added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index fdec2ec483c67f1d37c23477d1411b5c97e8a215..2c9399bda1dd363d04c1fed89ff9b12ea8c3aace 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -184,9 +184,6 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        string temp = validParameter.validFile(parameters, "all", false);                               if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "distance", false);                                 if (temp == "not found") { temp = "false"; }
-                       createPhylip = m->isTrue(temp);
-                       
             temp = validParameter.validFile(parameters, "iters", false);                       if (temp == "not found") { temp = "1000"; }
                        m->mothurConvert(temp, iters); 
             
@@ -204,6 +201,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             
             if (subsample == false) { iters = 0; }
             
+            temp = validParameter.validFile(parameters, "distance", false);                                    if (temp == "not found") { temp = "false"; }
+                       createPhylip = m->isTrue(temp);
+            if (subsample) { createPhylip = true; }
+            
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors); 
@@ -703,7 +704,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 vector<summarySharedData*> pDataArray; 
                 DWORD   dwThreadIdArray[processors-1];
-                HANDLE  hThreadArray[processors-1]; 
+                HANDLE  hThreadArray[processors-1];
                 
                 //Create processor worker threads.
                 for( int i=1; i<processors; i++ ){
@@ -716,6 +717,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                         temp->setGroup(thisLookup[k]->getGroup());
                         newLookup.push_back(temp);
                     }
+                
                     
                     //for each bin
                     for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
@@ -742,6 +744,9 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 //Close all thread handles and free memory allocations.
                 for(int i=0; i < pDataArray.size(); i++){
+                    if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                        m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+                    }
                     m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
                     m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
                     
@@ -809,58 +814,10 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 
         if (iters != 0) {
             //we need to find the average distance and standard deviation for each groups distance
-            
-            vector< vector<seqDist>  > calcAverages; calcAverages.resize(sumCalculators.size()); 
-            for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                calcAverages[i].resize(calcDistsTotals[0][i].size());
-                
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].seq1 = calcDists[i][j].seq1;
-                    calcAverages[i][j].seq2 = calcDists[i][j].seq2;
-                    calcAverages[i][j].dist = 0.0;
-                }
-            }
-            
-            for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
-                for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                    for (int j = 0; j < calcAverages[i].size(); j++) {
-                        calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
-                    }
-                }
-            }
-            
-            for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].dist /= (float) iters;
-                }
-            }
+            vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);
             
             //find standard deviation
-            vector< vector<seqDist>  > stdDev; stdDev.resize(sumCalculators.size());
-            for (int i = 0; i < stdDev.size(); i++) {  //initialize sums to zero.
-                stdDev[i].resize(calcDistsTotals[0][i].size());
-                
-                for (int j = 0; j < stdDev[i].size(); j++) {
-                    stdDev[i][j].seq1 = calcDists[i][j].seq1;
-                    stdDev[i][j].seq2 = calcDists[i][j].seq2;
-                    stdDev[i][j].dist = 0.0;
-                }
-            }
-            
-            for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
-                for (int i = 0; i < stdDev.size(); i++) {  
-                    for (int j = 0; j < stdDev[i].size(); j++) {
-                        stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
-                    }
-                }
-            }
-            
-            for (int i = 0; i < stdDev.size(); i++) {  //finds average.
-                for (int j = 0; j < stdDev[i].size(); j++) {
-                    stdDev[i][j].dist /= (float) iters;
-                    stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
-                }
-            }
+            vector< vector<seqDist>  > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages); 
             
             //print results
             for (int i = 0; i < calcDists.size(); i++) {