fixed phylo.diversity

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 7d0d539eddeeae6e3ee6bfbe3e114c6b90e1bb7a..eabcc7360bfd8c96793a577b3a98953d33199227 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -137,7 +137,6 @@ void ClearcutCommand::help(){
        try {
                m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
                m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
-               m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
                m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n");
                m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
                m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
@@ -255,6 +254,10 @@ int ClearcutCommand::execute() {
                
                clearcut_main(numArgs, clearcutParameters); 
                
+               //free memory
+               for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
+               delete[] clearcutParameters; 
+               
                if (!stdoutWanted) {    
                        m->mothurOutEndLine();
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();