finished sub.sample command

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 9f961a9a6658683a3661290757ebe01048002371..df73c9389b99b7ba18725d418d62b36184efa398 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,6 +24,7 @@ vector<string> UnifracWeightedCommand::getValidParameters(){
 //**********************************************************************************************************************
 UnifracWeightedCommand::UnifracWeightedCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["weighted"] = tempOutNames;
@@ -211,7 +212,6 @@ int UnifracWeightedCommand::execute() {
                        }
                        
                        if (random) { 
-                               vector<double> sums = weighted->getBranchLengthSums(T[i]); 
                        
                                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                                vector< vector<string> > namesOfGroupCombos;
@@ -245,12 +245,12 @@ int UnifracWeightedCommand::execute() {
                                
                                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                                if(processors == 1){
-                                                       driver(T[i],  namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+                                                       driver(T[i],  namesOfGroupCombos, 0, namesOfGroupCombos.size(),  rScores);
                                                }else{
-                                                       createProcesses(T[i],  namesOfGroupCombos, sums, rScores);
+                                                       createProcesses(T[i],  namesOfGroupCombos, rScores);
                                                }
                                        #else
-                                               driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+                                               driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
                                        #endif
                                        
                                        if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());  } return 0; }
@@ -322,7 +322,7 @@ int UnifracWeightedCommand::execute() {
 }
 /**************************************************************************************************/
 
-int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 1;
@@ -339,7 +339,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
+                               driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, scores);
                        
                                //pass numSeqs to parent
                                ofstream out;
@@ -349,10 +349,14 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
                                out.close();
                                
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
-               driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores);
+               driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
                
                //force parent to wait until all the processes are done
                for (int i=0;i<(processors-1);i++) { 
@@ -383,7 +387,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
 }
 
 /**************************************************************************************************/
-int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) { 
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector< vector<double> >& scores) { 
  try {
                Tree* randT = new Tree();
 
@@ -404,7 +408,7 @@ int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGrou
                        if (m->control_pressed) { delete randT;  return 0;  }
 
                        //get wscore of random tree
-                       EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
+                       EstOutput randomData = weighted->getValues(randT, groupA, groupB);
                
                        if (m->control_pressed) { delete randT;  return 0;  }