X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=bcff0fcd820a497da04405bef0ddb42d7d60ded9;hb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;hp=8e4f3274a490679c85f992f8584605c877c84850;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 8e4f327..bcff0fc 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -217,17 +217,19 @@ int PreClusterCommand::execute(){
 			m->mothurOutEndLine(); 
 			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 			m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-			
+			m->mothurCalling = true;
+            
 			Command* uniqueCommand = new DeconvoluteCommand(inputString);
 			uniqueCommand->execute();
 			
 			map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 			
 			delete uniqueCommand;
-			
+			m->mothurCalling = false;
 			m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 			
 			m->renameFile(filenames["fasta"][0], newFastaFile);
+            m->renameFile(filenames["name"][0], newNamesFile);
 			
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
@@ -302,7 +304,7 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -312,7 +314,17 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 				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){
+                outputNames.clear();
 				num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+                
+                string tempFile = toString(getpid()) + ".outputNames.temp";
+                ofstream outTemp;
+                m->openOutputFile(tempFile, outTemp);
+                
+                outTemp << outputNames.size();
+                for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
+                outTemp.close();
+                
 				exit(0);
 			}else { 
 				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
@@ -329,7 +341,23 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 			int temp = processIDS[i];
 			wait(&temp);
 		}
-		
+        
+        for (int i = 0; i < processIDS.size(); i++) {
+            string tempFile = toString(processIDS[i]) +  ".outputNames.temp";
+            ifstream intemp;
+            m->openInputFile(tempFile, intemp);
+            
+            int num;
+            intemp >> num;
+            for (int k = 0; k < num; k++) {
+                string name = "";
+                intemp >> name; m->gobble(intemp);
+                
+                outputNames.push_back(name); outputTypes["map"].push_back(name);
+            }
+            intemp.close();
+            m->mothurRemove(tempFile);
+        }
 #else
 		
 		//////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -553,6 +581,7 @@ int PreClusterCommand::readFASTA(){
 		//inNames.close();
         
         if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
         
 		return alignSeqs.size();
 	}
@@ -598,6 +627,7 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
 		}
 		
         if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
         
 		//sanity check
 		if (error) { m->control_pressed = true; }