fixes while testing 1.33.0

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 310e32bf23e048c73ae37579ac2e8e2d1cb8b0ff..2e6943f0eb7aed1c0b881b5dd5a5d079cdd4fb87 100644 (file)
--- 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());
                                                }
                                        }
                                }
@@ -652,7 +656,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
             }
             
             if (subsample && (thisIter != 0)) {  
-                if((thisIter) % 100 == 0){     m->mothurOut(toString(thisIter)); m->mothurOutEndLine();                }
+                if((thisIter) % 100 == 0){     m->mothurOutJustToScreen(toString(thisIter)+"\n");              }
                 calcDistsTotals.push_back(calcDists);
                 for (int i = 0; i < calcDists.size(); i++) {
                     for (int j = 0; j < calcDists[i].size(); j++) {
@@ -791,7 +795,7 @@ 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);
                                        }