changes while testing

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index a20679a1b352f0fc95f2329f0e536c54a029cced..c405e38060cec0db4b610c2e6c9e24a8810d7aed 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1690,10 +1690,8 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
             if (m->control_pressed) { break; }
             
             int index = 0;
-            int base = 0;
             
             if(nSeqsPerOTU[i] > 0){
-                qualities[i].assign(1024, -1);
                 
                 while(index < numFlowCells){
                     double maxPrValue = 1e8;
@@ -1742,8 +1740,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
                             value = (int)floor(temp);
                             if(value > 100){   value = 100;    }
                             
-                            qualities[i][base] = (int)value;
-                            base++;
+                            qualities[i].push_back((int)value);
                         }
                     }
                     
@@ -1754,12 +1751,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
             
             if(otuCounts[i] > 0){
                 qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-                
-                int j=4;       //need to get past the first four bases
-                while(qualities[i][j] != -1){
-                    qualityFile << qualities[i][j] << ' ';
-                    j++;
-                }
+                for (int j = 4; j < qualities[i].size(); j++) { qualityFile << qualities[i][j] << ' '; }
                 qualityFile << endl;
             }
         }
@@ -2394,16 +2386,22 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 m->mothurOut("\nFinalizing...\n");
                 fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: done fill().\n"); }
+
                 if (m->control_pressed) { break; }
                 
                 setOTUs(numOTUs, numSeqs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, otuData, singleTau, dist, aaP, aaI);
                 
+                if (m->debug) { m->mothurOut("[DEBUG]: done setOTUs().\n"); }
+                
                 if (m->control_pressed) { break; }
                 
                 vector<int> otuCounts(numOTUs, 0);
                 for(int j=0;j<numSeqs;j++)     {       otuCounts[otuData[j]]++;        }
                 
-                calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);        
+                calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: done calcCentroidsDriver().\n"); }
                 
                 if (m->control_pressed) { break; }
                 
@@ -2737,7 +2735,8 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
         
                RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
-               Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); 
+        float adjust = -1.0;
+               Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest", adjust);
                string tag = cluster->getTag();
                
                double clusterCutoff = cutoff;
@@ -3279,12 +3278,11 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                        if (m->control_pressed) { break; }
                        
                        int index = 0;
-                       int base = 0;
-                       
+            
                        if(nSeqsPerOTU[i] > 0){
-                               qualities[i].assign(1024, -1);
                                
                                while(index < numFlowCells){
+                    
                                        double maxPrValue = 1e8;
                                        short maxPrIndex = -1;
                                        double count = 0.0000;
@@ -3303,7 +3301,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                                                        pr[s] += tauValue * singleLookUp[s * NUMBINS + intensity];
                                                }
                                        }
-                                       
+                    
                                        maxPrIndex = uniqueFlowgrams[centroids[i] * numFlowCells + index];
                                        maxPrValue = pr[maxPrIndex];
                                        
@@ -3314,7 +3312,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                                                for(int s=0;s<HOMOPS;s++){
                                                        norm += exp(-(pr[s] - maxPrValue));
                                                }
-                                               
+                        
                                                for(int s=1;s<=maxPrIndex;s++){
                                                        int value = 0;
                                                        double temp = 0.0000;
@@ -3331,28 +3329,24 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                                                        value = (int)floor(temp);
                                                        if(value > 100){        value = 100;    }
                                                        
-                                                       qualities[i][base] = (int)value;
-                                                       base++;
+                            qualities[i].push_back((int)value);
                                                }
-                                       }
+                                       }//end if
                                        
                                        index++;
-                               }
-                       }
-                       
+                    
+                               }//end while
+                
+                       }//end if
                        
+            
                        if(otuCounts[i] > 0){
                                qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-                       
-                               int j=4;        //need to get past the first four bases
-                               while(qualities[i][j] != -1){
-                    qualityFile << qualities[i][j] << ' ';
-                    if (j > qualities[i].size()) { break; }
-                    j++;
-                               }
+                //need to get past the first four bases
+                for (int j = 4; j < qualities[i].size(); j++) { qualityFile << qualities[i][j] << ' '; }
                                qualityFile << endl;
                        }
-               }
+               }//end for
                qualityFile.close();
                outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);