added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / rarefact.cpp

diff --git a/rarefact.cpp b/rarefact.cpp
index 6acc24ce9df500338873829216e5c1b3754d7df7..691d01708bab5b5bef4118ab38662819280b56de 100644 (file)
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -12,13 +12,18 @@
 
 /***********************************************************************/
 
-void Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
        try {
                RarefactionCurveData* rcd = new RarefactionCurveData();
                for(int i=0;i<displays.size();i++){
                        rcd->registerDisplay(displays[i]);
                }
-       
+               
+               //convert freq percentage to number
+               int increment = 1;
+               if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+               else { increment = percentFreq;  }      
+                       
                for(int iter=0;iter<nIters;iter++){
                
                        for(int i=0;i<displays.size();i++){
@@ -31,6 +36,8 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
                
                        for(int i=0;i<numSeqs;i++){
                        
+                               if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0;  }
+                       
                                int binNumber = order->get(i);
                                int abundance = lookup->get(binNumber);
                        
@@ -61,6 +68,7 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
                        displays[i]->close();
                }
                delete rcd;
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "Rarefact", "getCurve");
@@ -70,7 +78,7 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 
 /***********************************************************************/
 
-void Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
 try {
                SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
                
@@ -84,6 +92,11 @@ try {
                //if jumble is false all iters will be the same
                if (globaldata->jumble == false)  {  nIters = 1;  }
                
+               //convert freq percentage to number
+               int increment = 1;
+               if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+               else { increment = percentFreq;  }
+               
                for(int iter=0;iter<nIters;iter++){
                
                        for(int i=0;i<displays.size();i++){
@@ -106,6 +119,8 @@ try {
                        vector<SharedRAbundVector*> subset;
                        //send each group one at a time
                        for (int k = 0; k < lookup.size(); k++) { 
+                               if (m->control_pressed) {  delete merge; delete rcd; return 0;  }
+                               
                                subset.clear(); //clears out old pair of sharedrabunds
                                //add in new pair of sharedrabunds
                                subset.push_back(merge); subset.push_back(lookup[k]);
@@ -127,6 +142,7 @@ try {
                }
                
                delete rcd;
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "Rarefact", "getSharedCurve");