X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=5665426e537deca591a971a560f58283020eb9d3;hb=HEAD;hp=a53a3dcb92837f112771f44ef39219d9e36a277a;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index a53a3dc..5665426 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -17,7 +17,7 @@ vector<string> MatrixOutputCommand::setParameters(){
 		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
-		CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+		CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
 		CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
         CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
 		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
@@ -281,6 +281,10 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
 							matrixCalculators.push_back(new MemEuclidean());
 						}else if (Estimators[i] == "mempearson") { 
 							matrixCalculators.push_back(new MemPearson());
+                        }else if (Estimators[i] == "jsd") {
+                                matrixCalculators.push_back(new JSD());
+                        }else if (Estimators[i] == "rjsd") {
+                            matrixCalculators.push_back(new RJSD());
 						}
 					}
 				}
@@ -428,7 +432,7 @@ int MatrixOutputCommand::execute(){
 		string current = "";
 		itTypes = outputTypes.find("phylip");
 		if (itTypes != outputTypes.end()) {
-			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; if (!subsample) { m->setPhylipFile(current); } }
 		}
 		
 		m->mothurOutEndLine();
@@ -527,7 +531,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                 //loop through and create all the processes you want
                 while (process != processors) {
-                    int pid = fork();
+                    pid_t pid = fork();
                     
                     if (pid > 0) {
                         processIDS.push_back(pid); 
@@ -536,7 +540,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                         
                         driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);   
                         
-                        string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
+                        string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + m->mothurGetpid(process) + ".dist";
                         ofstream outtemp;
                         m->openOutputFile(tempdistFileName, outtemp);
                             
@@ -735,6 +739,8 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                 variables["[calc]"] = matrixCalculators[i]->getName();
                 string distFileName = getOutputFileName("phylip",variables);
                 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+                //set current phylip file to average distance matrix
+                m->setPhylipFile(distFileName);
                 ofstream outAve;
                 m->openOutputFile(distFileName, outAve);
                 outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
@@ -791,7 +797,7 @@ int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int star
 						vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 						
 						if (m->control_pressed) { return 1; }
-						
+        
 						seqDist temp(l, k, tempdata[0]);
 						calcDists[i].push_back(temp);
 					}