citation changes for 1.31.0

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 0ac7ba85a278ffde691f78cf49f7101dd5aa51b1..e1a4dfa2c93e2aacff71b0c26f1a0172f0933f90 100644 (file)
--- 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 276b71ccdfbeda299125477eefbc3796a2c9aa7b..7a6907f47cc2030d9cab822db6c34b95c72e1504 100755 (executable)
--- 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 f5310bc1983b50eda0411c78061d7a58c6447ffd..1fd29240c156049f61abd9e9bc1f66132275d16c 100644 (file)
--- 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 2264c87b9af87c5f3363f5774116ff95bb691b8f..65e5770fdc7c9bc8f4b594fd884f523e4387e40c 100644 (file)
--- 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 142023e7a40881c1c6397a761ba350132490b75c..9538698a3fea181430056d11f16835f66186452e 100644 (file)
--- 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 de21717ce03df122f7df9ddc014cc49900768250..25ef4d4be2cbc15fe8a79657090531cc56183812 100644 (file)
--- 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 743e756544d29624d699acd7f50764403976c834..ca274e057532e5a3bbc0839c92cdcee8984e61e1 100644 (file)
--- 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 8add3eded2682f6e7568670e3c155d0fa40d1356..73e9f8a593072a34ba7f1f5b4efd6f5d81e972fc 100644 (file)
--- 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()); }