changed name of distance command to dist.seqs

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ea43c48e6b84e4c2e83de0c067e081c2a88da49f..c03751518e3e9a2ab54da2e38be693e08a3d6c34 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -92,7 +92,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand();                   }
                else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand();                  }
                else if(commandName == "concensus")                             {   command = new ConcensusCommand();                   }
-               else if(commandName == "distance")                              {   command = new DistanceCommand();                    }
+               else if(commandName == "dist.seq")                              {   command = new DistanceCommand();                    }
                else                                                                                    {       command = new NoCommand();                                      }
 
                return command;

diff --git a/errorchecking.cpp b/errorchecking.cpp
index f1279a4aaa57df50ab3f6606da3387d89e0718c0..c866ca0060960ab20f50f53ffbd774c066ffc628 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -246,7 +246,7 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if ((commandName == "filter.seqs") || (commandName == "distance")) { 
+               if ((commandName == "filter.seqs") || (commandName == "dist.seq")) { 
                        if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
                                 cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false; 
                        }

diff --git a/globaldata.cpp b/globaldata.cpp
index 494b664fb841389aff6dca6305963d68a1a5a8cf..fddb5c9caadb3e2e7fcaf7f940718eacb6c39e30 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -43,7 +43,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                }
                
                //set default value for cutoff
-               if (commandName == "distance") {        cutoff = "1.0";         }
+               if (commandName == "dist.seq") {        cutoff = "1.0";         }
 
                string key, value;              
                //reads in parameters and values
@@ -215,7 +215,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
-               if (commandName == "distance") {
+               if (commandName == "dist.seq") {
                        if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 5ea5158bf2e3b00456fe1b752a7623a8875bdae6..9d7f5c8e27fb95ba9cd404e484ef96f20ddc8594 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -70,17 +70,17 @@ int HelpCommand::execute(){
                cout << "The deconvolute command parameter is fasta and it is required." << "\n";
                cout << "The deconvolute command should be in the following format: " << "\n";
                cout << "deconvolute(fasta=yourFastaFile) " << "\n";
-       }else if (globaldata->helpRequest == "distance") {
-               cout << "The distance command reads a file containing sequences and creates a distance file." << "\n";
-               cout << "The distance command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors.  " << "\n";
+       }else if (globaldata->helpRequest == "dist.seq") {
+               cout << "The dist.seq command reads a file containing sequences and creates a distance file." << "\n";
+               cout << "The dist.seq command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors.  " << "\n";
                cout << "You must use one of the following parameters for your filename: fasta, phylip, clustal or nexus. " << "\n";
                cout << "The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
                cout << "The ends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T." << "\n";
                cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
                cout << "The processors parameter allows you to specify number of processors to use.  The default is 1, but you can use up to 4 processors." << "\n";
-               cout << "The distance command should be in the following format: " << "\n";
-               cout << "distance(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
-               cout << "Example distance(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
+               cout << "The dist.seq command should be in the following format: " << "\n";
+               cout << "dist.seq(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+               cout << "Example dist.seq(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "collect.single") {
                cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";

diff --git a/validcommands.cpp b/validcommands.cpp
index ad55d0d9c600594a908fb8e71a89b6c251f35aa9..5549e6396527c198a5131ba85c42ee356c07774f 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -22,7 +22,7 @@ ValidCommands::ValidCommands() {
                commands["get.oturep"]                  = "get.oturep";
                commands["cluster"]                             = "cluster"; 
                commands["deconvolute"]                 = "deconvolute"; 
-               commands["distance"]                    = "distance"; 
+               commands["dist.seqs"]                   = "dist.seqs"; 
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
                commands["rarefaction.single"]  = "rarefaction.single"; 

diff --git a/validparameter.cpp b/validparameter.cpp
index e97df8b0fc8e0efc9f02f6c61987f59ea1c75b89..8af4a8154e74fab87e3985222a0e0e8ac93a0bfd 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -290,7 +290,7 @@ void ValidParameters::initCommandParameters() {
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
                string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
-               commandParameters["distance"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+               commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));