X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=951b2008b062c26c5fabb54dfd8ef2d2a858da67;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=58fd99777a809afd6384861b4a3237218138c29f;hpb=5d77fd07180d1fb8561ff1962e6d7429caf8555e;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 58fd997..951b200 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -51,7 +51,28 @@ string PreClusterCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string PreClusterCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "precluster" + m->getExtension(inputName); }
+            else if (type == "name") {  outputFileName =  "precluster.names"; }
+            else if (type == "map") {  outputFileName =  "precluster.map"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PreClusterCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 PreClusterCommand::PreClusterCommand(){	
 	try {
@@ -184,9 +205,9 @@ int PreClusterCommand::execute(){
 		int start = time(NULL);
 		
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
-		string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
-		string newNamesFile = fileroot + "precluster.names";
-		string newMapFile = fileroot + "precluster.map"; //add group name if by group
+		string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
+		string newNamesFile = fileroot + getOutputFileNameTag("name");
+		string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
 		outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 		outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
 		
@@ -217,17 +238,19 @@ 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 +325,7 @@ 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 +335,17 @@ 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 +362,23 @@ 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
 		
 		//////////////////////////////////////////////////////////////////////////////////////////////////////