descriptions

diff --git a/amovacommand.h b/amovacommand.h
index 89720d6b93c6232a14562cd3c216855fed9a1d8d..50dc81a517dbbe89f39d9a4e1ca858ed3488a402 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -25,7 +25,7 @@ public:
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
        string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
-       string getDescription()         { return "calculate AMOVA statistic"; }
+       string getDescription()         { return "analysis of molecular variance"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/anosimcommand.h b/anosimcommand.h
index 9f8617acf5f087c38864d431786d9e3f2a4ba554..4b650705ace41501f3d85d672638a47f48a91ce3 100644 (file)
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -27,7 +27,7 @@ public:
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
        string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
-       string getDescription()         { return "anosim"; }
+       string getDescription()         { return "analysis of similarity"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index af427d8b6445e39185661bf51782bec1efc54fe6..f757fb956858ff6b244132bd44c0b83d8b9e16db 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -376,7 +376,7 @@ int ChimeraUchimeCommand::execute(){
                        int start = time(NULL); 
                        string nameFile = "";
                        
-                       if (templatefile == "self") { //you want to run uchime with a refernce template
+                       if (templatefile == "self") { //you want to run uchime with a reference template
                                
                                #ifdef USE_MPI  
                                        int pid; 
@@ -434,7 +434,7 @@ int ChimeraUchimeCommand::execute(){
                                
                                sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
                                
-                               string newFasta = fastaFileNames[s] + ".temp";
+                               string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
                                ofstream out;
                                m->openOutputFile(newFasta, out);
                                

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index 3a3234933e65c885c89490738db9e85e6b95d5e3..643551a35c0289efe46a9bd5f2e280566faea31e 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -29,7 +29,7 @@ public:
        string getCommandCategory()             { return "Clustering";                  }
        string getHelpString(); 
        string getCitation() { return "Schloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6. \nhttp://www.mothur.org/wiki/Cluster.classic"; }
-       string getDescription()         { return "cluster your sequences into OTUs using dotur's method"; }
+       string getDescription()         { return "cluster your sequences into OTUs using DOTUR’s method"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index ab9e275279e0399182d458b7a6a64b81ba56c205..966810b1438bd7e9b4072f6a8cccd6cb2d105cee 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -544,6 +544,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                        vector<float> terms; 
                        float AijDenominator = 0.0;
                        vector<float> Bij;
+                       
                        //get overall abundance of each grouping
                        for (int j = 0; j < groupings.size(); j++) {
                                
@@ -554,6 +555,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                                        if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
                                }
                                
+                               //mean abundance
                                float Aij = (totalAbund / (float) groupings[j].size());
                                terms.push_back(Aij);
                                
@@ -565,7 +567,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                        
                        float maxIndVal = 0.0;
                        for (int j = 0; j < terms.size(); j++) { 
-                               float thisAij = (terms[j] / AijDenominator); 
+                               float thisAij = (terms[j] / AijDenominator); //relative abundance
                                float thisValue = thisAij * Bij[j] * 100.0;
                                
                                //save largest
@@ -609,7 +611,8 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >&
                                        if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
                                        
                                }
-                                       
+                               
+                               //mean abundance        
                                float Aij = (totalAbund / (float) groupings[j].size());
                                terms.push_back(Aij);
                                
@@ -621,7 +624,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >&
                        
                        float maxIndVal = 0.0;
                        for (int j = 0; j < terms.size(); j++) { 
-                               float thisAij = (terms[j] / AijDenominator); 
+                               float thisAij = (terms[j] / AijDenominator); //relative abundance
                                float thisValue = thisAij * Bij[j] * 100.0;
                                        
                                //save largest

diff --git a/mantelcommand.h b/mantelcommand.h
index adffda857c4e4aa64ceb38c502f011d7ecefed2e..0a2c4045960911c65c4ea43213c08add648663a6 100644 (file)
--- a/mantelcommand.h
+++ b/mantelcommand.h
@@ -24,7 +24,7 @@ public:
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
        string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Mantel"; }
-       string getDescription()         { return "mantel"; }
+       string getDescription()         { return "Mantel’s test for correlation between matrices"; }
 
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/systemcommand.h b/systemcommand.h
index e0061f587ea6a3c7003fbc8b16a48763242ce964..6a4b884cba8ee21629219593cf43eae7b4c02447 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -26,7 +26,7 @@ class SystemCommand : public Command {
                string getCommandCategory()             { return "General";             }
                string getHelpString(); 
                string getCitation() { return "http://www.mothur.org/wiki/System"; }
-               string getDescription()         { return "excute system commands from within mothur"; }
+               string getDescription()         { return "execute system commands from within mothur"; }
 
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }