changed heatmap and venn command to use vector of sharedrabunds instead of order...

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index 3c0d797b4a246246af19a664b032017745e9f546..7c33dd7a7bb1237480c4e5d95b28187832a7b71d 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -18,7 +18,6 @@ Venn::Venn(){
        try {
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
-               util = new SharedUtil();
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -30,13 +29,11 @@ Venn::Venn(){
        }
 }
 //**********************************************************************************************************************
-void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
+void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
        try {
-               SAbundVector s;
-               s = order->getSAbundVector();  sabund = &s;
-               
+                               
                for(int i=0;i<vCalcs.size();i++){
-                       string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + vCalcs[i]->getName() + ".svg";
+                       string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
                        openOutputFile(filenamesvg, outsvg);
 
                        vector<double> data = vCalcs[i]->getValues(sabund);
@@ -46,7 +43,7 @@ void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
                        outsvg << "<g>\n";
                                
                        outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>"; 
-                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + order->getLabel() + "</text>\n";
+                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
                        outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>"; 
                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";  
                        
@@ -69,21 +66,21 @@ void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
        }
 }
 //**********************************************************************************************************************
-void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
+void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
        try {
                
                //fills vector of sharedsabunds - lookup
-               util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
+               //util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
                
                /******************* 1 Group **************************/
                if (lookup.size() == 1) {
                                        
                        SAbundVector s;
-                       s = lookup[0]->getSAbundVector();  sabund = &s;
+                       s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                        
                                //in essence you want to run it like a single 
@@ -102,7 +99,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
                                outsvg << "<g>\n";
                                
                                outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>"; 
-                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
+                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
                                outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>"; 
                                outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
                                outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";  
@@ -130,7 +127,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB
@@ -157,7 +154,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
 
                                //draw circles
                                outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>"; 
-                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
+                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
                                outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>"; 
                                outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>"; 
                                outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
@@ -200,7 +197,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB, sharedAC and sharedBC
@@ -276,7 +273,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
 
                                //draw circles
                                outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>"; 
-                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
+                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
                                outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>"; 
                                outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>"; 
                                outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>"; 
@@ -360,7 +357,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
                                if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0)) { sharedABCD++; }
                        }
                                
-                       string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn.sharedsobs.svg";
+                       string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn.sharedsobs.svg";
                        openOutputFile(filenamesvg, outsvg);
                
                        //image window
@@ -369,7 +366,7 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
 
                        //draw circles
                        outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>"; 
-                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
+                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
                        outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n "; 
                        outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
                        outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";