X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=8a7656cee9cda0086fd2aaedd1afd5fb27896952;hb=ffa535cf04326227080b02594616971a2c3a5195;hp=310e32bf23e048c73ae37579ac2e8e2d1cb8b0ff;hpb=4e3080b15a3d0c02f7ef2fd779ead433ffdece31;p=mothur.git

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 310e32b..8a7656c 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", "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 +281,9 @@ 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());
+
 						}
 					}
 				}
@@ -652,7 +655,7 @@ 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 +794,7 @@ 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);
 					}