        
@@ -375,13 +392,13 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
                                
                                vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca 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(PCAEuclidDists, observedEuclideanDistance);
                                                                
                                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; }
                        }
                }
                
@@ -394,7 +411,7 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 }
 /*********************************************************************************************************************************/
 
-void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+void PCACommand::output(string fbase, string label, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
        try {
 
                int numEigenValues = d.size();
@@ -403,17 +420,24 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                        dsum += d[i];
                }
                
-               ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
+               ofstream pcaData;
+        map<string, string> variables; 
+        variables["[filename]"] = fbase;
+        variables["[distance]"] = label;
+        string pcaFileName = getOutputFileName("pca",variables);
+        m->openOutputFile(pcaFileName, pcaData);
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
-               outputNames.push_back(fnameRoot+".pca.axes");
-               outputTypes["pca"].push_back(fnameRoot+".pca.axes");
+               outputNames.push_back(pcaFileName);
+               outputTypes["pca"].push_back(pcaFileName);
                
-               ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+               ofstream pcaLoadings;
+        string loadingsFilename = getOutputFileName("loadings",variables);
+         m->openOutputFile(loadingsFilename, pcaLoadings);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
                pcaLoadings.setf(ios::showpoint);
-               outputNames.push_back(fnameRoot+".pca.loadings");
-               outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");   
+               outputNames.push_back(loadingsFilename);
+               outputTypes["loadings"].push_back(loadingsFilename);    
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<numEigenValues;i++){
@@ -426,7 +450,7 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                }
                pcaData << endl;
                
-               for(int i=0;i<numEigenValues;i++){
+               for(int i=0;i<name_list.size();i++){
                        pcaData << name_list[i] << '\t';
                        for(int j=0;j<numEigenValues;j++){
                                pcaData << G[i][j] << '\t';