1.21.0

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 00bcf9abb0d7eb68be32387532647584da236157..49de82685f9d1a43325306eb1854b7011eee86b7 100644 (file)
--- 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 7c2916c54970c72f73942db5726fe3a0d8c85655..bac61c451854b96e256bae11545448fa38589ebd 100644 (file)
--- 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 6fccaba1381a22a618686b6f0bbd4c447026ca3e..905076b7dcd56b62102a3dbdbcef5de9024d0fef 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -38,7 +38,8 @@ vector<string> 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 fa214c476e15f32fb6be29cfda677a064de6e1e1..aa69ce10aad8589557369b1c9656942e1988950b 100644 (file)
--- 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 8cf332b54d0364e1c84084b6f4a599d500ea2681..6f705b979f8ba0cc41b5ceead966dc7b0cf7a918 100644 (file)
--- 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 c376218ce7332d18c17c336b683fedea17fab4da..6a834e96be802fe416949dc8910d8790a24ddf15 100644 (file)
--- 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<double> >& data, int secondGroupingStart) {

diff --git a/mothurmetastats.h b/mothurmetastats.h
index 37d616670973b6a55063b5df29c0411d4e1ea0dd..6c1f2f827dbdb4b0bdce33e573604ffe90082706 100644 (file)
--- a/mothurmetastats.h
+++ b/mothurmetastats.h
@@ -32,26 +32,7 @@ class MothurMetastats {
                int permute_matrix(vector<double>&, vector<double>&, int, vector<double>&, vector<double>&, vector<double>&);
                int permute_array(vector<int>&);
                int calc_twosample_ts(vector<double>&, int, vector<double>&, vector<double>&, vector<double>&);
-
-
-
-       
 };
        
-       //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