major change to the tree class to use the count table class instead of tree map....

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index ee50ab14e6183af4b2fe9979c97336ac1d9b75a5..869df029fdd35efa6c3e9a9a22d46c6c4fea6667 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -15,7 +15,8 @@ vector<string> AlignCheckCommand::setParameters(){
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
                CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+        CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
@@ -31,7 +32,7 @@ vector<string> AlignCheckCommand::setParameters(){
 string AlignCheckCommand::getHelpString(){     
        try {
                string helpString = "";
-               helpString += "The align.check command reads a fasta file and map file.\n";
+               helpString += "The align.check command reads a fasta file and map file as well as an optional name file.\n";
                helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
                helpString += "The align.check command parameters are fasta and map, both are required.\n";
                helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";