added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 60d300f177f1deec1720ceeefec71d73ccd7579b..bcecb7844e8a0348180884fbdb54993c286c53ac 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -22,7 +22,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir"};
+                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -119,9 +119,13 @@ ReadDistCommand::ReadDistCommand(string option) {
                        // ...at some point should added some additional type checking...
                        //get user cutoff and precision or use defaults
                        string temp;
-                       temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        convert(temp, precision); 
                        
+                       temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
+                       sim = isTrue(temp); 
+                       globaldata->sim = sim;
+                       
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
@@ -166,11 +170,12 @@ ReadDistCommand::ReadDistCommand(string option) {
 
 void ReadDistCommand::help(){
        try {
-               m->mothurOut("The read.dist command parameter options are phylip or column, group, name, cutoff and precision\n");
+               m->mothurOut("The read.dist command parameter options are phylip or column, group, name, sim, cutoff and precision\n");
                m->mothurOut("The read.dist command can be used in two ways.  The first is to read a phylip or column and run the cluster command\n");
                m->mothurOut("For this use the read.dist command should be in the following format: \n");
                m->mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
                m->mothurOut("The phylip or column parameter is required, but only one may be used.  If you use a column file the name filename is required. \n");
+               m->mothurOut("The sim parameter is used to indicate that your distance file contains similiarity values instead of distance values. The default is false, if sim=true then mothur will convert the similairity values to distances. \n");
                m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
                m->mothurOut("The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command.\n");
                m->mothurOut("For this use the read.dist command should be in the following format: \n");
@@ -204,7 +209,7 @@ int ReadDistCommand::execute(){
                size_t numDists = 0;
                
                vector<string> outputNames;
-cout << format << endl;                
+               
                if (format == "matrix") {
                        ifstream in;
                        openInputFile(distFileName, in);