From b72799e7908e2a3a0cf4f03e796b077a97ace6ac Mon Sep 17 00:00:00 2001 From: westcott Date: Tue, 21 Jun 2011 11:25:46 +0000 Subject: [PATCH] descriptions --- amovacommand.h | 2 +- anosimcommand.h | 2 +- chimerauchimecommand.cpp | 4 ++-- clusterdoturcommand.h | 2 +- indicatorcommand.cpp | 9 ++++++--- mantelcommand.h | 2 +- systemcommand.h | 2 +- 7 files changed, 13 insertions(+), 10 deletions(-) diff --git a/amovacommand.h b/amovacommand.h index 89720d6..50dc81a 100644 --- 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 9f8617a..4b65070 100644 --- 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 af427d8..f757fb9 100644 --- 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 3a32349..643551a 100644 --- 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 ab9e275..966810b 100644 --- a/indicatorcommand.cpp +++ b/indicatorcommand.cpp @@ -544,6 +544,7 @@ vector IndicatorCommand::getValues(vector< vector terms; float AijDenominator = 0.0; vector Bij; + //get overall abundance of each grouping for (int j = 0; j < groupings.size(); j++) { @@ -554,6 +555,7 @@ vector IndicatorCommand::getValues(vector< vectorgetAbundance(i) != 0) { numNotZero++; } } + //mean abundance float Aij = (totalAbund / (float) groupings[j].size()); terms.push_back(Aij); @@ -565,7 +567,7 @@ vector IndicatorCommand::getValues(vector< vector IndicatorCommand::getValues(vector< vector >& 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 IndicatorCommand::getValues(vector< vector >& 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 adffda8..0a2c404 100644 --- 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 e0061f5..6a4b884 100644 --- 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()); } -- 2.39.2