fixes while testing 1.33.0

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 56e60d88bc88200a1b21d82d70b4a9c1f22ebdef..966cc253552068ad1945a19e1aaaedfd9b3da506 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -50,6 +50,7 @@
 #include "memeuclidean.h"
 #include "mempearson.h"
 #include "sharedjsd.h"
+#include "sharedrjsd.h"
 
 
 //**********************************************************************************************************************
@@ -58,7 +59,7 @@ vector<string> CollectSharedCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
                CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
-               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
                CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -143,6 +144,7 @@ string CollectSharedCommand::getOutputPattern(string type) {
         else if (type == "memeuclidean")        {  pattern =  "[filename],memeuclidean";    }
         else if (type == "mempearson")          {  pattern =  "[filename],mempearson";      }
         else if (type == "jsd")                 {  pattern =  "[filename],jsd";             }
+        else if (type == "rjsd")                 {  pattern =  "[filename],rjsd";             }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;
@@ -199,6 +201,7 @@ CollectSharedCommand::CollectSharedCommand(){
                outputTypes["memeuclidean"] = tempOutNames;
                outputTypes["mempearson"] = tempOutNames;
         outputTypes["jsd"] = tempOutNames;
+        outputTypes["rjsd"] = tempOutNames;
                
        }
        catch(exception& e) {
@@ -272,6 +275,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        outputTypes["memeuclidean"] = tempOutNames;
                        outputTypes["mempearson"] = tempOutNames;
             outputTypes["jsd"] = tempOutNames;
+            outputTypes["rjsd"] = tempOutNames;
                        
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -467,7 +471,11 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                                                }else if (Estimators[i] == "jsd") {
                                                        cDisplays.push_back(new CollectDisplay(new JSD(), new SharedOneColumnFile(getOutputFileName("jsd", variables))));
                                                        outputNames.push_back(getOutputFileName("jsd", variables)); outputTypes["jsd"].push_back(getOutputFileName("jsd", variables));
+                                               }else if (Estimators[i] == "rjsd") {
+                                                       cDisplays.push_back(new CollectDisplay(new RJSD(), new SharedOneColumnFile(getOutputFileName("rjsd", variables))));
+                                                       outputNames.push_back(getOutputFileName("rjsd", variables)); outputTypes["rjsd"].push_back(getOutputFileName("rjsd", variables));
                                                }
+
                                                
                                        }
                                }