From 783b9ef8e739307aed392f35970701f6b53390fb Mon Sep 17 00:00:00 2001 From: westcott Date: Wed, 20 Jul 2011 14:53:48 +0000 Subject: [PATCH] 1.21.0 --- Mothur.xcodeproj/project.pbxproj | 4 ++-- alignmentdb.cpp | 2 +- indicatorcommand.cpp | 7 ++++--- makefile | 4 ++-- mothurfisher.cpp | 1 - mothurmetastats.cpp | 10 +--------- mothurmetastats.h | 19 ------------------- 7 files changed, 10 insertions(+), 37 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 00bcf9a..49de826 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -2177,8 +2177,8 @@ GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.20.2\\\"\"", - "RELEASE_DATE=\"\\\"7/05/2011\\\"\"", + "VERSION=\"\\\"1.21.0\\\"\"", + "RELEASE_DATE=\"\\\"7/25/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; diff --git a/alignmentdb.cpp b/alignmentdb.cpp index 7c2916c..bac61c4 100644 --- a/alignmentdb.cpp +++ b/alignmentdb.cpp @@ -129,7 +129,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap m->mothurOut("DONE."); m->mothurOutEndLine(); cout.flush(); - m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(rdb->referenceSeqs.size()) + " sequences."); m->mothurOutEndLine(); + m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine(); } diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp index 6fccaba..905076b 100644 --- a/indicatorcommand.cpp +++ b/indicatorcommand.cpp @@ -38,7 +38,8 @@ vector IndicatorCommand::setParameters(){ string IndicatorCommand::getHelpString(){ try { string helpString = ""; - helpString += "The indicator command reads a shared or relabund file and a tree or design file, and outputs a .indicator.tre and .indicator.summary file. \n"; + helpString += "The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. \n"; + helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n"; helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n"; helpString += "The summary file lists the indicator value for each OTU for each node.\n"; helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n"; @@ -229,7 +230,7 @@ int IndicatorCommand::execute(){ int start = time(NULL); - //read designfile if given and set up globaldatas groups for read of sharedfiles + //read designfile if given and set up groups for read of sharedfiles if (designfile != "") { designMap = new GroupMap(designfile); designMap->readDesignMap(); @@ -256,7 +257,7 @@ int IndicatorCommand::execute(){ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; } } - //reset Globaldatas groups if needed + //reset groups if needed if (designfile != "") { m->Groups = Groups; } /***************************************************/ diff --git a/makefile b/makefile index fa214c4..aa69ce1 100644 --- a/makefile +++ b/makefile @@ -15,8 +15,8 @@ USEREADLINE ?= yes CYGWIN_BUILD ?= no USECOMPRESSION ?= no MOTHUR_FILES="\"Enter_your_default_path_here\"" -RELEASE_DATE = "\"7/5/2011\"" -VERSION = "\"1.20.0\"" +RELEASE_DATE = "\"7/25/2011\"" +VERSION = "\"1.21.0\"" # Optimize to level 3: CXXFLAGS += -O3 diff --git a/mothurfisher.cpp b/mothurfisher.cpp index 8cf332b..6f705b9 100644 --- a/mothurfisher.cpp +++ b/mothurfisher.cpp @@ -90,7 +90,6 @@ double MothurFisher::hyper_323(double n11, double n1_, double n_1, double n){ } } /***********************************************************/ -//var sn11,sn1_,sn_1,sn,sprob; double MothurFisher::hyper(double n11){ try { return(hyper0(n11,0,0,0)); diff --git a/mothurmetastats.cpp b/mothurmetastats.cpp index c376218..6a834e9 100644 --- a/mothurmetastats.cpp +++ b/mothurmetastats.cpp @@ -23,15 +23,7 @@ MothurMetastats::MothurMetastats(double t, int n) { } } /***********************************************************/ -MothurMetastats::~MothurMetastats() { - try { - - - }catch(exception& e) { - m->errorOut(e, "MothurMetastats", "~MothurMetastats"); - exit(1); - } -} +MothurMetastats::~MothurMetastats() {} /***********************************************************/ //main metastats function int MothurMetastats::runMetastats(string outputFileName, vector< vector >& data, int secondGroupingStart) { diff --git a/mothurmetastats.h b/mothurmetastats.h index 37d6166..6c1f2f8 100644 --- a/mothurmetastats.h +++ b/mothurmetastats.h @@ -32,26 +32,7 @@ class MothurMetastats { int permute_matrix(vector&, vector&, int, vector&, vector&, vector&); int permute_array(vector&); int calc_twosample_ts(vector&, int, vector&, vector&, vector&); - - - - }; - //void testp(double *permuted_ttests,int *B,double *permuted,double - // *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double *ps); - //void permute_matrix(double *Imatrix,int *nc,int *nr,double - // *permuted,int *g,double *trial_ts,double *Tinitial,double - // *counter); - //void permute_array(int *array, int n); - //void calc_twosample_ts(double *Pmatrix,int *g,int *nc,int *nr,double - // *Ts,double *Tinitial,double *counter1); - //void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *storage); - //void start(double *Imatrix,int *g,int *nr,int *nc,double *testing, - // double storage[][9]); - - //int metastat_main (char*, int, int, double, int, double**, int); - - #endif -- 2.39.2