From ace98dda2bb2e1cffd6755fb8a27e5080af66f2b Mon Sep 17 00:00:00 2001 From: Sarah Westcott Date: Tue, 28 May 2013 09:45:57 -0400 Subject: [PATCH] citation changes for 1.31.0 --- Mothur.xcodeproj/project.pbxproj | 8 ++++---- classifysharedcommand.h | 2 +- decisiontree.cpp | 2 +- getmetacommunitycommand.h | 4 ++-- getseqscommand.cpp | 2 +- makefile | 2 +- makelookupcommand.h | 4 ++-- sparcccommand.h | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 0ac7ba8..e1a4dfa 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -2416,8 +2416,8 @@ GCC_OPTIMIZATION_LEVEL = s; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../../release\\\"\"", - "VERSION=\"\\\"1.29.2\\\"\"", - "RELEASE_DATE=\"\\\"2/12/2013\\\"\"", + "VERSION=\"\\\"1.31.0\\\"\"", + "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", ); "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; @@ -2452,8 +2452,8 @@ GCC_MODEL_TUNING = ""; GCC_OPTIMIZATION_LEVEL = s; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.30.0\\\"\"", - "RELEASE_DATE=\"\\\"4/01/2013\\\"\"", + "VERSION=\"\\\"1.31.0\\\"\"", + "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; diff --git a/classifysharedcommand.h b/classifysharedcommand.h index 276b71c..7a6907f 100755 --- a/classifysharedcommand.h +++ b/classifysharedcommand.h @@ -24,7 +24,7 @@ public: string getHelpString(); string getOutputPattern(string); string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; } - string getDescription() { return "description"; } + string getDescription() { return "implements the random forest machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; } int execute(); void help() { m->mothurOut(getHelpString()); } diff --git a/decisiontree.cpp b/decisiontree.cpp index f5310bc..1fd2924 100644 --- a/decisiontree.cpp +++ b/decisiontree.cpp @@ -440,7 +440,7 @@ void DecisionTree::deleteTreeNodesRecursively(RFTreeNode* treeNode) { if (treeNode == NULL) { return; } deleteTreeNodesRecursively(treeNode->leftChildNode); deleteTreeNodesRecursively(treeNode->rightChildNode); - delete treeNode; + delete treeNode; treeNode = NULL; } catch(exception& e) { m->errorOut(e, "DecisionTree", "deleteTreeNodesRecursively"); diff --git a/getmetacommunitycommand.h b/getmetacommunitycommand.h index 2264c87..65e5770 100644 --- a/getmetacommunitycommand.h +++ b/getmetacommunitycommand.h @@ -28,8 +28,8 @@ public: string getOutputPattern(string); string getHelpString(); - string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; } - string getDescription() { return "brief description"; } + string getCitation() { return "Holmes I, Harris K, Quince C (2012) Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126 http://www.mothur.org/wiki/Get.metacommunity"; } + string getDescription() { return "Assigns samples to bins using a Dirichlet multinomial mixture model"; } int execute(); void help() { m->mothurOut(getHelpString()); } diff --git a/getseqscommand.cpp b/getseqscommand.cpp index 142023e..9538698 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -45,7 +45,7 @@ string GetSeqsCommand::getHelpString(){ helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n"; helpString += "It outputs a file containing only the sequences in the .accnos file.\n"; helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n"; - helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n"; + helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=true. \n"; helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"; helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"; helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; diff --git a/makefile b/makefile index de21717..25ef4d4 100644 --- a/makefile +++ b/makefile @@ -15,7 +15,7 @@ USEREADLINE ?= yes CYGWIN_BUILD ?= no USECOMPRESSION ?= no MOTHUR_FILES="\"Enter_your_default_path_here\"" -RELEASE_DATE = "\"5/24/2013\"" +RELEASE_DATE = "\"5/28/2013\"" VERSION = "\"1.31.0\"" FORTAN_COMPILER = gfortran FORTRAN_FLAGS = diff --git a/makelookupcommand.h b/makelookupcommand.h index 743e756..ca274e0 100644 --- a/makelookupcommand.h +++ b/makelookupcommand.h @@ -26,8 +26,8 @@ public: string getOutputPattern(string); string getHelpString(); - string getCitation() { return "http://www.mothur.org/wiki/Make.lookup"; } - string getDescription() { return "create custom lookup files for use with shhh.flows"; } + string getCitation() { return "Quince, C., A. Lanzén, T. P. Curtis, R. J. Davenport, N. Hall, I. M. Head, L. F. Read, and W. T. Sloan. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6:639-41. http://www.mothur.org/wiki/Make.lookup"; } + string getDescription() { return "Creates a lookup file for use with shhh.flows using user-supplied mock community data and flow grams"; } int execute(); void help() { m->mothurOut(getHelpString()); } diff --git a/sparcccommand.h b/sparcccommand.h index 8add3ed..73e9f8a 100644 --- a/sparcccommand.h +++ b/sparcccommand.h @@ -29,7 +29,7 @@ public: //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden string getHelpString(); string getCitation() { return "Friedman J, Alm EJ (2012) Inferring Correlation Networks from Genomic Survey Data. PLoS Comput Biol 8(9): e1002687. doi:10.1371/journal.pcbi.1002687 http://www.mothur.org/wiki/Sparcc"; } - string getDescription() { return "brief description"; } + string getDescription() { return "Calculates correlations between OTUs using a method that is insensitive to the use of relative abundance data"; } int execute(); void help() { m->mothurOut(getHelpString()); } -- 2.39.2