X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhercommand.cpp;h=c405e38060cec0db4b610c2e6c9e24a8810d7aed;hp=9bd437ad3cb7b2a75b69770769c8ddbc942f4a35;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ac663461b19ad1436a06aa63f97221d1ff105482

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 9bd437a..c405e38 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -266,7 +266,17 @@ ShhherCommand::ShhherCommand(string option) {
 			string temp;
 			temp = validParameter.validFile(parameters, "lookup", true);
 			if (temp == "not found")	{	
-				lookupFileName = "LookUp_Titanium.pat";	
+				string path = m->argv;
+                string tempPath = path;
+                for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                path = path.substr(0, (tempPath.find_last_of('m')));
+                
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                path += "lookupFiles/";
+#else
+                path += "lookupFiles\\";
+#endif
+				lookupFileName = m->getFullPathName(path) + "LookUp_Titanium.pat";
 				
 				int ableToOpen;
 				ifstream in;
@@ -276,7 +286,7 @@ ShhherCommand::ShhherCommand(string option) {
 				//if you can't open it, try input location
 				if (ableToOpen == 1) {
 					if (inputDir != "") { //default path is set
-						string tryPath = inputDir + lookupFileName;
+						string tryPath = inputDir + m->getSimpleName(lookupFileName);
 						m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine();
 						ifstream in2;
 						ableToOpen = m->openInputFile(tryPath, in2, "noerror");
@@ -324,7 +334,7 @@ ShhherCommand::ShhherCommand(string option) {
 				for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
 				exepath = exepath.substr(0, (tempPath.find_last_of('m')));
 					
-				string tryPath = m->getFullPathName(exepath) + lookupFileName;
+				string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
 				m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
 				ifstream in2;
 				int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
@@ -1680,10 +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;
@@ -1732,8 +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);
                         }
                     }
                     
@@ -1744,12 +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;
             }
         }
@@ -2384,16 +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; }
                 
@@ -2727,7 +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;
@@ -3269,12 +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;
@@ -3293,7 +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];
 					
@@ -3304,7 +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;
@@ -3321,28 +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);