citation changes for 1.31.0

mothur · May 28, 2013 · ace98dd · ace98dd
1 parent bd27c2b
commit ace98dd
Show file tree

Hide file tree

Showing 8 changed files with 13 additions and 13 deletions.
diff --git 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
@@ -24,7 +24,7 @@ class ClassifySharedCommand : public Command {
   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
@@ -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
@@ -28,8 +28,8 @@ class GetMetaCommunityCommand : public Command {
     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
@@ -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
@@ -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
@@ -26,8 +26,8 @@ class MakeLookupCommand : public Command {
 
     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
@@ -29,7 +29,7 @@ class SparccCommand : public Command {
     //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()); }