added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index bd4086988a6f304833cabdfa2235a8536eefc8ae..986c68db1f4942e8242aef7514f78441ef0e37e0 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -16,7 +16,7 @@
 
 
 //**********************************************************************************************************************
-Venn::Venn(){
+Venn::Venn(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
 
@@ -31,7 +31,7 @@ void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
        try {
                                
                for(int i=0;i<vCalcs.size();i++){
-                       string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
+                       string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
                        openOutputFile(filenamesvg, outsvg);
 
                        vector<double> data = vCalcs[i]->getValues(sabund);
@@ -73,7 +73,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                        
                                //in essence you want to run it like a single 
@@ -122,7 +122,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
-                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB
@@ -168,7 +168,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                }else { outsvg << "</text>\n"; }
 
                                outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
-                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))) + "</text>\n";
+                               outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
                                outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"540\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
                                
                                //close file
@@ -191,7 +191,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        for(int i=0;i<vCalcs.size();i++){
                        
                                                                                                
-                               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                               string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                if (vCalcs[i]->getName() == "sharedace") {
@@ -232,7 +232,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                                //merge BC and estimate with shared with A
                                                SharedRAbundVector* merge = new SharedRAbundVector();
                                                for (int j = 0; j < lookup[1]->size(); j++) {
-                                                       merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
+                                                       merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
                                                }
                                        
                                                subset.clear();
@@ -243,7 +243,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                                //merge AC and estimate with shared with B
                                                merge = new SharedRAbundVector();
                                                for (int j = 0; j < lookup[0]->size(); j++) {
-                                                       merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
+                                                       merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
                                                }
                                        
                                                subset.clear();
@@ -254,7 +254,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                                //merge AB and estimate with shared with C
                                                merge = new SharedRAbundVector();
                                                for (int j = 0; j < lookup[0]->size(); j++) {
-                                                       merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
+                                                       merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
                                                }
                                        
                                                subset.clear();
@@ -306,12 +306,12 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";  
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n"; 
                                
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"740\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"760\">The number of sepecies shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"740\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"760\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
                                        if (numA.size() == 3) { 
                                                outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
@@ -389,9 +389,9 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"305\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";  
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedabc[0]).length() / 2)) + "\"  y=\"280\">" + toString(sharedabc[0]) + "</text>\n"; 
                                
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
                                        if (numA.size() == 3) { 
                                                outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
@@ -446,7 +446,7 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                
                                if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); mothurOutEndLine(); }
                                else{
-                                       string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+                                       string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                        openOutputFile(filenamesvg, outsvg);
 
                                
@@ -546,17 +546,17 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"530\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
                                        outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"550\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</text>\n";
                                        
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"570\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"590\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"610\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"630\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"650\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"670\">The number of sepecies shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"570\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"590\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"610\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"630\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"650\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"670\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
                                        
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"690\">The number of sepecies shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"710\">The number of sepecies shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"730\">The number of sepecies shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
-                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"750\">The number of sepecies shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"690\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"710\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"730\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
+                                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"750\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
                                                                        
                                        //make adjustments
                                        sharedABC = sharedABC - sharedABCD;